Source compatibility report for the CDK library between 1.2.10 and 1.4.0 versions

Test Info

Library Name	CDK
Version #1	1.2.10
Version #2	1.4.0

Test Results

Total Java ARchives	1
Total Methods / Classes	35280 / 2522
Verdict	Incompatible (18.9%)

Problem Summary

	Severity	Count
Added Methods	-	9961
Removed Methods	High	4833
Problems with Data Types	High	584
	Medium	0
	Low	8
Problems with Methods	High	15
	Medium	10
	Low	0
Other Changes in Data Types	-	14

Added Methods (9961)

cdk-1.4.0.jar, AbstractAWTDrawVisitor.class
package org.openscience.cdk.renderer.visitor
AbstractAWTDrawVisitor.AbstractAWTDrawVisitor ( )
AbstractAWTDrawVisitor.getTextBasePoint ( String text, double xCoord, double yCoord, Graphics2D graphics ) :  Point
AbstractAWTDrawVisitor.getTextBounds ( String text, double xCoord, double yCoord, Graphics2D graphics ) :  Rectangle2D
AbstractAWTDrawVisitor.setTransform ( AffineTransform transform ) :  void
AbstractAWTDrawVisitor.transformPoint ( double xCoord, double yCoord ) :  int[ ]

cdk-1.4.0.jar, AbstractDateTime.class
package com.hp.hpl.jena.datatypes.xsd
AbstractDateTime.AbstractDateTime ( Object value )
AbstractDateTime.compare ( AbstractDateTime other ) :  int
AbstractDateTime.compareDates ( int[ ] date1, int[ ] date2, boolean strict ) :  short
AbstractDateTime.compareOrder ( int[ ] date1, int[ ] date2 ) :  short
AbstractDateTime.equals ( Object obj ) :  boolean
AbstractDateTime.extractFractionalSeconds ( ) :  void
AbstractDateTime.fQuotient ( int a, int b ) [static] :  int
AbstractDateTime.fQuotient ( int temp, int low, int high ) [static] :  int
AbstractDateTime.hashCode ( ) :  int
AbstractDateTime.maxDayInMonthFor ( int year, int month ) [static] :  int
AbstractDateTime.mod ( int a, int b, int quotient ) [static] :  int
AbstractDateTime.modulo ( int temp, int low, int high ) [static] :  int
AbstractDateTime.normalize ( int[ ] date, int[ ] timeZone ) [static] :  void
AbstractDateTime.resetDateObj ( int[ ] data ) :  void

cdk-1.4.0.jar, AbstractFontManager.class
package org.openscience.cdk.renderer.font
AbstractFontManager.AbstractFontManager ( )
AbstractFontManager.atLowerBoundary ( ) :  boolean
AbstractFontManager.atMax ( ) :  boolean
AbstractFontManager.atMin ( ) :  boolean
AbstractFontManager.atUpperBoundary ( ) :  boolean
AbstractFontManager.decreaseFontSize ( ) :  void
AbstractFontManager.getFontName ( ) :  String
AbstractFontManager.getFontSizeForZoom ( double zoom ) :  Integer
AbstractFontManager.getFontStyle ( ) :  IFontManager.FontStyle
AbstractFontManager.getNumberOfFontSizes ( ) :  int
AbstractFontManager.increaseFontSize ( ) :  void
AbstractFontManager.inLower ( ) :  boolean
AbstractFontManager.inRange ( ) :  boolean
AbstractFontManager.inUpper ( ) :  boolean
AbstractFontManager.makeFonts ( ) [abstract] :  void
AbstractFontManager.registerFontSizeMapping ( double zoom, int size ) :  void
AbstractFontManager.resetVirtualCounts ( ) :  void
AbstractFontManager.setFontName ( String fontName ) :  void
AbstractFontManager.setFontStyle ( IFontManager.FontStyle fontStyle ) :  void
AbstractFontManager.toMiddle ( ) :  void

cdk-1.4.0.jar, AbstractGeneratorParameter.class
package org.openscience.cdk.renderer.generators.parameter
AbstractGeneratorParameter.AbstractGeneratorParameter ( )
AbstractGeneratorParameter.getValue ( ) :  Object
AbstractGeneratorParameter.setValue ( Object value ) :  void

cdk-1.4.0.jar, AbstractGraphBuilder.class
package signature
AbstractGraphBuilder.AbstractGraphBuilder ( )
AbstractGraphBuilder.makeEdge ( int p1, int p2, String p3, String p4, String p5 ) [abstract] :  void
AbstractGraphBuilder.makeFromColoredTree ( ColoredTree tree ) :  void
AbstractGraphBuilder.makeGraph ( ) [abstract] :  void
AbstractGraphBuilder.makeVertex ( String p1 ) [abstract] :  void

cdk-1.4.0.jar, AbstractGraphSignature.class
package signature
AbstractGraphSignature.AbstractGraphSignature ( )
AbstractGraphSignature.AbstractGraphSignature ( int height )
AbstractGraphSignature.AbstractGraphSignature ( String separator )
AbstractGraphSignature.AbstractGraphSignature ( String separator, int height )
AbstractGraphSignature.getCanonicalLabels ( ) :  int[ ]
AbstractGraphSignature.getGraphSignature ( ) :  String
AbstractGraphSignature.getHeight ( ) :  int
AbstractGraphSignature.getMaximalSignature ( ) :  String
AbstractGraphSignature.getMinimalSignature ( ) :  String
AbstractGraphSignature.getSortedSignatures ( ) :  List
AbstractGraphSignature.getSymmetryClasses ( ) :  List
AbstractGraphSignature.getSymmetryClasses ( int height ) :  List
AbstractGraphSignature.getVertexCount ( ) [abstract] :  int
AbstractGraphSignature.getVertexSignatures ( ) :  List
AbstractGraphSignature.getVertexSignatureStrings ( ) :  List
AbstractGraphSignature.isCanonicallyLabelled ( ) :  boolean
AbstractGraphSignature.reconstructCanonicalEdgeString ( ) :  String
AbstractGraphSignature.reconstructCanonicalGraph ( AbstractVertexSignature signature, AbstractGraphBuilder builder ) :  void
AbstractGraphSignature.signatureForVertex ( int p1 ) [abstract] :  AbstractVertexSignature
AbstractGraphSignature.signatureStringForVertex ( int p1 ) [abstract] :  String
AbstractGraphSignature.signatureStringForVertex ( int p1, int p2 ) [abstract] :  String
AbstractGraphSignature.toCanonicalString ( ) :  String
AbstractGraphSignature.toFullString ( ) :  String

cdk-1.4.0.jar, AbstractMCS.class
package org.openscience.cdk.smsd.interfaces
AbstractMCS.AbstractMCS ( )
AbstractMCS.getAllAtomMapping ( ) [abstract] :  List
AbstractMCS.getAllMapping ( ) [abstract] :  List
AbstractMCS.getBondInSensitiveTimeOut ( ) [abstract] :  double
AbstractMCS.getBondSensitiveTimeOut ( ) [abstract] :  double
AbstractMCS.getEnergyScore ( int p1 ) [abstract] :  Double
AbstractMCS.getEuclideanDistance ( ) [abstract] :  double
AbstractMCS.getFirstAtomMapping ( ) [abstract] :  Map
AbstractMCS.getFirstMapping ( ) [abstract] :  Map
AbstractMCS.getFragmentSize ( int p1 ) [abstract] :  Integer
AbstractMCS.getProductMolecule ( ) [abstract] :  IAtomContainer
AbstractMCS.getReactantMolecule ( ) [abstract] :  IAtomContainer
AbstractMCS.getStereoScore ( int p1 ) [abstract] :  Integer
AbstractMCS.getTanimotoSimilarity ( ) [abstract] :  double
AbstractMCS.init ( IAtomContainer p1, IAtomContainer p2, boolean p3, boolean p4 ) [abstract] :  void
AbstractMCS.init ( IMolecule p1, IMolecule p2, boolean p3, boolean p4 ) [abstract] :  void
AbstractMCS.init ( IQueryAtomContainer p1, IAtomContainer p2 ) [abstract] :  void
AbstractMCS.isStereoMisMatch ( ) [abstract] :  boolean
AbstractMCS.isSubgraph ( ) [abstract] :  boolean
AbstractMCS.setBondInSensitiveTimeOut ( double p1 ) [abstract] :  void
AbstractMCS.setBondSensitiveTimeOut ( double p1 ) [abstract] :  void
AbstractMCS.setChemFilters ( boolean p1, boolean p2, boolean p3 ) [abstract] :  void

cdk-1.4.0.jar, AbstractMCSAlgorithm.class
package org.openscience.cdk.smsd.interfaces
AbstractMCSAlgorithm.AbstractMCSAlgorithm ( )
AbstractMCSAlgorithm.searchMCS ( boolean p1 ) [abstract] :  void

cdk-1.4.0.jar, AbstractQuotientGraph.class
package signature
AbstractQuotientGraph.AbstractQuotientGraph ( )
AbstractQuotientGraph.construct ( List symmetryClasses ) :  void
AbstractQuotientGraph.getEdgeCount ( ) :  int
AbstractQuotientGraph.getVertexCount ( ) :  int
AbstractQuotientGraph.getVertexSignatureStrings ( ) :  List
AbstractQuotientGraph.isConnected ( int p1, int p2 ) [abstract] :  boolean
AbstractQuotientGraph.numberOfLoopEdges ( ) :  int
AbstractQuotientGraph.toString ( ) :  String

cdk-1.4.0.jar, AbstractReactionLabeller.class
package org.openscience.cdk.smsd.labelling
AbstractReactionLabeller.AbstractReactionLabeller ( )
AbstractReactionLabeller.labelReaction ( IReaction reaction, ICanonicalMoleculeLabeller labeller ) :  IReaction

cdk-1.4.0.jar, AbstractRenderer.class
package org.openscience.cdk.renderer
AbstractRenderer.AbstractRenderer ( )
AbstractRenderer.calculateScaleForBondLength ( double p1 ) [abstract] :  double
AbstractRenderer.calculateScreenBounds ( Rectangle2D modelBounds ) :  Rectangle
AbstractRenderer.convertToDiagramBounds ( Rectangle2D modelBounds ) :  Rectangle
AbstractRenderer.generateDiagram ( IChemObject object ) :  IRenderingElement
AbstractRenderer.getDrawCenter ( ) :  Point2d
AbstractRenderer.getModelCenter ( ) :  Point2d
AbstractRenderer.getRenderer2DModel ( ) :  RendererModel
AbstractRenderer.paint ( IDrawVisitor drawVisitor, IRenderingElement diagram ) :  void
AbstractRenderer.repaint ( IDrawVisitor drawVisitor ) :  void
AbstractRenderer.setDrawCenter ( double modelX, double modelY ) :  void
AbstractRenderer.setModelCenter ( double modelX, double modelY ) :  void
AbstractRenderer.setup ( ) :  void
AbstractRenderer.setupTransformNatural ( Rectangle2D modelBounds ) :  void
AbstractRenderer.setupTransformToFit ( Rectangle2D screenBounds, Rectangle2D modelBounds, double bondLength, boolean reset ) :  void
AbstractRenderer.setZoom ( double zoom ) :  void
AbstractRenderer.setZoomToFit ( double drawWidth, double drawHeight, double diagramWidth, double diagramHeight ) :  void
AbstractRenderer.shift ( Rectangle screenBounds, Rectangle diagramBounds ) :  Rectangle
AbstractRenderer.shiftDrawCenter ( double shiftX, double shiftY ) :  void
AbstractRenderer.toModelCoordinates ( double screenX, double screenY ) :  Point2d
AbstractRenderer.toScreenCoordinates ( double modelX, double modelY ) :  Point2d

cdk-1.4.0.jar, AbstractSelection.class
package org.openscience.cdk.renderer.selection
AbstractSelection.AbstractSelection ( )
AbstractSelection.addToAtomContainer ( IAtomContainer ac, IChemObject item ) :  void
AbstractSelection.select ( IChemModel chemModel ) :  void

cdk-1.4.0.jar, AbstractSubGraph.class
package org.openscience.cdk.smsd.interfaces
AbstractSubGraph.AbstractSubGraph ( )
AbstractSubGraph.isSubgraph ( boolean p1 ) [abstract] :  boolean

cdk-1.4.0.jar, AbstractVertexSignature.class
package signature
AbstractVertexSignature.AbstractVertexSignature ( )
AbstractVertexSignature.AbstractVertexSignature ( AbstractVertexSignature.InvariantType invariantType )
AbstractVertexSignature.accept ( DAGVisitor visitor ) :  void
AbstractVertexSignature.canonize ( int color, StringBuffer canonicalVertexSignature ) :  void
AbstractVertexSignature.create ( int rootVertexIndex, int graphVertexCount, int height ) :  void
AbstractVertexSignature.createMaximumHeight ( int rootVertexIndex, int graphVertexCount ) :  void
AbstractVertexSignature.getCanonicalLabelling ( int totalVertexCount ) :  int[ ]
AbstractVertexSignature.getConnected ( int p1 ) [abstract] :  int[ ]
AbstractVertexSignature.getEdgeLabel ( int p1, int p2 ) [abstract] :  String
AbstractVertexSignature.getHeight ( ) :  int
AbstractVertexSignature.getIntLabel ( int p1 ) [abstract] :  int
AbstractVertexSignature.getOriginalVertexIndex ( int vertexIndex ) :  int
AbstractVertexSignature.getVertexCount ( ) :  int
AbstractVertexSignature.getVertexSymbol ( int p1 ) [abstract] :  String
AbstractVertexSignature.parse ( String s ) [static] :  ColoredTree
AbstractVertexSignature.toCanonicalString ( ) :  String
AbstractVertexSignature.toString ( ) :  String

cdk-1.4.0.jar, AbsXMLLiteral.class
package com.hp.hpl.jena.rdf.arp.states
AbsXMLLiteral.AbsXMLLiteral ( AbsXMLLiteral p, Map ns )
AbsXMLLiteral.AbsXMLLiteral ( FrameI p, AbsXMLContext x, StringBuffer r )
AbsXMLLiteral.AbsXMLLiteral ( XMLHandler h, AbsXMLContext x )
AbsXMLLiteral.append ( char s ) :  void
AbsXMLLiteral.append ( String s ) :  void
AbsXMLLiteral.characters ( char[ ] chrs, int start, int length ) :  void
AbsXMLLiteral.comment ( char[ ] ch, int start, int length ) :  void
AbsXMLLiteral.endElement ( ) [abstract] :  void
AbsXMLLiteral.processingInstruction ( String target, String data ) :  void
AbsXMLLiteral.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI

cdk-1.4.0.jar, AcidicGroupCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AcidicGroupCountDescriptor.AcidicGroupCountDescriptor ( )
AcidicGroupCountDescriptor.calculate ( IAtomContainer atomContainer ) :  DescriptorValue
AcidicGroupCountDescriptor.getDescriptorNames ( ) :  String[ ]
AcidicGroupCountDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
AcidicGroupCountDescriptor.getParameterNames ( ) :  String[ ]
AcidicGroupCountDescriptor.getParameters ( ) :  Object[ ]
AcidicGroupCountDescriptor.getParameterType ( String name ) :  Object
AcidicGroupCountDescriptor.getSpecification ( ) :  DescriptorSpecification
AcidicGroupCountDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.0.jar, AddDeniedException.class
package com.hp.hpl.jena.shared
AddDeniedException.AddDeniedException ( String message )
AddDeniedException.AddDeniedException ( String message, Triple triple )

cdk-1.4.0.jar, AddOne.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
AddOne.AddOne ( )
AddOne.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
AddOne.getArgLength ( ) :  int
AddOne.getName ( ) :  String

cdk-1.4.0.jar, Algorithm.class
package org.openscience.cdk.smsd.interfaces
Algorithm.compareTo ( Algorithm obj ) :  int
Algorithm.description ( ) :  String
Algorithm.type ( ) :  int
Algorithm.valueOf ( String name ) [static] :  Algorithm
Algorithm.values ( ) [static] :  Algorithm[ ]

cdk-1.4.0.jar, ALiteral.class
package com.hp.hpl.jena.rdf.arp
ALiteral.getDatatypeURI ( ) [abstract] :  String
ALiteral.getLang ( ) [abstract] :  String
ALiteral.getParseType ( ) [abstract] :  String
ALiteral.isWellFormedXML ( ) [abstract] :  boolean
ALiteral.toString ( ) [abstract] :  String

cdk-1.4.0.jar, AllAccept.class
package com.hp.hpl.jena.assembler.acceptance
AllAccept.AllAccept ( String name )
AllAccept.suite ( ) [static] :  TestSuite
AllAccept.testUnadornedInferenceModel ( ) :  void
AllAccept.testWithContent ( ) :  void

cdk-1.4.0.jar, AllDifferent.class
package com.hp.hpl.jena.ontology
AllDifferent.addDistinctMember ( Resource p1 ) [abstract] :  void
AllDifferent.addDistinctMembers ( Iterator p1 ) [abstract] :  void
AllDifferent.getDistinctMembers ( ) [abstract] :  RDFList
AllDifferent.hasDistinctMember ( Resource p1 ) [abstract] :  boolean
AllDifferent.listDistinctMembers ( ) [abstract] :  ExtendedIterator
AllDifferent.removeDistinctMember ( Resource p1 ) [abstract] :  void
AllDifferent.setDistinctMembers ( RDFList p1 ) [abstract] :  void

cdk-1.4.0.jar, AllRingsFinder.class
package org.openscience.cdk.ringsearch
AllRingsFinder.AllRingsFinder ( boolean logging )

cdk-1.4.0.jar, AllValuesFromRestriction.class
package com.hp.hpl.jena.ontology
AllValuesFromRestriction.getAllValuesFrom ( ) [abstract] :  Resource
AllValuesFromRestriction.hasAllValuesFrom ( Resource p1 ) [abstract] :  boolean
AllValuesFromRestriction.removeAllValuesFrom ( Resource p1 ) [abstract] :  void
AllValuesFromRestriction.setAllValuesFrom ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, AlreadyExistsException.class
package com.hp.hpl.jena.shared
AlreadyExistsException.AlreadyExistsException ( String name )

cdk-1.4.0.jar, AlreadyLinkedViewException.class
package com.hp.hpl.jena.enhanced
AlreadyLinkedViewException.AlreadyLinkedViewException ( Polymorphic other )

cdk-1.4.0.jar, AlreadyReifiedException.class
package com.hp.hpl.jena.shared
AlreadyReifiedException.AlreadyReifiedException ( Node n )

cdk-1.4.0.jar, AlreadySelectedException.class
package org.apache.commons.cli
AlreadySelectedException.AlreadySelectedException ( String message )

cdk-1.4.0.jar, Alt.class
package com.hp.hpl.jena.rdf.model
Alt.getDefault ( ) [abstract] :  RDFNode
Alt.getDefaultAlt ( ) [abstract] :  Alt
Alt.getDefaultBag ( ) [abstract] :  Bag
Alt.getDefaultBoolean ( ) [abstract] :  boolean
Alt.getDefaultByte ( ) [abstract] :  byte
Alt.getDefaultChar ( ) [abstract] :  char
Alt.getDefaultDouble ( ) [abstract] :  double
Alt.getDefaultFloat ( ) [abstract] :  float
Alt.getDefaultInt ( ) [abstract] :  int
Alt.getDefaultLanguage ( ) [abstract] :  String
Alt.getDefaultLiteral ( ) [abstract] :  Literal
Alt.getDefaultLong ( ) [abstract] :  long
Alt.getDefaultObject ( ObjectF p1 ) [abstract] :  Object *DEPRECATED*
Alt.getDefaultResource ( ) [abstract] :  Resource
Alt.getDefaultResource ( ResourceF p1 ) [abstract] :  Resource
Alt.getDefaultSeq ( ) [abstract] :  Seq
Alt.getDefaultShort ( ) [abstract] :  short
Alt.getDefaultString ( ) [abstract] :  String
Alt.remove ( Statement p1 ) [abstract] :  Container
Alt.setDefault ( boolean p1 ) [abstract] :  Alt
Alt.setDefault ( char p1 ) [abstract] :  Alt
Alt.setDefault ( double p1 ) [abstract] :  Alt
Alt.setDefault ( float p1 ) [abstract] :  Alt
Alt.setDefault ( long p1 ) [abstract] :  Alt
Alt.setDefault ( Object p1 ) [abstract] :  Alt
Alt.setDefault ( RDFNode p1 ) [abstract] :  Alt
Alt.setDefault ( String p1 ) [abstract] :  Alt
Alt.setDefault ( String p1, String p2 ) [abstract] :  Alt

cdk-1.4.0.jar, Alternatives.class
package com.hp.hpl.jena.graph.query.regexptrees
Alternatives.Alternatives ( RegexpTree[ ] operands )
Alternatives.create ( List operands ) [static] :  RegexpTree
Alternatives.equals ( Object other ) :  boolean
Alternatives.hashCode ( ) :  int
Alternatives.toString ( ) :  String

cdk-1.4.0.jar, AltHasNoDefaultException.class
package com.hp.hpl.jena.rdf.model
AltHasNoDefaultException.AltHasNoDefaultException ( Alt a )

cdk-1.4.0.jar, AmbiguousSpecificTypeException.class
package com.hp.hpl.jena.assembler.exceptions
AmbiguousSpecificTypeException.AmbiguousSpecificTypeException ( Resource root, ArrayList types )
AmbiguousSpecificTypeException.getTypes ( ) :  List

cdk-1.4.0.jar, AngularMomentum.class
package org.openscience.cdk.math.qm
AngularMomentum.AngularMomentum ( double J )
AngularMomentum.getIminus ( ) :  Matrix
AngularMomentum.getIplus ( ) :  Matrix
AngularMomentum.getIx ( ) :  IMatrix
AngularMomentum.getIy ( ) :  IMatrix
AngularMomentum.getIz ( ) :  IMatrix
AngularMomentum.getSpinVector ( double theta, double phi ) :  Vector

cdk-1.4.0.jar, AnonId.class
package com.hp.hpl.jena.rdf.model
AnonId.AnonId ( )
AnonId.AnonId ( String id )
AnonId.create ( ) [static] :  AnonId
AnonId.create ( String id ) [static] :  AnonId
AnonId.equals ( Object o ) :  boolean
AnonId.getLabelString ( ) :  String
AnonId.hashCode ( ) :  int
AnonId.toString ( ) :  String

cdk-1.4.0.jar, Any.class
package com.hp.hpl.jena.graph.query
QueryNode.Any.matchOrBind ( Domain d, Node x ) :  boolean
QueryNode.Any.QueryNode.Any ( )
QueryNode.Any.toString ( ) :  String

cdk-1.4.0.jar, AnyOf.class
package com.hp.hpl.jena.graph.query.regexptrees
AnyOf.AnyOf ( String possibles )
AnyOf.equals ( Object other ) :  boolean
AnyOf.hashCode ( ) :  int
AnyOf.toString ( ) :  String

cdk-1.4.0.jar, AnySingle.class
package com.hp.hpl.jena.graph.query.regexptrees
AnySingle.AnySingle ( )
AnySingle.equals ( Object x ) :  boolean
AnySingle.hashCode ( ) :  int
AnySingle.toString ( ) :  String

cdk-1.4.0.jar, Application.class
package com.hp.hpl.jena.graph.query
Expression.Application.argCount ( ) [abstract] :  int
Expression.Application.Expression.Application ( )
Expression.Application.getArg ( int p1 ) [abstract] :  Expression
Expression.Application.getFun ( ) [abstract] :  String
Expression.Application.isApply ( ) :  boolean

cdk-1.4.0.jar, Applyer.class
package com.hp.hpl.jena.graph.query
Applyer.Applyer ( )
Applyer.applyToTriples ( Domain p1, Matcher p2, StageElement p3 ) [abstract] :  void

cdk-1.4.0.jar, ApplyFn.class
package com.hp.hpl.jena.rdf.model
RDFList.ApplyFn.apply ( RDFNode p1 ) [abstract] :  void

cdk-1.4.0.jar, ArabicShaping.class
package com.ibm.icu.text
ArabicShaping.ArabicShaping ( int options )
ArabicShaping.equals ( Object rhs ) :  boolean
ArabicShaping.hashCode ( ) :  int
ArabicShaping.shape ( char[ ] source, int sourceStart, int sourceLength, char[ ] dest, int destStart, int destSize ) :  int
ArabicShaping.shape ( char[ ] source, int start, int length ) :  void
ArabicShaping.shape ( String text ) :  String
ArabicShaping.toString ( ) :  String

cdk-1.4.0.jar, Arc.class
package signature
DAG.Arc.DAG.Arc ( DAG a, int b, int p3 )
DAG.Arc.equals ( Object other ) :  boolean

cdk-1.4.0.jar, AResource.class
package com.hp.hpl.jena.rdf.arp
AResource.getAnonymousID ( ) [abstract] :  String
AResource.getURI ( ) [abstract] :  String
AResource.getUserData ( ) [abstract] :  Object
AResource.hasNodeID ( ) [abstract] :  boolean
AResource.isAnonymous ( ) [abstract] :  boolean
AResource.setUserData ( Object p1 ) [abstract] :  void

cdk-1.4.0.jar, Arg.class
package jena.cmdline
Arg.getName ( ) :  String
Arg.getValue ( ) :  String
Arg.getValues ( ) :  List
Arg.hasValue ( ) :  boolean
Arg.matches ( ArgDecl decl ) :  boolean

cdk-1.4.0.jar, ArgDecl.class
package jena.cmdline
ArgDecl.addHook ( ArgHandler argHandler ) :  void
ArgDecl.addName ( String name ) :  void
ArgDecl.ArgDecl ( boolean hasValue )
ArgDecl.ArgDecl ( boolean hasValue, String name )
ArgDecl.ArgDecl ( boolean hasValue, String name, ArgHandler handler )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2 )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, ArgHandler handler )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, String name3 )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, String name3, ArgHandler handler )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, String name3, String name4 )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, String name3, String name4, ArgHandler handler )
ArgDecl.ArgDecl ( boolean hasValue, String name1, String name2, String name3, String name4, String name5, ArgHandler handler )
ArgDecl.getNames ( ) :  Set
ArgDecl.matches ( Arg a ) :  boolean
ArgDecl.matches ( String arg ) :  boolean
ArgDecl.names ( ) :  Iterator
ArgDecl.takesValue ( ) :  boolean
ArgDecl.trigger ( Arg arg ) :  void

cdk-1.4.0.jar, ArgHandler.class
package jena.cmdline
ArgHandler.action ( String p1, String p2 ) [abstract] :  void

cdk-1.4.0.jar, ARP.class
package com.hp.hpl.jena.rdf.arp
ARP.ARP ( )
ARP.getHandlers ( ) :  ARPHandlers
ARP.getLocator ( ) :  Locator
ARP.getOptions ( ) :  ARPOptions
ARP.load ( InputStream in ) :  void
ARP.load ( InputStream in, String xmlBase ) :  void
ARP.load ( Reader in ) :  void
ARP.load ( Reader in, String xmlBase ) :  void
ARP.setHandlersWith ( ARPHandlers handlers ) :  void
ARP.setOptionsWith ( ARPOptions opts ) :  void

cdk-1.4.0.jar, ARPConfig.class
package com.hp.hpl.jena.rdf.arp
ARPConfig.getHandlers ( ) [abstract] :  ARPHandlers
ARPConfig.getOptions ( ) [abstract] :  ARPOptions
ARPConfig.setHandlersWith ( ARPHandlers p1 ) [abstract] :  void
ARPConfig.setOptionsWith ( ARPOptions p1 ) [abstract] :  void

cdk-1.4.0.jar, ARPHandlers.class
package com.hp.hpl.jena.rdf.arp
ARPHandlers.createNewHandlers ( ) [static] :  ARPHandlers
ARPHandlers.getErrorHandler ( ) :  ErrorHandler
ARPHandlers.getExtendedHandler ( ) :  ExtendedHandler
ARPHandlers.getNamespaceHandler ( ) :  NamespaceHandler
ARPHandlers.getStatementHandler ( ) :  StatementHandler
ARPHandlers.setErrorHandler ( ErrorHandler eh ) :  ErrorHandler
ARPHandlers.setExtendedHandler ( ExtendedHandler sh ) :  ExtendedHandler
ARPHandlers.setNamespaceHandler ( NamespaceHandler sh ) :  NamespaceHandler
ARPHandlers.setStatementHandler ( StatementHandler sh ) :  StatementHandler

cdk-1.4.0.jar, ARPOptions.class
package com.hp.hpl.jena.rdf.arp
ARPOptions.copy ( ) :  ARPOptions
ARPOptions.createNewOptions ( ) [static] :  ARPOptions
ARPOptions.getEmbedding ( ) :  boolean
ARPOptions.getErrorMode ( int eCode ) :  int
ARPOptions.getIRIFactory ( ) :  IRIFactory
ARPOptions.getIRIFactoryGlobal ( ) [static] :  IRIFactory
ARPOptions.setDefaultErrorMode ( ) :  void
ARPOptions.setEmbedding ( boolean embed ) :  boolean
ARPOptions.setErrorMode ( int errno, int mode ) :  int
ARPOptions.setIRIFactory ( IRIFactory f ) :  void
ARPOptions.setIRIFactoryGlobal ( IRIFactory f ) [static] :  void
ARPOptions.setLaxErrorMode ( ) :  void
ARPOptions.setStrictErrorMode ( ) :  void
ARPOptions.setStrictErrorMode ( int nonErrorMode ) :  void

cdk-1.4.0.jar, ArrayBunch.class
package com.hp.hpl.jena.mem
ArrayBunch.add ( Triple t ) :  void
ArrayBunch.app ( Domain d, StageElement next, MatchOrBind s ) :  void
ArrayBunch.ArrayBunch ( )
ArrayBunch.contains ( Triple t ) :  boolean
ArrayBunch.containsBySameValueAs ( Triple t ) :  boolean
ArrayBunch.grow ( ) :  void
ArrayBunch.iterator ( ) :  ExtendedIterator
ArrayBunch.iterator ( HashCommon.NotifyEmpty container ) :  ExtendedIterator
ArrayBunch.remove ( Triple t ) :  void
ArrayBunch.size ( ) :  int

cdk-1.4.0.jar, ArrayIterator.class
package com.hp.hpl.jena.util.iterator
ArrayIterator.ArrayIterator ( Object[ ] array )
ArrayIterator.hasNext ( ) :  boolean
ArrayIterator.next ( ) :  Object
ArrayIterator.remove ( ) :  void

cdk-1.4.0.jar, Artefact.class
package net.sf.jnati.deploy.artefact
Artefact.getArtefactLocation ( ) :  ArtefactDescriptor
Artefact.getConfiguration ( ) :  Configuration
Artefact.setConfiguration ( Configuration config ) :  void

cdk-1.4.0.jar, ArtefactDescriptor.class
package net.sf.jnati
ArtefactDescriptor.ArtefactDescriptor ( String id, String version, String osarch, File root )
ArtefactDescriptor.getId ( ) :  String
ArtefactDescriptor.getOsArch ( ) :  String
ArtefactDescriptor.getPath ( ) :  File
ArtefactDescriptor.getVersion ( ) :  String

cdk-1.4.0.jar, Assembler.class
package com.hp.hpl.jena.assembler
Assembler.open ( Assembler p1, Resource p2 ) [abstract] :  Object
Assembler.open ( Assembler p1, Resource p2, Mode p3 ) [abstract] :  Object
Assembler.open ( Resource p1 ) [abstract] :  Object
Assembler.openModel ( Resource p1 ) [abstract] :  Model
Assembler.openModel ( Resource p1, Mode p2 ) [abstract] :  Model

cdk-1.4.0.jar, AssemblerBase.class
package com.hp.hpl.jena.assembler.assemblers
AssemblerBase.AssemblerBase ( )
AssemblerBase.checkType ( Resource root, Resource type ) :  void
AssemblerBase.getOptionalClassName ( Resource root, Property classProperty ) [static] :  String
AssemblerBase.getRequiredLiteral ( Resource root, Property p ) :  Literal
AssemblerBase.getRequiredResource ( Resource root, Property p ) [static] :  Resource
AssemblerBase.getResource ( Statement s ) [static] :  Resource
AssemblerBase.getString ( Statement s ) [static] :  String
AssemblerBase.getUnique ( Resource root, Property property ) [static] :  RDFNode
AssemblerBase.getUniqueLiteral ( Resource root, Property property ) [static] :  Literal
AssemblerBase.getUniqueResource ( Resource root, Property property ) [static] :  Resource
AssemblerBase.getUniqueStatement ( Resource root, Property property ) [static] :  Statement
AssemblerBase.getUniqueString ( Resource root, Property property ) [static] :  String
AssemblerBase.loadClass ( Resource root, String className ) [static] :  Class
AssemblerBase.open ( Assembler a, Resource root ) :  Object
AssemblerBase.open ( Assembler p1, Resource p2, Mode p3 ) [abstract] :  Object
AssemblerBase.open ( Resource root ) :  Object
AssemblerBase.openModel ( Resource root ) :  Model
AssemblerBase.openModel ( Resource root, Mode mode ) :  Model

cdk-1.4.0.jar, AssemblerException.class
package com.hp.hpl.jena.assembler.exceptions
AssemblerException.AssemblerException ( Resource root, String message )
AssemblerException.AssemblerException ( Resource root, String string, Throwable t )
AssemblerException.frameStrings ( ) :  String
AssemblerException.getDoing ( ) :  List
AssemblerException.getRoot ( ) :  Resource
AssemblerException.nice ( RDFNode r ) [static] :  String
AssemblerException.nice ( Resource r ) [static] :  String
AssemblerException.pushDoing ( AssemblerGroup.Frame frame ) :  AssemblerException
AssemblerException.toString ( ) :  String

cdk-1.4.0.jar, AssemblerGroup.class
package com.hp.hpl.jena.assembler.assemblers
AssemblerGroup.assemblerFor ( Resource p1 ) [abstract] :  Assembler
AssemblerGroup.AssemblerGroup ( )
AssemblerGroup.copy ( ) :  AssemblerGroup
AssemblerGroup.create ( ) [static] :  AssemblerGroup
AssemblerGroup.implementWith ( Resource p1, Assembler p2 ) [abstract] :  AssemblerGroup
AssemblerGroup.openModel ( Resource resource ) :  Model

cdk-1.4.0.jar, AssemblerHelp.class
package com.hp.hpl.jena.assembler
AssemblerHelp.AssemblerHelp ( )
AssemblerHelp.findAssemblerRoots ( Model model ) [static] :  Set
AssemblerHelp.findAssemblerRoots ( Model model, Resource type ) [static] :  Set
AssemblerHelp.findSpecificType ( Resource root ) [static] :  Resource
AssemblerHelp.findSpecificType ( Resource root, Resource baseType ) [static] :  Resource
AssemblerHelp.findSpecificTypes ( Resource root, Resource baseType ) [static] :  Set
AssemblerHelp.fullModel ( ImportManager im, Model m ) [static] :  Model
AssemblerHelp.fullModel ( Model m ) [static] :  Model
AssemblerHelp.getResource ( Statement s ) [static] :  Resource
AssemblerHelp.getString ( Statement s ) [static] :  String
AssemblerHelp.getString ( Statement s, Literal L ) [static] :  String
AssemblerHelp.loadArbitraryClasses ( AssemblerGroup g, Model m ) [static] :  void
AssemblerHelp.loadAssemblerClasses ( AssemblerGroup group, Model m ) [static] :  void
AssemblerHelp.singleModelRoot ( Model singleRoot ) [static] :  Resource
AssemblerHelp.singleRoot ( Model singleRoot, Resource type ) [static] :  Resource
AssemblerHelp.withFullModel ( Resource root ) [static] :  Resource

cdk-1.4.0.jar, AssertDisjointPairs.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
AssertDisjointPairs.AssertDisjointPairs ( )
AssertDisjointPairs.getArgLength ( ) :  int
AssertDisjointPairs.getName ( ) :  String
AssertDisjointPairs.headAction ( Node[ ] args, int length, RuleContext context ) :  void

cdk-1.4.0.jar, AssertionFailureException.class
package com.hp.hpl.jena.shared
AssertionFailureException.AssertionFailureException ( String message )

cdk-1.4.0.jar, Atom.class
package org.openscience.cdk
Atom.getImplicitHydrogenCount ( ) :  Integer
Atom.setImplicitHydrogenCount ( Integer hydrogenCount ) :  void
package signature.chemistry
Molecule.Atom.equals ( Molecule.Atom other ) :  boolean
Molecule.Atom.Molecule.Atom ( Molecule index, int symbol, String p3 )
Molecule.Atom.Molecule.Atom ( Molecule other, Molecule.Atom p2 )
Molecule.Atom.toString ( ) :  String

cdk-1.4.0.jar, AtomColor.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.AtomColor.BasicAtomGenerator.AtomColor ( )
BasicAtomGenerator.AtomColor.getDefault ( ) :  Color
BasicAtomGenerator.AtomColor.getDefault ( ) :  Object

cdk-1.4.0.jar, AtomColorer.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.AtomColorer.BasicAtomGenerator.AtomColorer ( )
BasicAtomGenerator.AtomColorer.getDefault ( ) :  IAtomColorer
BasicAtomGenerator.AtomColorer.getDefault ( ) :  Object

cdk-1.4.0.jar, AtomContainer.class
package org.openscience.cdk
AtomContainer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
AtomContainer.addStereoElement ( IStereoElement element ) :  void
AtomContainer.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, AtomContainerAtomPermutor.class
package org.openscience.cdk.graph
AtomContainerAtomPermutor.AtomContainerAtomPermutor ( IAtomContainer ac )
package org.openscience.cdk.smsd.labelling
AtomContainerAtomPermutor.AtomContainerAtomPermutor ( IAtomContainer atomContainer )
AtomContainerAtomPermutor.next ( ) :  IAtomContainer
AtomContainerAtomPermutor.next ( ) :  Object
AtomContainerAtomPermutor.permute ( int[ ] p, IAtomContainer atomContainer ) [static] :  IAtomContainer
AtomContainerAtomPermutor.remove ( ) :  void

cdk-1.4.0.jar, AtomContainerBondPermutor.class
package org.openscience.cdk.graph
AtomContainerBondPermutor.AtomContainerBondPermutor ( IAtomContainer ac )

cdk-1.4.0.jar, AtomContainerComparator.class
package org.openscience.cdk.tools.manipulator
AtomContainerComparator.compare ( IAtomContainer o1, IAtomContainer o2 ) :  int

cdk-1.4.0.jar, AtomContainerComparatorBy2DCenter.class
package org.openscience.cdk.tools.manipulator
AtomContainerComparatorBy2DCenter.AtomContainerComparatorBy2DCenter ( )
AtomContainerComparatorBy2DCenter.compare ( IAtomContainer atCont1, IAtomContainer atCont2 ) :  int
AtomContainerComparatorBy2DCenter.compare ( Object x0, Object x1 ) :  int

cdk-1.4.0.jar, AtomContainerManipulator.class
package org.openscience.cdk.tools.manipulator
AtomContainerManipulator.extractSubstructure ( IAtomContainer atomContainer, int[ ] atomIndices ) [static] :  IAtomContainer
AtomContainerManipulator.getAtomParity ( IAtomContainer container, IAtom atom ) [static] :  IAtomParity

cdk-1.4.0.jar, AtomContainerPermutor.class
package org.openscience.cdk.graph
AtomContainerPermutor.next ( ) :  IAtomContainer
AtomContainerPermutor.setAtomContainer ( IAtomContainer ac ) :  void

cdk-1.4.0.jar, AtomContainerPrinter.class
package org.openscience.cdk.smsd.labelling
AtomContainerPrinter.AtomContainerPrinter ( )
AtomContainerPrinter.toString ( IAtomContainer atomContainer ) :  String

cdk-1.4.0.jar, AtomContainerRenderer.class
package org.openscience.cdk.renderer
AtomContainerRenderer.AtomContainerRenderer ( List generators, IFontManager fontManager )
AtomContainerRenderer.calculateDiagramBounds ( IAtomContainer atomContainer ) :  Rectangle
AtomContainerRenderer.calculateDiagramBounds ( IChemObject x0 ) :  Rectangle
AtomContainerRenderer.calculateScaleForBondLength ( double modelBondLength ) :  double
AtomContainerRenderer.getGenerators ( ) :  List
AtomContainerRenderer.paint ( IAtomContainer atomContainer, IDrawVisitor drawVisitor ) :  Rectangle
AtomContainerRenderer.paint ( IAtomContainer atomContainer, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) :  void
AtomContainerRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) :  Rectangle
AtomContainerRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) :  void
AtomContainerRenderer.reset ( ) :  void
AtomContainerRenderer.setScale ( IAtomContainer atomContainer ) :  void
AtomContainerRenderer.setScale ( IChemObject x0 ) :  void
AtomContainerRenderer.setup ( IAtomContainer atomContainer, Rectangle screen ) :  void
AtomContainerRenderer.setup ( IChemObject x0, Rectangle x1 ) :  void

cdk-1.4.0.jar, AtomContainerSet.class
package org.openscience.cdk
AtomContainerSet.sortAtomContainers ( Comparator comparator ) :  void

cdk-1.4.0.jar, AtomMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
AtomMatcher.matches ( IAtomContainer p1, IAtom p2 ) [abstract] :  boolean

cdk-1.4.0.jar, AtomParity.class
package org.openscience.cdk
AtomParity.getBuilder ( ) :  IChemObjectBuilder

cdk-1.4.0.jar, AtomPermutor.class
package signature.chemistry
AtomPermutor.AtomPermutor ( Molecule molecule )
AtomPermutor.next ( ) :  Molecule
AtomPermutor.next ( ) :  Object
AtomPermutor.remove ( ) :  void

cdk-1.4.0.jar, AtomRadius.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.AtomRadius.BasicAtomGenerator.AtomRadius ( )
BasicAtomGenerator.AtomRadius.getDefault ( ) :  Double
BasicAtomGenerator.AtomRadius.getDefault ( ) :  Object

cdk-1.4.0.jar, AtomSignature.class
package org.openscience.cdk.signature
AtomSignature.AtomSignature ( IAtom atom, IAtomContainer molecule )
AtomSignature.AtomSignature ( IAtom atom, int height, AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule )
AtomSignature.AtomSignature ( IAtom atom, int height, IAtomContainer molecule )
AtomSignature.AtomSignature ( int atomIndex, IAtomContainer molecule )
AtomSignature.AtomSignature ( int atomIndex, int height, AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule )
AtomSignature.AtomSignature ( int atomIndex, int height, IAtomContainer molecule )
AtomSignature.getConnected ( int vertexIndex ) :  int[ ]
AtomSignature.getEdgeLabel ( int vertexIndex, int otherVertexIndex ) :  String
AtomSignature.getIntLabel ( int vertexIndex ) :  int
AtomSignature.getVertexSymbol ( int vertexIndex ) :  String
package signature.chemistry
AtomSignature.AtomSignature ( Molecule molecule, int atomNumber )
AtomSignature.AtomSignature ( Molecule molecule, int atomNumber, int height )
AtomSignature.AtomSignature ( Molecule molecule, int atomNumber, int height, AbstractVertexSignature.InvariantType invariantType )
AtomSignature.getConnected ( int vertexIndex ) :  int[ ]
AtomSignature.getEdgeLabel ( int vertexIndex, int otherVertexIndex ) :  String
AtomSignature.getIntLabel ( int vertexIndex ) :  int
AtomSignature.getVertexSymbol ( int vertexIndex ) :  String

cdk-1.4.0.jar, AtomSymbolElement.class
package org.openscience.cdk.renderer.elements
AtomSymbolElement.accept ( IRenderingVisitor v ) :  void
AtomSymbolElement.AtomSymbolElement ( double x, double y, String symbol, Integer formalCharge, Integer hydrogenCount, int alignment, Color color )

cdk-1.4.0.jar, AWTDrawVisitor.class
package org.openscience.cdk.renderer.visitor
AWTDrawVisitor.AWTDrawVisitor ( Graphics2D graphics )
AWTDrawVisitor.setFontManager ( IFontManager fontManager ) :  void
AWTDrawVisitor.setRendererModel ( RendererModel rendererModel ) :  void
AWTDrawVisitor.visit ( IRenderingElement element ) :  void

cdk-1.4.0.jar, AWTFontManager.class
package org.openscience.cdk.renderer.font
AWTFontManager.AWTFontManager ( )
AWTFontManager.getFont ( ) :  Font
AWTFontManager.makeFonts ( ) :  void
AWTFontManager.setFontForZoom ( double zoom ) :  void

cdk-1.4.0.jar, BackgroundColor.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.BackgroundColor.BasicSceneGenerator.BackgroundColor ( )
BasicSceneGenerator.BackgroundColor.getDefault ( ) :  Color
BasicSceneGenerator.BackgroundColor.getDefault ( ) :  Object

cdk-1.4.0.jar, BackReference.class
package com.hp.hpl.jena.graph.query.regexptrees
BackReference.BackReference ( int n )
BackReference.equals ( Object other ) :  boolean
BackReference.getIndex ( ) :  int
BackReference.hashCode ( ) :  int
BackReference.toString ( ) :  String

cdk-1.4.0.jar, BackwardRuleInfGraphI.class
package com.hp.hpl.jena.reasoner.rulesys
BackwardRuleInfGraphI.findDataMatches ( TriplePattern p1 ) [abstract] :  ExtendedIterator
BackwardRuleInfGraphI.getTemp ( Node p1, Node p2, Node p3 ) [abstract] :  Node
BackwardRuleInfGraphI.getVersion ( ) [abstract] :  int
BackwardRuleInfGraphI.logDerivation ( Triple p1, Derivation p2 ) [abstract] :  void
BackwardRuleInfGraphI.processBuiltin ( ClauseEntry p1, Rule p2, BindingEnvironment p3 ) [abstract] :  boolean

cdk-1.4.0.jar, BadBooleanException.class
package com.hp.hpl.jena.shared
BadBooleanException.BadBooleanException ( String spelling )

cdk-1.4.0.jar, BadCharLiteralException.class
package com.hp.hpl.jena.shared
BadCharLiteralException.BadCharLiteralException ( String spelling )

cdk-1.4.0.jar, BadDescriptionException.class
package com.hp.hpl.jena.shared
BadDescriptionException.BadDescriptionException ( String message, Model badModel )

cdk-1.4.0.jar, BadDescriptionMultipleRootsException.class
package com.hp.hpl.jena.shared
BadDescriptionMultipleRootsException.BadDescriptionMultipleRootsException ( Model badModel, Resource type )

cdk-1.4.0.jar, BadDescriptionNoRootException.class
package com.hp.hpl.jena.shared
BadDescriptionNoRootException.BadDescriptionNoRootException ( Model badModel, Resource type )

cdk-1.4.0.jar, BadObjectException.class
package com.hp.hpl.jena.assembler
BadObjectException.BadObjectException ( Statement s )
BadObjectException.getObject ( ) :  RDFNode

cdk-1.4.0.jar, BadURIException.class
package com.hp.hpl.jena.shared
BadURIException.BadURIException ( String message )

cdk-1.4.0.jar, Bag.class
package com.hp.hpl.jena.rdf.model
Bag.remove ( Statement p1 ) [abstract] :  Container

cdk-1.4.0.jar, Base.class
package com.hp.hpl.jena.graph.query
Expression.Base.argCount ( ) :  int
Expression.Base.equals ( Object other ) :  boolean
Expression.Base.Expression.Base ( )
Expression.Base.getArg ( int i ) :  Expression
Expression.Base.getFun ( ) :  String
Expression.Base.getName ( ) :  String
Expression.Base.getValue ( ) :  Object
Expression.Base.isApply ( ) :  boolean
Expression.Base.isConstant ( ) :  boolean
Expression.Base.isVariable ( ) :  boolean

cdk-1.4.0.jar, BaseBuiltin.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
BaseBuiltin.BaseBuiltin ( )
BaseBuiltin.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
BaseBuiltin.checkArgs ( int length, RuleContext context ) :  void
BaseBuiltin.getArg ( int n, Node[ ] args, RuleContext context ) :  Node
BaseBuiltin.getArgLength ( ) :  int
BaseBuiltin.getURI ( ) :  String
BaseBuiltin.headAction ( Node[ ] args, int length, RuleContext context ) :  void
BaseBuiltin.isMonotonic ( ) :  boolean
BaseBuiltin.isSafe ( ) :  boolean

cdk-1.4.0.jar, BaseDatatype.class
package com.hp.hpl.jena.datatypes
BaseDatatype.BaseDatatype ( String uri )
BaseDatatype.cannonicalise ( Object value ) :  Object
BaseDatatype.extendedTypeDefinition ( ) :  Object
BaseDatatype.getHashCode ( LiteralLabel lit ) :  int
BaseDatatype.getJavaClass ( ) :  Class
BaseDatatype.getURI ( ) :  String
BaseDatatype.isEqual ( LiteralLabel value1, LiteralLabel value2 ) :  boolean
BaseDatatype.isValid ( String lexicalForm ) :  boolean
BaseDatatype.isValidLiteral ( LiteralLabel lit ) :  boolean
BaseDatatype.isValidValue ( Object valueForm ) :  boolean
BaseDatatype.langTagCompatible ( LiteralLabel value1, LiteralLabel value2 ) :  boolean
BaseDatatype.normalizeSubType ( Object value, RDFDatatype dt ) :  RDFDatatype
BaseDatatype.parse ( String lexicalForm ) :  Object
BaseDatatype.toString ( ) :  String
BaseDatatype.unparse ( Object value ) :  String

cdk-1.4.0.jar, BaseInfGraph.class
package com.hp.hpl.jena.reasoner
BaseInfGraph.BaseInfGraph ( Graph data, Reasoner reasoner )
BaseInfGraph.BaseInfGraph ( Graph data, Reasoner reasoner, ReificationStyle style )
BaseInfGraph.cloneWithPremises ( Graph premises ) :  InfGraph
BaseInfGraph.close ( ) :  void
BaseInfGraph.constructReifier ( ) :  Reifier
BaseInfGraph.discardState ( ) :  void
BaseInfGraph.find ( Node subject, Node property, Node object, Graph param ) :  ExtendedIterator
BaseInfGraph.find ( TriplePattern pattern ) :  ExtendedIterator
BaseInfGraph.findWithContinuation ( TriplePattern p1, Finder p2 ) [abstract] :  ExtendedIterator
BaseInfGraph.getBulkUpdateHandler ( ) :  BulkUpdateHandler
BaseInfGraph.getCapabilities ( ) :  Capabilities
BaseInfGraph.getDeductionsGraph ( ) :  Graph
BaseInfGraph.getDerivation ( Triple triple ) :  Iterator
BaseInfGraph.getGlobalProperty ( Node property ) :  Node
BaseInfGraph.getPrefixMapping ( ) :  PrefixMapping
BaseInfGraph.getRawGraph ( ) :  Graph
BaseInfGraph.getReasoner ( ) :  Reasoner
BaseInfGraph.getSchemaGraph ( ) [abstract] :  Graph
BaseInfGraph.getTransactionHandler ( ) :  TransactionHandler
BaseInfGraph.getVersion ( ) :  int
BaseInfGraph.graphBaseFind ( Node subject, Node property, Node object ) :  ExtendedIterator
BaseInfGraph.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
BaseInfGraph.graphBaseSize ( ) :  int
BaseInfGraph.isEmpty ( ) :  boolean
BaseInfGraph.isPrepared ( ) :  boolean
BaseInfGraph.performAdd ( Triple t ) :  void
BaseInfGraph.performDelete ( Triple t ) :  void
BaseInfGraph.prepare ( ) :  void
BaseInfGraph.rebind ( ) :  void
BaseInfGraph.rebind ( Graph data ) :  void
BaseInfGraph.reset ( ) :  void
BaseInfGraph.setDerivationLogging ( boolean logOn ) :  void
BaseInfGraph.testGlobalProperty ( Node property ) :  boolean
BaseInfGraph.validate ( ) :  ValidityReport

cdk-1.4.0.jar, BasicAtomGenerator.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.BasicAtomGenerator ( )
BasicAtomGenerator.canDraw ( IAtom atom, IAtomContainer container, RendererModel model ) :  boolean
BasicAtomGenerator.generate ( IAtomContainer atomContainer, IAtom atom, RendererModel model ) :  IRenderingElement
BasicAtomGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
BasicAtomGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
BasicAtomGenerator.generateCompactElement ( IAtom atom, RendererModel model ) :  IRenderingElement
BasicAtomGenerator.generateElement ( IAtom atom, int alignment, RendererModel model ) :  AtomSymbolElement
BasicAtomGenerator.getAtomColor ( IAtom atom, RendererModel model ) :  Color
BasicAtomGenerator.getParameters ( ) :  List
BasicAtomGenerator.hasCoordinates ( IAtom atom ) :  boolean
BasicAtomGenerator.invisibleCarbon ( IAtom atom, IAtomContainer atomContainer, RendererModel model ) :  boolean
BasicAtomGenerator.invisibleHydrogen ( IAtom atom, RendererModel model ) :  boolean
BasicAtomGenerator.isHydrogen ( IAtom atom ) :  boolean
BasicAtomGenerator.showCarbon ( IAtom carbonAtom, IAtomContainer container, RendererModel model ) :  boolean

cdk-1.4.0.jar, BasicBondGenerator.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.BasicBondGenerator ( )
BasicBondGenerator.bindsHydrogen ( IBond bond ) :  boolean
BasicBondGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
BasicBondGenerator.generate ( IBond currentBond, RendererModel model ) :  IRenderingElement
BasicBondGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
BasicBondGenerator.generateBond ( IBond bond, RendererModel model ) :  IRenderingElement
BasicBondGenerator.generateBondElement ( IBond bond, IBond.Order type, RendererModel model ) :  IRenderingElement
BasicBondGenerator.generateBondElement ( IBond bond, RendererModel model ) :  IRenderingElement
BasicBondGenerator.generateInnerElement ( IBond bond, IRing ring, RendererModel model ) :  LineElement
BasicBondGenerator.generateRingElements ( IBond bond, IRing ring, RendererModel model ) :  IRenderingElement
BasicBondGenerator.getColorForBond ( IBond bond, RendererModel model ) :  Color
BasicBondGenerator.getParameters ( ) :  List
BasicBondGenerator.getRingSet ( IAtomContainer atomContainer ) :  IRingSet
BasicBondGenerator.getWidthForBond ( IBond bond, RendererModel model ) :  double
BasicBondGenerator.setOverrideBondWidth ( double bondWidth ) :  void
BasicBondGenerator.setOverrideColor ( Color color ) :  void

cdk-1.4.0.jar, BasicFBReifier.class
package com.hp.hpl.jena.reasoner.rulesys
BasicFBReifier.allNodes ( ) :  ExtendedIterator
BasicFBReifier.allNodes ( Triple t ) :  ExtendedIterator
BasicFBReifier.BasicFBReifier ( BasicForwardRuleInfGraph parent, Reifier base, BasicFBReifier.GetReifier deductions, ReificationStyle style )
BasicFBReifier.close ( ) :  void
BasicFBReifier.find ( TripleMatch m ) :  ExtendedIterator
BasicFBReifier.findEither ( TripleMatch m, boolean showHidden ) :  ExtendedIterator
BasicFBReifier.findExposed ( TripleMatch m ) :  ExtendedIterator
BasicFBReifier.getParentGraph ( ) :  Graph
BasicFBReifier.getStyle ( ) :  ReificationStyle
BasicFBReifier.getTriple ( Node n ) :  Triple
BasicFBReifier.handledAdd ( Triple t ) :  boolean
BasicFBReifier.handledRemove ( Triple t ) :  boolean
BasicFBReifier.hasTriple ( Node n ) :  boolean
BasicFBReifier.hasTriple ( Triple t ) :  boolean
BasicFBReifier.reifyAs ( Node n, Triple t ) :  Node
BasicFBReifier.remove ( Node n, Triple t ) :  void
BasicFBReifier.remove ( Triple t ) :  void
BasicFBReifier.size ( ) :  int

cdk-1.4.0.jar, BasicForwardRuleInfGraph.class
package com.hp.hpl.jena.reasoner.rulesys
BasicForwardRuleInfGraph.addBRule ( Rule brule ) :  void
BasicForwardRuleInfGraph.addDeduction ( Triple t ) :  void
BasicForwardRuleInfGraph.BasicForwardRuleInfGraph ( Reasoner reasoner, Graph schema )
BasicForwardRuleInfGraph.BasicForwardRuleInfGraph ( Reasoner reasoner, List rules, Graph schema )
BasicForwardRuleInfGraph.BasicForwardRuleInfGraph ( Reasoner reasoner, List rules, Graph schema, Graph data )
BasicForwardRuleInfGraph.BasicForwardRuleInfGraph ( Reasoner reasoner, List rules, Graph schema, ReificationStyle style )
BasicForwardRuleInfGraph.close ( ) :  void
BasicForwardRuleInfGraph.constructReifier ( ) :  Reifier
BasicForwardRuleInfGraph.createDeductionsGraph ( ) :  Graph
BasicForwardRuleInfGraph.deleteBRule ( Rule brule ) :  void
BasicForwardRuleInfGraph.find ( TriplePattern pattern ) :  ExtendedIterator
BasicForwardRuleInfGraph.findDataMatches ( Node subject, Node predicate, Node object ) :  ExtendedIterator
BasicForwardRuleInfGraph.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
BasicForwardRuleInfGraph.getCurrentDeductionsGraph ( ) :  Graph
BasicForwardRuleInfGraph.getDeductionsGraph ( ) :  Graph
BasicForwardRuleInfGraph.getDerivation ( Triple t ) :  Iterator
BasicForwardRuleInfGraph.getNRulesFired ( ) :  long
BasicForwardRuleInfGraph.getSchemaGraph ( ) :  Graph
BasicForwardRuleInfGraph.graphBaseFind ( Node subject, Node property, Node object ) :  ExtendedIterator
BasicForwardRuleInfGraph.graphBaseSize ( ) :  int
BasicForwardRuleInfGraph.instantiateRuleEngine ( List rules ) :  void
BasicForwardRuleInfGraph.logDerivation ( Triple t, Derivation derivation ) :  void
BasicForwardRuleInfGraph.performAdd ( Triple t ) :  void
BasicForwardRuleInfGraph.performDelete ( Triple t ) :  void
BasicForwardRuleInfGraph.preloadDeductions ( Graph preloadIn ) :  boolean
BasicForwardRuleInfGraph.prepare ( ) :  void
BasicForwardRuleInfGraph.rebind ( ) :  void
BasicForwardRuleInfGraph.rebind ( Graph data ) :  void
BasicForwardRuleInfGraph.setDerivationLogging ( boolean recordDerivations ) :  void
BasicForwardRuleInfGraph.setRuleStore ( Object ruleStore ) :  void
BasicForwardRuleInfGraph.setTraceOn ( boolean state ) :  void
BasicForwardRuleInfGraph.shouldLogDerivations ( ) :  boolean
BasicForwardRuleInfGraph.shouldTrace ( ) :  boolean
BasicForwardRuleInfGraph.silentAdd ( Triple t ) :  void

cdk-1.4.0.jar, BasicForwardRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
BasicForwardRuleReasoner.addDescription ( Model configSpec, Resource base ) :  void
BasicForwardRuleReasoner.BasicForwardRuleReasoner ( List rules )
BasicForwardRuleReasoner.BasicForwardRuleReasoner ( List rules, ReasonerFactory factory )
BasicForwardRuleReasoner.bind ( Graph data ) :  InfGraph
BasicForwardRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
BasicForwardRuleReasoner.bindSchema ( Model tbox ) :  Reasoner
BasicForwardRuleReasoner.getGraphCapabilities ( ) :  Capabilities
BasicForwardRuleReasoner.getReasonerCapabilities ( ) :  Model
BasicForwardRuleReasoner.getRules ( ) :  List
BasicForwardRuleReasoner.setDerivationLogging ( boolean logOn ) :  void
BasicForwardRuleReasoner.setParameter ( Property parameter, Object value ) :  void
BasicForwardRuleReasoner.setTraceOn ( boolean state ) :  void
BasicForwardRuleReasoner.supportsProperty ( Property property ) :  boolean

cdk-1.4.0.jar, BasicGenerator.class
package org.openscience.cdk.renderer.generators
BasicGenerator.BasicGenerator ( )
BasicGenerator.generate ( IAtomContainer ac, RendererModel model ) :  IRenderingElement
BasicGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
BasicGenerator.getParameters ( ) :  List

cdk-1.4.0.jar, BasicGroupCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
BasicGroupCountDescriptor.BasicGroupCountDescriptor ( )
BasicGroupCountDescriptor.calculate ( IAtomContainer atomContainer ) :  DescriptorValue
BasicGroupCountDescriptor.getDescriptorNames ( ) :  String[ ]
BasicGroupCountDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
BasicGroupCountDescriptor.getParameterNames ( ) :  String[ ]
BasicGroupCountDescriptor.getParameters ( ) :  Object[ ]
BasicGroupCountDescriptor.getParameterType ( String name ) :  Object
BasicGroupCountDescriptor.getSpecification ( ) :  DescriptorSpecification
BasicGroupCountDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.0.jar, BasicKeyIterator.class
package com.hp.hpl.jena.mem
HashCommon.BasicKeyIterator.HashCommon.BasicKeyIterator ( HashCommon initialChanges, int container, HashCommon.NotifyEmpty movedKeys, List p4 )
HashCommon.BasicKeyIterator.hasNext ( ) :  boolean
HashCommon.BasicKeyIterator.next ( ) :  Object
HashCommon.BasicKeyIterator.remove ( ) :  void

cdk-1.4.0.jar, BasicMarker.class
package org.slf4j.helpers
BasicMarker.add ( Marker reference ) :  void
BasicMarker.contains ( Marker other ) :  boolean
BasicMarker.contains ( String name ) :  boolean
BasicMarker.equals ( Object obj ) :  boolean
BasicMarker.getName ( ) :  String
BasicMarker.hasChildren ( ) :  boolean
BasicMarker.hashCode ( ) :  int
BasicMarker.hasReferences ( ) :  boolean
BasicMarker.iterator ( ) :  Iterator
BasicMarker.remove ( Marker referenceToRemove ) :  boolean
BasicMarker.toString ( ) :  String

cdk-1.4.0.jar, BasicMarkerFactory.class
package org.slf4j.helpers
BasicMarkerFactory.BasicMarkerFactory ( )
BasicMarkerFactory.detachMarker ( String name ) :  boolean
BasicMarkerFactory.exists ( String name ) :  boolean
BasicMarkerFactory.getDetachedMarker ( String name ) :  Marker
BasicMarkerFactory.getMarker ( String name ) :  Marker

cdk-1.4.0.jar, BasicMDCAdapter.class
package org.slf4j.helpers
BasicMDCAdapter.BasicMDCAdapter ( )
BasicMDCAdapter.clear ( ) :  void
BasicMDCAdapter.get ( String key ) :  String
BasicMDCAdapter.getCopyOfContextMap ( ) :  Map
BasicMDCAdapter.getKeys ( ) :  Set
BasicMDCAdapter.put ( String key, String val ) :  void
BasicMDCAdapter.remove ( String key ) :  void
BasicMDCAdapter.setContextMap ( Map contextMap ) :  void

cdk-1.4.0.jar, BasicParser.class
package org.apache.commons.cli
BasicParser.BasicParser ( )
BasicParser.flatten ( Options options, String[ ] arguments, boolean stopAtNonOption ) :  String[ ]

cdk-1.4.0.jar, BasicSceneGenerator.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.BasicSceneGenerator ( )
BasicSceneGenerator.generate ( IAtomContainer ac, RendererModel model ) :  IRenderingElement
BasicSceneGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
BasicSceneGenerator.getParameters ( ) :  List

cdk-1.4.0.jar, BasicValidator.class
package org.openscience.cdk.validate
BasicValidator.validateAtom ( IAtom subject ) :  ValidationReport
BasicValidator.validateBond ( IBond subject ) :  ValidationReport
BasicValidator.validateMolecule ( IMolecule subject ) :  ValidationReport
BasicValidator.validateReaction ( IReaction subject ) :  ValidationReport

cdk-1.4.0.jar, BigDecimal.class
package com.ibm.icu.math
BigDecimal.abs ( ) :  BigDecimal
BigDecimal.abs ( MathContext set ) :  BigDecimal
BigDecimal.add ( BigDecimal rhs ) :  BigDecimal
BigDecimal.add ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.BigDecimal ( BigDecimal bd )
BigDecimal.BigDecimal ( BigInteger bi )
BigDecimal.BigDecimal ( BigInteger bi, int scale )
BigDecimal.BigDecimal ( char[ ] inchars )
BigDecimal.BigDecimal ( char[ ] inchars, int offset, int length )
BigDecimal.BigDecimal ( double num )
BigDecimal.BigDecimal ( int num )
BigDecimal.BigDecimal ( long num )
BigDecimal.BigDecimal ( String string )
BigDecimal.byteValueExact ( ) :  byte
BigDecimal.compareTo ( BigDecimal rhs ) :  int
BigDecimal.compareTo ( BigDecimal rhs, MathContext set ) :  int
BigDecimal.compareTo ( Object rhsobj ) :  int
BigDecimal.divide ( BigDecimal rhs ) :  BigDecimal
BigDecimal.divide ( BigDecimal rhs, int round ) :  BigDecimal
BigDecimal.divide ( BigDecimal rhs, int scale, int round ) :  BigDecimal
BigDecimal.divide ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.divideInteger ( BigDecimal rhs ) :  BigDecimal
BigDecimal.divideInteger ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.doubleValue ( ) :  double
BigDecimal.equals ( Object obj ) :  boolean
BigDecimal.floatValue ( ) :  float
BigDecimal.format ( int before, int after ) :  String
BigDecimal.format ( int before, int after, int explaces, int exdigits, int exformint, int exround ) :  String
BigDecimal.hashCode ( ) :  int
BigDecimal.intValue ( ) :  int
BigDecimal.intValueExact ( ) :  int
BigDecimal.longValue ( ) :  long
BigDecimal.longValueExact ( ) :  long
BigDecimal.max ( BigDecimal rhs ) :  BigDecimal
BigDecimal.max ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.min ( BigDecimal rhs ) :  BigDecimal
BigDecimal.min ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.movePointLeft ( int n ) :  BigDecimal
BigDecimal.movePointRight ( int n ) :  BigDecimal
BigDecimal.multiply ( BigDecimal rhs ) :  BigDecimal
BigDecimal.multiply ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.negate ( ) :  BigDecimal
BigDecimal.negate ( MathContext set ) :  BigDecimal
BigDecimal.plus ( ) :  BigDecimal
BigDecimal.plus ( MathContext set ) :  BigDecimal
BigDecimal.pow ( BigDecimal rhs ) :  BigDecimal
BigDecimal.pow ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.remainder ( BigDecimal rhs ) :  BigDecimal
BigDecimal.remainder ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.scale ( ) :  int
BigDecimal.setScale ( int scale ) :  BigDecimal
BigDecimal.setScale ( int scale, int round ) :  BigDecimal
BigDecimal.shortValueExact ( ) :  short
BigDecimal.signum ( ) :  int
BigDecimal.subtract ( BigDecimal rhs ) :  BigDecimal
BigDecimal.subtract ( BigDecimal rhs, MathContext set ) :  BigDecimal
BigDecimal.toBigDecimal ( ) :  BigDecimal
BigDecimal.toBigInteger ( ) :  BigInteger
BigDecimal.toBigIntegerExact ( ) :  BigInteger
BigDecimal.toCharArray ( ) :  char[ ]
BigDecimal.toString ( ) :  String
BigDecimal.unscaledValue ( ) :  BigInteger
BigDecimal.valueOf ( double dub ) [static] :  BigDecimal
BigDecimal.valueOf ( long lint ) [static] :  BigDecimal
BigDecimal.valueOf ( long lint, int scale ) [static] :  BigDecimal

cdk-1.4.0.jar, BinaryTree.class
package org.openscience.cdk.smsd.helper
BinaryTree.BinaryTree ( int value )
BinaryTree.getEqual ( ) :  BinaryTree
BinaryTree.getNotEqual ( ) :  BinaryTree
BinaryTree.getValue ( ) :  int
BinaryTree.setEqual ( BinaryTree equal ) :  void
BinaryTree.setNotEqual ( BinaryTree notEqual ) :  void

cdk-1.4.0.jar, Bind.class
package com.hp.hpl.jena.graph.query
Bind.asNodeMatch ( Domain d ) :  Node
Bind.Bind ( int n )
Bind.match ( Domain d, Node x ) :  boolean
Bind.toString ( ) :  String
QueryNode.Bind.isFrozen ( ) :  boolean
QueryNode.Bind.match ( Domain d, Node value ) :  boolean
QueryNode.Bind.matchOrBind ( Domain d, Node value ) :  boolean
QueryNode.Bind.mustMatch ( ) :  boolean
QueryNode.Bind.QueryNode.Bind ( Node n, int index )
QueryNode.Bind.toString ( ) :  String

cdk-1.4.0.jar, BindingEnvironment.class
package com.hp.hpl.jena.reasoner.rulesys
BindingEnvironment.bind ( Node p1, Node p2 ) [abstract] :  boolean
BindingEnvironment.getGroundVersion ( Node p1 ) [abstract] :  Node
BindingEnvironment.instantiate ( TriplePattern p1 ) [abstract] :  Triple

cdk-1.4.0.jar, BindingQueryPlan.class
package com.hp.hpl.jena.graph.query
BindingQueryPlan.executeBindings ( ) [abstract] :  ExtendedIterator

cdk-1.4.0.jar, Bits.class
package com.hp.hpl.jena.shared.uuid
Bits.access ( long bits, int start, int finish ) [static] :  long
Bits.Bits ( )
Bits.clear ( long bits, int start, int finish ) [static] :  long
Bits.mask ( int start, int finish ) [static] :  long
Bits.maskZero ( int start, int finish ) [static] :  long
Bits.pack ( long bits, long value, int start, int finish ) [static] :  long
Bits.set ( long bits, int bitIndex ) [static] :  long
Bits.set ( long bits, int start, int finish ) [static] :  long
Bits.test ( long bits, boolean isSet, int bitIndex ) [static] :  boolean
Bits.test ( long bits, long value, int start, int finish ) [static] :  boolean
Bits.unpack ( long bits, int start, int finish ) [static] :  long
Bits.unpack ( String str, int startChar, int finishChar ) [static] :  long

cdk-1.4.0.jar, BKKCKCF.class
package org.openscience.cdk.smsd.algorithm.mcsplus
BKKCKCF.BKKCKCF ( List comp_graph_nodes_org, List C_edges_org, List D_edges_org )
BKKCKCF.getBestCliqueSize ( ) :  int
BKKCKCF.getMaxCliqueSet ( ) :  Stack

cdk-1.4.0.jar, Bond.class
package org.openscience.cdk
Bond.Bond ( IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo )
Bond.getStereo ( ) :  IBond.Stereo
Bond.setStereo ( IBond.Stereo stereo ) :  void
package signature.chemistry
Molecule.Bond.compareTo ( Molecule.Bond o ) :  int
Molecule.Bond.compareTo ( Object p1 ) :  int
Molecule.Bond.equals ( Object o ) :  boolean
Molecule.Bond.getConnected ( int i ) :  int
Molecule.Bond.hasBoth ( int atomIndexA, int atomIndexB ) :  boolean
Molecule.Bond.Molecule.Bond ( Molecule a, Molecule.Atom b, Molecule.Atom order, int p4 )
Molecule.Bond.Molecule.Bond ( Molecule other, Molecule.Bond p2 )
Molecule.Bond.toString ( ) :  String

cdk-1.4.0.jar, BondDistance.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.BondDistance.BasicBondGenerator.BondDistance ( )
BasicBondGenerator.BondDistance.getDefault ( ) :  Double
BasicBondGenerator.BondDistance.getDefault ( ) :  Object

cdk-1.4.0.jar, BondEnergies.class
package org.openscience.cdk.smsd.tools
BondEnergies.BondEnergies ( )
BondEnergies.getEnergies ( IAtom sourceAtom, IAtom targetAtom, IBond.Order bondOrder ) :  int
BondEnergies.getEnergies ( IBond bond ) :  int
BondEnergies.getEnergies ( String sourceAtom, String targetAtom, IBond.Order bondOrder ) :  int
BondEnergies.getInstance ( ) [static] :  BondEnergies

cdk-1.4.0.jar, BondEnergy.class
package org.openscience.cdk.smsd.helper
BondEnergy.BondEnergy ( String symbol1, String symbol2, IBond.Order order, int energy )
BondEnergy.getBondOrder ( ) :  IBond.Order
BondEnergy.getEnergy ( ) :  int
BondEnergy.getSymbolFirstAtom ( ) :  String
BondEnergy.getSymbolSecondAtom ( ) :  String
BondEnergy.matches ( IBond bond ) :  boolean

cdk-1.4.0.jar, BondLength.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.BondLength.BasicBondGenerator.BondLength ( )
BasicBondGenerator.BondLength.getDefault ( ) :  Double
BasicBondGenerator.BondLength.getDefault ( ) :  Object

cdk-1.4.0.jar, BondMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
BondMatcher.matches ( IAtomContainer p1, IBond p2 ) [abstract] :  boolean

cdk-1.4.0.jar, BondWidth.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.BondWidth.BasicBondGenerator.BondWidth ( )
BasicBondGenerator.BondWidth.getDefault ( ) :  Double
BasicBondGenerator.BondWidth.getDefault ( ) :  Object

cdk-1.4.0.jar, BoolConstant.class
package com.hp.hpl.jena.graph.query
Expression.BoolConstant.evalBool ( IndexValues vv ) :  boolean
Expression.BoolConstant.evalBool ( VariableValues vv ) :  boolean
Expression.BoolConstant.evalObject ( IndexValues iv ) :  Object
Expression.BoolConstant.Expression.BoolConstant ( boolean value )
Expression.BoolConstant.getValue ( ) :  Object
Expression.BoolConstant.isConstant ( ) :  boolean
Expression.BoolConstant.prepare ( VariableIndexes vi ) :  Valuator

cdk-1.4.0.jar, BooleanClassDescription.class
package com.hp.hpl.jena.ontology
BooleanClassDescription.addOperand ( Resource p1 ) [abstract] :  void
BooleanClassDescription.addOperands ( Iterator p1 ) [abstract] :  void
BooleanClassDescription.getOperands ( ) [abstract] :  RDFList
BooleanClassDescription.hasOperand ( Resource p1 ) [abstract] :  boolean
BooleanClassDescription.listOperands ( ) [abstract] :  ExtendedIterator
BooleanClassDescription.operator ( ) [abstract] :  Property
BooleanClassDescription.removeOperand ( Resource p1 ) [abstract] :  void
BooleanClassDescription.setOperands ( RDFList p1 ) [abstract] :  void

cdk-1.4.0.jar, Bound.class
package com.hp.hpl.jena.graph.query
Bound.asNodeMatch ( Domain d ) :  Node
Bound.Bound ( int n )
Bound.match ( Domain d, Node x ) :  boolean
Bound.toString ( ) :  String
QueryNode.Bound.finder ( Domain d ) :  Node
QueryNode.Bound.matchOrBind ( Domain d, Node x ) :  boolean
QueryNode.Bound.QueryNode.Bound ( Node n, int index )
QueryNode.Bound.toString ( ) :  String
package com.hp.hpl.jena.reasoner.rulesys.builtins
Bound.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Bound.Bound ( )
Bound.getName ( ) :  String

cdk-1.4.0.jar, BoundsCalculator.class
package org.openscience.cdk.renderer
BoundsCalculator.BoundsCalculator ( )
BoundsCalculator.calculateBounds ( IAtomContainer atomContainer ) [static] :  Rectangle2D
BoundsCalculator.calculateBounds ( IChemModel chemModel ) [static] :  Rectangle2D
BoundsCalculator.calculateBounds ( IMoleculeSet moleculeSet ) [static] :  Rectangle2D
BoundsCalculator.calculateBounds ( IReaction reaction ) [static] :  Rectangle2D
BoundsCalculator.calculateBounds ( IReactionSet reactionSet ) [static] :  Rectangle2D

cdk-1.4.0.jar, BreakDictionary.class
package com.ibm.icu.text
BreakDictionary.at ( int row, char ch ) :  short
BreakDictionary.at ( int row, int col ) :  short
BreakDictionary.BreakDictionary ( InputStream dictionaryStream )
BreakDictionary.main ( String[ ] args ) [static] :  void
BreakDictionary.printWordList ( String partialWord, int state, PrintWriter out ) :  void
BreakDictionary.readDictionaryFile ( DataInputStream in ) :  void

cdk-1.4.0.jar, BreakIterator.class
package com.ibm.icu.text
BreakIterator.BreakIterator ( )
BreakIterator.clone ( ) :  Object
BreakIterator.current ( ) [abstract] :  int
BreakIterator.first ( ) [abstract] :  int
BreakIterator.following ( int p1 ) [abstract] :  int
BreakIterator.getAvailableLocales ( ) [static] :  Locale[ ]
BreakIterator.getAvailableULocales ( ) [static] :  ULocale[ ] *DEPRECATED*
BreakIterator.getCharacterInstance ( ) [static] :  BreakIterator
BreakIterator.getCharacterInstance ( Locale where ) [static] :  BreakIterator
BreakIterator.getCharacterInstance ( ULocale where ) [static] :  BreakIterator *DEPRECATED*
BreakIterator.getLineInstance ( ) [static] :  BreakIterator
BreakIterator.getLineInstance ( Locale where ) [static] :  BreakIterator
BreakIterator.getLineInstance ( ULocale where ) [static] :  BreakIterator *DEPRECATED*
BreakIterator.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
BreakIterator.getSentenceInstance ( ) [static] :  BreakIterator
BreakIterator.getSentenceInstance ( Locale where ) [static] :  BreakIterator
BreakIterator.getSentenceInstance ( ULocale where ) [static] :  BreakIterator *DEPRECATED*
BreakIterator.getText ( ) [abstract] :  CharacterIterator
BreakIterator.getTitleInstance ( ) [static] :  BreakIterator
BreakIterator.getTitleInstance ( Locale where ) [static] :  BreakIterator
BreakIterator.getTitleInstance ( ULocale where ) [static] :  BreakIterator *DEPRECATED*
BreakIterator.getWordInstance ( ) [static] :  BreakIterator
BreakIterator.getWordInstance ( Locale where ) [static] :  BreakIterator
BreakIterator.getWordInstance ( ULocale where ) [static] :  BreakIterator *DEPRECATED*
BreakIterator.isBoundary ( int offset ) :  boolean
BreakIterator.last ( ) [abstract] :  int
BreakIterator.next ( ) [abstract] :  int
BreakIterator.next ( int p1 ) [abstract] :  int
BreakIterator.preceding ( int offset ) :  int
BreakIterator.previous ( ) [abstract] :  int
BreakIterator.registerInstance ( BreakIterator iter, Locale locale, int kind ) [static] :  Object
BreakIterator.registerInstance ( BreakIterator iter, ULocale locale, int kind ) [static] :  Object *DEPRECATED*
BreakIterator.setText ( CharacterIterator p1 ) [abstract] :  void
BreakIterator.setText ( String newText ) :  void
BreakIterator.unregister ( Object key ) [static] :  boolean

cdk-1.4.0.jar, BrokenException.class
package com.hp.hpl.jena.shared
BrokenException.BrokenException ( String message )
BrokenException.BrokenException ( String message, Throwable cause )
BrokenException.BrokenException ( Throwable cause )

cdk-1.4.0.jar, BuddhistCalendar.class
package com.ibm.icu.util
BuddhistCalendar.BuddhistCalendar ( )
BuddhistCalendar.BuddhistCalendar ( Date date )
BuddhistCalendar.BuddhistCalendar ( int year, int month, int date )
BuddhistCalendar.BuddhistCalendar ( int year, int month, int date, int hour, int minute, int second )
BuddhistCalendar.BuddhistCalendar ( Locale aLocale )
BuddhistCalendar.BuddhistCalendar ( TimeZone zone )
BuddhistCalendar.BuddhistCalendar ( TimeZone zone, Locale aLocale )
BuddhistCalendar.BuddhistCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
BuddhistCalendar.BuddhistCalendar ( ULocale locale ) *DEPRECATED*
BuddhistCalendar.getType ( ) :  String
BuddhistCalendar.handleComputeFields ( int julianDay ) :  void
BuddhistCalendar.handleComputeMonthStart ( int eyear, int month, boolean useMonth ) :  int
BuddhistCalendar.handleGetExtendedYear ( ) :  int
BuddhistCalendar.handleGetLimit ( int field, int limitType ) :  int

cdk-1.4.0.jar, BufferPipe.class
package com.hp.hpl.jena.graph.query
BufferPipe.BufferPipe ( )
BufferPipe.close ( ) :  void
BufferPipe.close ( Exception e ) :  void
BufferPipe.get ( ) :  Domain
BufferPipe.hasNext ( ) :  boolean
BufferPipe.put ( Domain d ) :  void

cdk-1.4.0.jar, Builder.class
package com.ibm.icu.text
DictionaryBasedBreakIterator.Builder.buildCharCategories ( Vector tempRuleList ) :  void
DictionaryBasedBreakIterator.Builder.DictionaryBasedBreakIterator.Builder ( DictionaryBasedBreakIterator p1 )
DictionaryBasedBreakIterator.Builder.handleSpecialSubstitution ( String replace, String replaceWith, int startPos, String description ) :  void
DictionaryBasedBreakIterator.Builder.mungeExpressionList ( Hashtable expressions ) :  void
RuleBasedBreakIterator_Old.Builder.buildBreakIterator ( ) :  void
RuleBasedBreakIterator_Old.Builder.buildCharCategories ( Vector tempRuleList ) :  void
RuleBasedBreakIterator_Old.Builder.debugPrintTempStateTable ( ) :  void
RuleBasedBreakIterator_Old.Builder.debugPrintVector ( String label, Vector v ) :  void
RuleBasedBreakIterator_Old.Builder.debugPrintVectorOfVectors ( String label1, String label2, Vector v ) :  void
RuleBasedBreakIterator_Old.Builder.error ( String message, int position, String context ) :  void
RuleBasedBreakIterator_Old.Builder.handleSpecialSubstitution ( String replace, String replaceWith, int startPos, String description ) :  void
RuleBasedBreakIterator_Old.Builder.mungeExpressionList ( Hashtable expressions ) :  void
RuleBasedBreakIterator_Old.Builder.processSubstitution ( String substitutionRule, String description, int startPos ) :  String
RuleBasedBreakIterator_Old.Builder.RuleBasedBreakIterator_Old.Builder ( RuleBasedBreakIterator_Old p1 )

cdk-1.4.0.jar, Builtin.class
package com.hp.hpl.jena.reasoner.rulesys
Builtin.bodyCall ( Node[ ] p1, int p2, RuleContext p3 ) [abstract] :  boolean
Builtin.getArgLength ( ) [abstract] :  int
Builtin.getName ( ) [abstract] :  String
Builtin.getURI ( ) [abstract] :  String
Builtin.headAction ( Node[ ] p1, int p2, RuleContext p3 ) [abstract] :  void
Builtin.isMonotonic ( ) [abstract] :  boolean
Builtin.isSafe ( ) [abstract] :  boolean

cdk-1.4.0.jar, BuiltinException.class
package com.hp.hpl.jena.reasoner.rulesys
BuiltinException.BuiltinException ( Builtin builtin, RuleContext context, String message )

cdk-1.4.0.jar, BuiltinPersonalities.class
package com.hp.hpl.jena.enhanced
BuiltinPersonalities.BuiltinPersonalities ( )
BuiltinPersonalities.listPersonalities ( PrintWriter writer ) [static] :  void

cdk-1.4.0.jar, BuiltinRegistry.class
package com.hp.hpl.jena.reasoner.rulesys
BuiltinRegistry.BuiltinRegistry ( )
BuiltinRegistry.getImplementation ( String functor ) :  Builtin
BuiltinRegistry.getImplementationByURI ( String uri ) :  Builtin
BuiltinRegistry.register ( Builtin impl ) :  void
BuiltinRegistry.register ( String functor, Builtin impl ) :  void

cdk-1.4.0.jar, BulkUpdateHandler.class
package com.hp.hpl.jena.graph
BulkUpdateHandler.add ( Graph p1 ) [abstract] :  void
BulkUpdateHandler.add ( Graph p1, boolean p2 ) [abstract] :  void
BulkUpdateHandler.add ( Iterator p1 ) [abstract] :  void
BulkUpdateHandler.add ( List p1 ) [abstract] :  void
BulkUpdateHandler.add ( Triple[ ] p1 ) [abstract] :  void
BulkUpdateHandler.delete ( Graph p1 ) [abstract] :  void
BulkUpdateHandler.delete ( Graph p1, boolean p2 ) [abstract] :  void
BulkUpdateHandler.delete ( Iterator p1 ) [abstract] :  void
BulkUpdateHandler.delete ( List p1 ) [abstract] :  void
BulkUpdateHandler.delete ( Triple[ ] p1 ) [abstract] :  void
BulkUpdateHandler.remove ( Node p1, Node p2, Node p3 ) [abstract] :  void
BulkUpdateHandler.removeAll ( ) [abstract] :  void

cdk-1.4.0.jar, BunchMap.class
package com.hp.hpl.jena.mem
BunchMap.clear ( ) [abstract] :  void
BunchMap.get ( Object p1 ) [abstract] :  TripleBunch
BunchMap.keyIterator ( ) [abstract] :  ExtendedIterator
BunchMap.put ( Object p1, TripleBunch p2 ) [abstract] :  void
BunchMap.remove ( Object p1 ) [abstract] :  void
BunchMap.size ( ) [abstract] :  long

cdk-1.4.0.jar, ByteArrayWrapper.class
package com.ibm.icu.util
ByteArrayWrapper.append ( byte[ ] src, int start, int limit ) :  ByteArrayWrapper *DEPRECATED*
ByteArrayWrapper.ByteArrayWrapper ( )
ByteArrayWrapper.ByteArrayWrapper ( byte[ ] bytesToAdopt, int size ) *DEPRECATED*
ByteArrayWrapper.ByteArrayWrapper ( ByteBuffer source ) *DEPRECATED*
ByteArrayWrapper.compareTo ( Object other ) :  int *DEPRECATED*
ByteArrayWrapper.ensureCapacity ( int capacity ) :  ByteArrayWrapper *DEPRECATED*
ByteArrayWrapper.equals ( Object other ) :  boolean *DEPRECATED*
ByteArrayWrapper.hashCode ( ) :  int *DEPRECATED*
ByteArrayWrapper.releaseBytes ( ) :  byte[ ]
ByteArrayWrapper.set ( byte[ ] src, int start, int limit ) :  ByteArrayWrapper *DEPRECATED*
ByteArrayWrapper.toString ( ) :  String *DEPRECATED*

cdk-1.4.0.jar, Cache.class
package com.hp.hpl.jena.util.cache
Cache.get ( Object p1 ) [abstract] :  Object
Cache.put ( Object p1, Object p2 ) [abstract] :  void

cdk-1.4.0.jar, CacheControl.class
package com.hp.hpl.jena.util.cache
CacheControl.clear ( ) [abstract] :  void
CacheControl.getEnabled ( ) [abstract] :  boolean
CacheControl.getGets ( ) [abstract] :  long
CacheControl.getHits ( ) [abstract] :  long
CacheControl.getPuts ( ) [abstract] :  long
CacheControl.setEnabled ( boolean p1 ) [abstract] :  boolean

cdk-1.4.0.jar, CacheManager.class
package com.hp.hpl.jena.util.cache
CacheManager.createCache ( String type, String name, int size ) [static] :  Cache

cdk-1.4.0.jar, Calendar.class
package com.ibm.icu.util
Calendar.add ( int field, int amount ) :  void
Calendar.after ( Object when ) :  boolean
Calendar.before ( Object when ) :  boolean
Calendar.Calendar ( )
Calendar.Calendar ( TimeZone zone, Locale aLocale )
Calendar.Calendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
Calendar.clear ( ) :  void
Calendar.clear ( int field ) :  void
Calendar.clone ( ) :  Object
Calendar.compareTo ( Calendar that ) :  int *DEPRECATED*
Calendar.compareTo ( Object that ) :  int *DEPRECATED*
Calendar.complete ( ) :  void
Calendar.computeFields ( ) :  void
Calendar.computeGregorianFields ( int julianDay ) :  void
Calendar.computeGregorianMonthStart ( int year, int month ) :  int
Calendar.computeJulianDay ( ) :  int
Calendar.computeMillisInDay ( ) :  int
Calendar.computeTime ( ) :  void
Calendar.computeZoneOffset ( long millis, int millisInDay ) :  int
Calendar.equals ( Object obj ) :  boolean
Calendar.fieldDifference ( Date when, int field ) :  int
Calendar.fieldName ( int field ) :  String
Calendar.floorDivide ( int numerator, int denominator ) [static] :  int
Calendar.floorDivide ( int numerator, int denominator, int[ ] remainder ) [static] :  int
Calendar.floorDivide ( long numerator, int denominator, int[ ] remainder ) [static] :  int
Calendar.floorDivide ( long numerator, long denominator ) [static] :  long
Calendar.get ( int field ) :  int
Calendar.getActualMaximum ( int field ) :  int
Calendar.getActualMinimum ( int field ) :  int
Calendar.getAvailableLocales ( ) [static] :  Locale[ ]
Calendar.getAvailableULocales ( ) [static] :  ULocale[ ] *DEPRECATED*
Calendar.getDateTimeFormat ( int dateStyle, int timeStyle, Locale loc ) :  DateFormat
Calendar.getDateTimeFormat ( int dateStyle, int timeStyle, ULocale loc ) :  DateFormat *DEPRECATED*
Calendar.getDayOfWeekType ( int dayOfWeek ) :  int
Calendar.getDisplayName ( Locale loc ) :  String
Calendar.getDisplayName ( ULocale loc ) :  String *DEPRECATED*
Calendar.getFieldCount ( ) :  int
Calendar.getFieldResolutionTable ( ) :  int[ ][ ][ ]
Calendar.getFirstDayOfWeek ( ) :  int
Calendar.getGreatestMinimum ( int field ) :  int
Calendar.getGregorianDayOfMonth ( ) :  int
Calendar.getGregorianDayOfYear ( ) :  int
Calendar.getGregorianMonth ( ) :  int
Calendar.getGregorianYear ( ) :  int
Calendar.getInstance ( ) [static] :  Calendar
Calendar.getInstance ( Locale aLocale ) [static] :  Calendar
Calendar.getInstance ( TimeZone zone ) [static] :  Calendar
Calendar.getInstance ( TimeZone zone, Locale aLocale ) [static] :  Calendar
Calendar.getInstance ( TimeZone zone, ULocale locale ) [static] :  Calendar *DEPRECATED*
Calendar.getInstance ( ULocale locale ) [static] :  Calendar *DEPRECATED*
Calendar.getLeastMaximum ( int field ) :  int
Calendar.getLimit ( int field, int limitType ) :  int
Calendar.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
Calendar.getMaximum ( int field ) :  int
Calendar.getMinimalDaysInFirstWeek ( ) :  int
Calendar.getMinimum ( int field ) :  int
Calendar.getStamp ( int field ) :  int
Calendar.getTime ( ) :  Date
Calendar.getTimeInMillis ( ) :  long
Calendar.getTimeZone ( ) :  TimeZone
Calendar.getType ( ) :  String
Calendar.getWeekendTransition ( int dayOfWeek ) :  int
Calendar.gregorianMonthLength ( int y, int m ) [static] :  int
Calendar.gregorianPreviousMonthLength ( int y, int m ) [static] :  int
Calendar.handleComputeFields ( int julianDay ) :  void
Calendar.handleComputeJulianDay ( int bestField ) :  int
Calendar.handleComputeMonthStart ( int p1, int p2, boolean p3 ) [abstract] :  int
Calendar.handleCreateFields ( ) :  int[ ]
Calendar.handleGetDateFormat ( String pattern, Locale locale ) :  DateFormat
Calendar.handleGetDateFormat ( String pattern, ULocale locale ) :  DateFormat *DEPRECATED*
Calendar.handleGetExtendedYear ( ) [abstract] :  int
Calendar.handleGetLimit ( int p1, int p2 ) [abstract] :  int
Calendar.handleGetMonthLength ( int extendedYear, int month ) :  int
Calendar.handleGetYearLength ( int eyear ) :  int
Calendar.hashCode ( ) :  int
Calendar.internalGet ( int field ) :  int
Calendar.internalGet ( int field, int defaultValue ) :  int
Calendar.internalGetTimeInMillis ( ) :  long
Calendar.internalSet ( int field, int value ) :  void
Calendar.isEquivalentTo ( Calendar other ) :  boolean
Calendar.isGregorianLeapYear ( int year ) [static] :  boolean
Calendar.isLenient ( ) :  boolean
Calendar.isSet ( int field ) :  boolean
Calendar.isWeekend ( ) :  boolean
Calendar.isWeekend ( Date date ) :  boolean
Calendar.julianDayToDayOfWeek ( int julian ) [static] :  int
Calendar.julianDayToMillis ( int julian ) [static] :  long
Calendar.millisToJulianDay ( long millis ) [static] :  int
Calendar.newerField ( int defaultField, int alternateField ) :  int
Calendar.newestStamp ( int first, int last, int bestStampSoFar ) :  int
Calendar.pinField ( int field ) :  void
Calendar.prepareGetActual ( int field, boolean isMinimum ) :  void
Calendar.resolveFields ( int[ ][ ][ ] precedenceTable ) :  int
Calendar.roll ( int field, boolean up ) :  void
Calendar.roll ( int field, int amount ) :  void
Calendar.set ( int field, int value ) :  void
Calendar.set ( int year, int month, int date ) :  void
Calendar.set ( int year, int month, int date, int hour, int minute ) :  void
Calendar.set ( int year, int month, int date, int hour, int minute, int second ) :  void
Calendar.setFirstDayOfWeek ( int value ) :  void
Calendar.setLenient ( boolean lenient ) :  void
Calendar.setMinimalDaysInFirstWeek ( int value ) :  void
Calendar.setTime ( Date date ) :  void
Calendar.setTimeInMillis ( long millis ) :  void
Calendar.setTimeZone ( TimeZone value ) :  void
Calendar.toString ( ) :  String
Calendar.validateField ( int field ) :  void
Calendar.validateField ( int field, int min, int max ) :  void
Calendar.validateFields ( ) :  void
Calendar.weekNumber ( int dayOfPeriod, int dayOfWeek ) :  int
Calendar.weekNumber ( int desiredDay, int dayOfPeriod, int dayOfWeek ) :  int

cdk-1.4.0.jar, CannotConstructException.class
package com.hp.hpl.jena.assembler.exceptions
CannotConstructException.CannotConstructException ( Class assemblerClass, Resource root, Resource type )
CannotConstructException.getAssemblerClass ( ) :  Class
CannotConstructException.getType ( ) :  Resource

cdk-1.4.0.jar, CannotCreateException.class
package com.hp.hpl.jena.shared
CannotCreateException.CannotCreateException ( String message )
CannotCreateException.CannotCreateException ( String message, Throwable cause )

cdk-1.4.0.jar, CannotEncodeCharacterException.class
package com.hp.hpl.jena.shared
CannotEncodeCharacterException.CannotEncodeCharacterException ( char badChar, String encodingContext )
CannotEncodeCharacterException.getBadChar ( ) :  char
CannotEncodeCharacterException.getEncodingContext ( ) :  String

cdk-1.4.0.jar, CannotHaveRulesException.class
package com.hp.hpl.jena.assembler.exceptions
CannotHaveRulesException.CannotHaveRulesException ( Resource root )

cdk-1.4.0.jar, CannotLoadClassException.class
package com.hp.hpl.jena.assembler.exceptions
CannotLoadClassException.CannotLoadClassException ( Resource root, String className, ClassNotFoundException e )
CannotLoadClassException.getClassName ( ) :  String

cdk-1.4.0.jar, CannotReifyException.class
package com.hp.hpl.jena.shared
CannotReifyException.CannotReifyException ( Node n )

cdk-1.4.0.jar, CanonicalIterator.class
package com.ibm.icu.text
CanonicalIterator.CanonicalIterator ( String source )
CanonicalIterator.getSource ( ) :  String
CanonicalIterator.next ( ) :  String
CanonicalIterator.permute ( String source, boolean skipZeros, Set output ) [static] :  void
CanonicalIterator.reset ( ) :  void
CanonicalIterator.setSource ( String newSource ) :  void

cdk-1.4.0.jar, CanonicalLabellingAdaptor.class
package org.openscience.cdk.smsd.labelling
CanonicalLabellingAdaptor.CanonicalLabellingAdaptor ( )
CanonicalLabellingAdaptor.getCanonicalMolecule ( IAtomContainer container ) :  IAtomContainer
CanonicalLabellingAdaptor.getCanonicalPermutation ( IAtomContainer container ) :  int[ ]

cdk-1.4.0.jar, CanonicalLabellingTest.class
package signature.simple
CanonicalLabellingTest.CanonicalLabellingTest ( )
CanonicalLabellingTest.fiveCycleTest ( ) :  void
CanonicalLabellingTest.fourCycleTest ( ) :  void
CanonicalLabellingTest.getLabels ( SimpleGraph graph ) :  int[ ]
CanonicalLabellingTest.isIdentity ( int[ ] permutation ) :  boolean
CanonicalLabellingTest.permuteTest ( SimpleGraph graph ) :  void
CanonicalLabellingTest.testSimpleGraphLabelling ( ) :  void
CanonicalLabellingTest.threeFourFusedCycle ( ) :  void
CanonicalLabellingTest.threeThreeFusedCycle ( ) :  void

cdk-1.4.0.jar, CanonicalLabellingVisitor.class
package signature
CanonicalLabellingVisitor.CanonicalLabellingVisitor ( int vertexCount, Comparator comparator )
CanonicalLabellingVisitor.getLabelling ( ) :  int[ ]
CanonicalLabellingVisitor.visit ( DAG.Node node ) :  void

cdk-1.4.0.jar, Capabilities.class
package com.hp.hpl.jena.graph
Capabilities.addAllowed ( ) [abstract] :  boolean
Capabilities.addAllowed ( boolean p1 ) [abstract] :  boolean
Capabilities.canBeEmpty ( ) [abstract] :  boolean
Capabilities.deleteAllowed ( ) [abstract] :  boolean
Capabilities.deleteAllowed ( boolean p1 ) [abstract] :  boolean
Capabilities.findContractSafe ( ) [abstract] :  boolean
Capabilities.handlesLiteralTyping ( ) [abstract] :  boolean
Capabilities.iteratorRemoveAllowed ( ) [abstract] :  boolean
Capabilities.sizeAccurate ( ) [abstract] :  boolean

cdk-1.4.0.jar, CardinalityQRestriction.class
package com.hp.hpl.jena.ontology
CardinalityQRestriction.getCardinalityQ ( ) [abstract] :  int
CardinalityQRestriction.hasCardinalityQ ( int p1 ) [abstract] :  boolean
CardinalityQRestriction.removeCardinalityQ ( int p1 ) [abstract] :  void
CardinalityQRestriction.setCardinalityQ ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, CardinalityRestriction.class
package com.hp.hpl.jena.ontology
CardinalityRestriction.getCardinality ( ) [abstract] :  int
CardinalityRestriction.hasCardinality ( int p1 ) [abstract] :  boolean
CardinalityRestriction.removeCardinality ( int p1 ) [abstract] :  void
CardinalityRestriction.setCardinality ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, CaseInsensitiveString.class
package com.ibm.icu.util
CaseInsensitiveString.CaseInsensitiveString ( String s )
CaseInsensitiveString.equals ( Object o ) :  boolean
CaseInsensitiveString.getString ( ) :  String
CaseInsensitiveString.hashCode ( ) :  int

cdk-1.4.0.jar, CDK.class
package org.openscience.cdk
CDK.CDK ( )
CDK.getVersion ( ) [static] :  String
package org.openscience.cdk.libio.jena
CDK.CDK ( )

cdk-1.4.0.jar, CDKMCS.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKMCS.buildRGraph ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  CDKRGraph
CDKMCS.CDKMCS ( )
CDKMCS.checkSingleAtomCases ( IAtomContainer sourceGraph, IAtomContainer targetGraph ) [static] :  List
CDKMCS.getBitSet ( IAtomContainer atomContainer ) [static] :  BitSet
CDKMCS.getIsomorphAtomsMap ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getIsomorphMap ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getIsomorphMaps ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getOverlaps ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getSubgraphAtomsMap ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getSubgraphAtomsMaps ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getSubgraphMap ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getSubgraphMaps ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  List
CDKMCS.getTimeManager ( ) [static] :  TimeManager
CDKMCS.getTimeout ( ) [static] :  double
CDKMCS.isIsomorph ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  boolean
CDKMCS.isSubgraph ( IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds ) [static] :  boolean
CDKMCS.isTimeOut ( ) [static] :  boolean
CDKMCS.makeAtomsMapOfBondsMap ( List list, IAtomContainer sourceGraph, IAtomContainer targetGraph ) [static] :  List
CDKMCS.makeAtomsMapsOfBondsMaps ( List list, IAtomContainer sourceGraph, IAtomContainer targetGraph ) [static] :  List
CDKMCS.project ( List rMapList, IAtomContainer graph, int key ) [static] :  IAtomContainer
CDKMCS.projectList ( List rMapsList, IAtomContainer graph, int key ) [static] :  ArrayList
CDKMCS.search ( IAtomContainer sourceGraph, IAtomContainer targetGraph, BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, boolean shouldMatchBonds ) [static] :  List
CDKMCS.setTimeManager ( TimeManager aTimeManager ) [static] :  void

cdk-1.4.0.jar, CDKMCSHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKMCSHandler.CDKMCSHandler ( )
CDKMCSHandler.getAllAtomMapping ( ) :  List
CDKMCSHandler.getAllMapping ( ) :  List
CDKMCSHandler.getFirstAtomMapping ( ) :  Map
CDKMCSHandler.getFirstMapping ( ) :  Map
CDKMCSHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IMoleculeSet
CDKMCSHandler.searchMCS ( boolean shouldMatchBonds ) :  void
CDKMCSHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
CDKMCSHandler.set ( MolHandler source, MolHandler target ) :  void

cdk-1.4.0.jar, CDKOWLFormat.class
package org.openscience.cdk.io.formats
CDKOWLFormat.getFormatName ( ) :  String
CDKOWLFormat.getInstance ( ) [static] :  IResourceFormat
CDKOWLFormat.getMIMEType ( ) :  String
CDKOWLFormat.getNameExtensions ( ) :  String[ ]
CDKOWLFormat.getPreferredNameExtension ( ) :  String
CDKOWLFormat.getReaderClassName ( ) :  String
CDKOWLFormat.getRequiredDataFeatures ( ) :  int
CDKOWLFormat.getSupportedDataFeatures ( ) :  int
CDKOWLFormat.getWriterClassName ( ) :  String
CDKOWLFormat.isXMLBased ( ) :  boolean
CDKOWLFormat.matches ( int lineNumber, String line ) :  boolean

cdk-1.4.0.jar, CDKOWLReader.class
package org.openscience.cdk.io.rdf
CDKOWLReader.accepts ( Class classObject ) :  boolean
CDKOWLReader.CDKOWLReader ( )
CDKOWLReader.CDKOWLReader ( Reader input )
CDKOWLReader.close ( ) :  void
CDKOWLReader.getFormat ( ) :  IResourceFormat
CDKOWLReader.read ( IChemObject object ) :  IChemObject
CDKOWLReader.setReader ( InputStream input ) :  void
CDKOWLReader.setReader ( Reader reader ) :  void *DEPRECATED*

cdk-1.4.0.jar, CDKOWLWriter.class
package org.openscience.cdk.io.rdf
CDKOWLWriter.accepts ( Class classObject ) :  boolean
CDKOWLWriter.CDKOWLWriter ( )
CDKOWLWriter.CDKOWLWriter ( Writer output )
CDKOWLWriter.close ( ) :  void
CDKOWLWriter.getFormat ( ) :  IResourceFormat
CDKOWLWriter.setWriter ( OutputStream output ) :  void
CDKOWLWriter.setWriter ( Writer out ) :  void
CDKOWLWriter.write ( IChemObject object ) :  void

cdk-1.4.0.jar, CDKRGraph.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKRGraph.addNode ( CDKRNode newNode ) :  void
CDKRGraph.bitSetToRMap ( BitSet set ) :  List
CDKRGraph.CDKRGraph ( )
CDKRGraph.clear ( ) :  void
CDKRGraph.getFirstGraphSize ( ) :  int
CDKRGraph.getGraph ( ) :  List
CDKRGraph.getSecondGraphSize ( ) :  int
CDKRGraph.getSolutions ( ) :  List
CDKRGraph.parse ( BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, TimeManager timeManager ) :  void
CDKRGraph.projectG1 ( BitSet set ) :  BitSet
CDKRGraph.projectG2 ( BitSet set ) :  BitSet
CDKRGraph.setAllMap ( boolean findAllMap ) :  void
CDKRGraph.setAllStructure ( boolean findAllStructure ) :  void
CDKRGraph.setFirstGraphSize ( int graphSize ) :  void
CDKRGraph.setMaxIteration ( int maxIterator ) :  void
CDKRGraph.setSecondGraphSize ( int graphSize ) :  void
CDKRGraph.toString ( ) :  String

cdk-1.4.0.jar, CDKRMap.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKRMap.CDKRMap ( int id1, int id2 )
CDKRMap.equals ( Object obj ) :  boolean
CDKRMap.getId1 ( ) :  int
CDKRMap.getId2 ( ) :  int
CDKRMap.hashCode ( ) :  int
CDKRMap.setId1 ( int id1 ) :  void
CDKRMap.setId2 ( int id2 ) :  void

cdk-1.4.0.jar, CDKRMapHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKRMapHandler.calculateIsomorphs ( IAtomContainer Molecule1, IAtomContainer Molecule2, boolean shouldMatchBonds ) :  void
CDKRMapHandler.calculateOverlapsAndReduce ( IAtomContainer Molecule1, IAtomContainer Molecule2, boolean shouldMatchBonds ) :  void
CDKRMapHandler.calculateOverlapsAndReduceExactMatch ( IAtomContainer Molecule1, IAtomContainer Molecule2, boolean shouldMatchBonds ) :  void
CDKRMapHandler.calculateSubGraphs ( IAtomContainer Molecule1, IAtomContainer Molecule2, boolean shouldMatchBonds ) :  void
CDKRMapHandler.CDKRMapHandler ( )
CDKRMapHandler.getAllMaximum ( List overlaps ) :  Stack
CDKRMapHandler.getMappings ( ) :  List
CDKRMapHandler.getMaximum ( List overlaps ) :  List
CDKRMapHandler.getSource ( ) [static] :  IAtomContainer
CDKRMapHandler.getTarget ( ) [static] :  IAtomContainer
CDKRMapHandler.identifyMatchedParts ( List list, IAtomContainer source, IAtomContainer target ) :  void
CDKRMapHandler.identifySingleAtomsMatchedParts ( List list, IAtomContainer source, IAtomContainer target ) :  void
CDKRMapHandler.isSameRMap ( CDKRMap sourceRMap, CDKRMap targetRMap ) :  boolean
CDKRMapHandler.isSubgraph ( List rmaps1, List rmaps2 ) :  boolean
CDKRMapHandler.isTimeoutFlag ( ) :  boolean
CDKRMapHandler.removeRedundantMappingsForSingleAtomCase ( List overlaps ) :  List
CDKRMapHandler.removeSubGraph ( List overlaps ) :  List
CDKRMapHandler.setMappings ( List mappings ) :  void
CDKRMapHandler.setSource ( IAtomContainer aSource ) [static] :  void
CDKRMapHandler.setTarget ( IAtomContainer aTarget ) [static] :  void
CDKRMapHandler.setTimeoutFlag ( boolean timeoutFlag ) :  void

cdk-1.4.0.jar, CDKRNode.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKRNode.CDKRNode ( int id1, int id2 )
CDKRNode.getExtension ( ) :  BitSet
CDKRNode.getForbidden ( ) :  BitSet
CDKRNode.getRMap ( ) :  CDKRMap
CDKRNode.getrMap ( ) :  CDKRMap
CDKRNode.setExtension ( BitSet extension ) :  void
CDKRNode.setForbidden ( BitSet forbidden ) :  void
CDKRNode.setRMap ( CDKRMap rMap ) :  void
CDKRNode.setrMap ( CDKRMap rMap ) :  void
CDKRNode.toString ( ) :  String

cdk-1.4.0.jar, CDKStyleAromaticity.class
package org.openscience.cdk.renderer.generators
RingGenerator.CDKStyleAromaticity.getDefault ( ) :  Boolean
RingGenerator.CDKStyleAromaticity.getDefault ( ) :  Object
RingGenerator.CDKStyleAromaticity.RingGenerator.CDKStyleAromaticity ( )

cdk-1.4.0.jar, CDKSubGraphHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKSubGraphHandler.CDKSubGraphHandler ( )
CDKSubGraphHandler.getAllAtomMapping ( ) :  List
CDKSubGraphHandler.getAllMapping ( ) :  List
CDKSubGraphHandler.getFirstAtomMapping ( ) :  Map
CDKSubGraphHandler.getFirstMapping ( ) :  Map
CDKSubGraphHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IMoleculeSet
CDKSubGraphHandler.isSubgraph ( boolean shouldMatchBonds ) :  boolean
CDKSubGraphHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
CDKSubGraphHandler.set ( MolHandler source, MolHandler target ) :  void

cdk-1.4.0.jar, ChangedListener.class
package com.hp.hpl.jena.rdf.listeners
ChangedListener.addedStatement ( Statement s ) :  void
ChangedListener.addedStatements ( List statements ) :  void
ChangedListener.addedStatements ( Model m ) :  void
ChangedListener.addedStatements ( Statement[ ] statements ) :  void
ChangedListener.addedStatements ( StmtIterator statements ) :  void
ChangedListener.ChangedListener ( )
ChangedListener.hasChanged ( ) :  boolean
ChangedListener.notifyEvent ( Model m, Object event ) :  void
ChangedListener.removedStatement ( Statement s ) :  void
ChangedListener.removedStatements ( List statements ) :  void
ChangedListener.removedStatements ( Model m ) :  void
ChangedListener.removedStatements ( Statement[ ] statements ) :  void
ChangedListener.removedStatements ( StmtIterator statements ) :  void
ChangedListener.setChanged ( ) :  void

cdk-1.4.0.jar, CharEncoding.class
package com.hp.hpl.jena.util
CharEncoding.create ( String enc ) [static] :  CharEncoding
CharEncoding.isIANA ( ) [abstract] :  boolean
CharEncoding.isInNIO ( ) [abstract] :  boolean
CharEncoding.name ( ) :  String
CharEncoding.warningMessage ( ) [abstract] :  String

cdk-1.4.0.jar, CharsetDetector.class
package com.ibm.icu.text
CharsetDetector.CharsetDetector ( ) *DEPRECATED*
CharsetDetector.detect ( ) :  CharsetMatch *DEPRECATED*
CharsetDetector.detectAll ( ) :  CharsetMatch[ ] *DEPRECATED*
CharsetDetector.enableInputFilter ( boolean filter ) :  boolean *DEPRECATED*
CharsetDetector.getAllDetectableCharsets ( ) [static] :  String[ ] *DEPRECATED*
CharsetDetector.getReader ( InputStream in, String declaredEncoding ) :  Reader *DEPRECATED*
CharsetDetector.getString ( byte[ ] in, String declaredEncoding ) :  String *DEPRECATED*
CharsetDetector.inputFilterEnabled ( ) :  boolean *DEPRECATED*
CharsetDetector.setDeclaredEncoding ( String encoding ) :  CharsetDetector *DEPRECATED*
CharsetDetector.setText ( byte[ ] in ) :  CharsetDetector *DEPRECATED*
CharsetDetector.setText ( InputStream in ) :  CharsetDetector *DEPRECATED*

cdk-1.4.0.jar, CharsetMatch.class
package com.ibm.icu.text
CharsetMatch.compareTo ( Object o ) :  int *DEPRECATED*
CharsetMatch.getConfidence ( ) :  int *DEPRECATED*
CharsetMatch.getLanguage ( ) :  String *DEPRECATED*
CharsetMatch.getMatchType ( ) :  int *DEPRECATED*
CharsetMatch.getName ( ) :  String *DEPRECATED*
CharsetMatch.getReader ( ) :  Reader *DEPRECATED*
CharsetMatch.getString ( ) :  String *DEPRECATED*
CharsetMatch.getString ( int maxLength ) :  String *DEPRECATED*

cdk-1.4.0.jar, ChemicalFilters.class
package org.openscience.cdk.smsd.filters
ChemicalFilters.ChemicalFilters ( List allMCS, List allAtomMCS, Map firstSolution, Map firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol )
ChemicalFilters.convertBondOrder ( IBond bond ) [static] :  int
ChemicalFilters.convertBondStereo ( IBond bond ) [static] :  int
ChemicalFilters.convertOrder ( double srcOrder ) [static] :  IBond.Order
ChemicalFilters.convertStereo ( int stereoValue ) [static] :  IBond.Stereo
ChemicalFilters.getSortedEnergy ( ) :  List
ChemicalFilters.getSortedFragment ( ) :  List
ChemicalFilters.getStereoMatches ( ) :  List
ChemicalFilters.sortResultsByEnergies ( ) :  void
ChemicalFilters.sortResultsByFragments ( ) :  void
ChemicalFilters.sortResultsByStereoAndBondMatch ( ) :  void

cdk-1.4.0.jar, Child.class
package org.openscience.cdk.renderer.elements
TextGroupElement.Child.TextGroupElement.Child ( TextGroupElement text, String position, TextGroupElement.Position p3 )
TextGroupElement.Child.TextGroupElement.Child ( TextGroupElement text, String subscript, String position, TextGroupElement.Position p4 )

cdk-1.4.0.jar, ChineseCalendar.class
package com.ibm.icu.util
ChineseCalendar.add ( int field, int amount ) :  void
ChineseCalendar.ChineseCalendar ( )
ChineseCalendar.ChineseCalendar ( TimeZone zone, Locale locale )
ChineseCalendar.ChineseCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
ChineseCalendar.getFieldResolutionTable ( ) :  int[ ][ ][ ]
ChineseCalendar.getType ( ) :  String
ChineseCalendar.handleComputeFields ( int julianDay ) :  void
ChineseCalendar.handleComputeMonthStart ( int eyear, int month, boolean useMonth ) :  int
ChineseCalendar.handleCreateFields ( ) :  int[ ]
ChineseCalendar.handleGetDateFormat ( String pattern, ULocale locale ) :  DateFormat
ChineseCalendar.handleGetExtendedYear ( ) :  int
ChineseCalendar.handleGetLimit ( int field, int limitType ) :  int
ChineseCalendar.handleGetMonthLength ( int extendedYear, int month ) :  int
ChineseCalendar.roll ( int field, int amount ) :  void

cdk-1.4.0.jar, ChineseDateFormat.class
package com.ibm.icu.text
ChineseDateFormat.ChineseDateFormat ( String pattern, Locale locale )
ChineseDateFormat.ChineseDateFormat ( String pattern, ULocale locale ) *DEPRECATED*
ChineseDateFormat.subFormat ( StringBuffer buf, char ch, int count, int beginOffset, FieldPosition pos, Calendar cal ) :  void
ChineseDateFormat.subParse ( String text, int start, char ch, int count, boolean obeyCount, boolean allowNegative, boolean[ ] ambiguousYear, Calendar cal ) :  int

cdk-1.4.0.jar, ChineseDateFormatSymbols.class
package com.ibm.icu.text
ChineseDateFormatSymbols.ChineseDateFormatSymbols ( )
ChineseDateFormatSymbols.ChineseDateFormatSymbols ( Calendar cal, Locale locale )
ChineseDateFormatSymbols.ChineseDateFormatSymbols ( Calendar cal, ULocale locale ) *DEPRECATED*
ChineseDateFormatSymbols.ChineseDateFormatSymbols ( Locale locale )
ChineseDateFormatSymbols.ChineseDateFormatSymbols ( ULocale locale ) *DEPRECATED*
ChineseDateFormatSymbols.getLeapMonth ( int isLeapMonth ) :  String
ChineseDateFormatSymbols.initializeData ( ULocale loc, CalendarData calData ) :  void *DEPRECATED*

cdk-1.4.0.jar, ChiralCenterFinder.class
package signature.chemistry
ChiralCenterFinder.ChiralCenterFinder ( )
ChiralCenterFinder.findTetrahedralChiralCenters ( Molecule molecule ) [static] :  List

cdk-1.4.0.jar, ChiralityTest.class
package signature.chemistry
ChiralityTest.ChiralityTest ( )
ChiralityTest.dichlorocyclopropaneTest ( ) :  void
ChiralityTest.dihydroxyCyclohexane ( ) :  void
ChiralityTest.spiranTest ( ) :  void

cdk-1.4.0.jar, CIP_CHIRALITY.class
package org.openscience.cdk.geometry.cip
CIPTool.CIP_CHIRALITY.valueOf ( String name ) [static] :  CIPTool.CIP_CHIRALITY
CIPTool.CIP_CHIRALITY.values ( ) [static] :  CIPTool.CIP_CHIRALITY[ ]

cdk-1.4.0.jar, CIPLigandRule.class
package org.openscience.cdk.geometry.cip.rules
CIPLigandRule.CIPLigandRule ( )
CIPLigandRule.compare ( ILigand ligand1, ILigand ligand2 ) :  int
CIPLigandRule.compare ( Object x0, Object x1 ) :  int

cdk-1.4.0.jar, CIPTool.class
package org.openscience.cdk.geometry.cip
CIPTool.checkIfAllLigandsAreDifferent ( ILigand[ ] ligands ) [static] :  boolean
CIPTool.CIPTool ( )
CIPTool.defineLigancyFourChirality ( IAtomContainer container, int chiralAtom, int ligand1, int ligand2, int ligand3, int ligand4, ITetrahedralChirality.Stereo stereo ) [static] :  LigancyFourChirality
CIPTool.defineLigand ( IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom, int ligandAtom ) [static] :  ILigand
CIPTool.getCIPChirality ( IAtomContainer container, ITetrahedralChirality stereoCenter ) [static] :  CIPTool.CIP_CHIRALITY
CIPTool.getCIPChirality ( LigancyFourChirality stereoCenter ) [static] :  CIPTool.CIP_CHIRALITY
CIPTool.getLigandLigands ( ILigand ligand ) [static] :  ILigand[ ]
CIPTool.order ( ILigand[ ] ligands ) [static] :  ILigand[ ]

cdk-1.4.0.jar, ClauseEntry.class
package com.hp.hpl.jena.reasoner.rulesys
ClauseEntry.sameAs ( Object p1 ) [abstract] :  boolean

cdk-1.4.0.jar, ClosableIterator.class
package com.hp.hpl.jena.util.iterator
ClosableIterator.close ( ) [abstract] :  void

cdk-1.4.0.jar, Close.class
package org.openscience.cdk.renderer.elements.path
Close.Close ( )
Close.points ( ) :  float[ ]

cdk-1.4.0.jar, ClosedException.class
package com.hp.hpl.jena.shared
ClosedException.ClosedException ( String message, Graph graph )
ClosedException.getGraph ( ) :  Graph

cdk-1.4.0.jar, ClosedShellJob.class
package org.openscience.cdk.math.qm
ClosedShellJob.calculate ( ) :  Orbitals
ClosedShellJob.ClosedShellJob ( Orbitals orbitals )
ClosedShellJob.getEnergies ( ) :  Vector

cdk-1.4.0.jar, CmdLineUtils.class
package jena.cmdline
CmdLineUtils.CmdLineUtils ( )
CmdLineUtils.readWholeFileAsUTF8 ( String filename ) [static] :  String

cdk-1.4.0.jar, CollationElementIterator.class
package com.ibm.icu.text
CollationElementIterator.equals ( Object that ) :  boolean
CollationElementIterator.getMaxExpansion ( int ce ) :  int
CollationElementIterator.getOffset ( ) :  int
CollationElementIterator.next ( ) :  int
CollationElementIterator.previous ( ) :  int
CollationElementIterator.primaryOrder ( int ce ) [static] :  int
CollationElementIterator.reset ( ) :  void
CollationElementIterator.secondaryOrder ( int ce ) [static] :  int
CollationElementIterator.setOffset ( int offset ) :  void
CollationElementIterator.setText ( CharacterIterator source ) :  void
CollationElementIterator.setText ( String source ) :  void
CollationElementIterator.setText ( UCharacterIterator source ) :  void
CollationElementIterator.tertiaryOrder ( int ce ) [static] :  int

cdk-1.4.0.jar, CollationKey.class
package com.ibm.icu.text
CollationKey.CollationKey ( String source, byte[ ] key )
CollationKey.CollationKey ( String source, RawCollationKey key )
CollationKey.compareTo ( CollationKey target ) :  int
CollationKey.compareTo ( Object obj ) :  int
CollationKey.equals ( CollationKey target ) :  boolean
CollationKey.equals ( Object target ) :  boolean
CollationKey.getBound ( int boundType, int noOfLevels ) :  CollationKey
CollationKey.getSourceString ( ) :  String
CollationKey.hashCode ( ) :  int
CollationKey.merge ( CollationKey source ) :  CollationKey
CollationKey.toByteArray ( ) :  byte[ ]

cdk-1.4.0.jar, Collator.class
package com.ibm.icu.text
Collator.clone ( ) :  Object
Collator.Collator ( )
Collator.compare ( Object source, Object target ) :  int
Collator.compare ( String p1, String p2 ) [abstract] :  int
Collator.equals ( String source, String target ) :  boolean
Collator.getAvailableLocales ( ) [static] :  Locale[ ]
Collator.getAvailableULocales ( ) [static] :  ULocale[ ] *DEPRECATED*
Collator.getCollationKey ( String p1 ) [abstract] :  CollationKey
Collator.getDecomposition ( ) :  int
Collator.getDisplayName ( Locale objectLocale ) [static] :  String
Collator.getDisplayName ( Locale objectLocale, Locale displayLocale ) [static] :  String
Collator.getDisplayName ( ULocale objectLocale ) [static] :  String *DEPRECATED*
Collator.getDisplayName ( ULocale objectLocale, ULocale displayLocale ) [static] :  String *DEPRECATED*
Collator.getFunctionalEquivalent ( String keyword, ULocale locID ) [static] :  ULocale *DEPRECATED*
Collator.getFunctionalEquivalent ( String keyword, ULocale locID, boolean[ ] isAvailable ) [static] :  ULocale *DEPRECATED*
Collator.getInstance ( ) [static] :  Collator
Collator.getInstance ( Locale locale ) [static] :  Collator
Collator.getInstance ( ULocale locale ) [static] :  Collator *DEPRECATED*
Collator.getKeywords ( ) [static] :  String[ ] *DEPRECATED*
Collator.getKeywordValues ( String keyword ) [static] :  String[ ] *DEPRECATED*
Collator.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
Collator.getRawCollationKey ( String p1, RawCollationKey p2 ) [abstract] :  RawCollationKey
Collator.getStrength ( ) :  int
Collator.getTailoredSet ( ) :  UnicodeSet
Collator.getUCAVersion ( ) [abstract] :  VersionInfo
Collator.getVariableTop ( ) [abstract] :  int
Collator.getVersion ( ) [abstract] :  VersionInfo
Collator.registerFactory ( Collator.CollatorFactory factory ) [static] :  Object
Collator.registerInstance ( Collator collator, ULocale locale ) [static] :  Object *DEPRECATED*
Collator.setDecomposition ( int decomposition ) :  void
Collator.setStrength ( int newStrength ) :  void
Collator.setVariableTop ( int p1 ) [abstract] :  void
Collator.setVariableTop ( String p1 ) [abstract] :  int
Collator.unregister ( Object registryKey ) [static] :  boolean

cdk-1.4.0.jar, CollatorFactory.class
package com.ibm.icu.text
Collator.CollatorFactory.Collator.CollatorFactory ( )
Collator.CollatorFactory.createCollator ( Locale loc ) :  Collator
Collator.CollatorFactory.createCollator ( ULocale loc ) :  Collator *DEPRECATED*
Collator.CollatorFactory.getDisplayName ( Locale objectLocale, Locale displayLocale ) :  String
Collator.CollatorFactory.getDisplayName ( ULocale objectLocale, ULocale displayLocale ) :  String *DEPRECATED*
Collator.CollatorFactory.getSupportedLocaleIDs ( ) [abstract] :  Set
Collator.CollatorFactory.visible ( ) :  boolean

cdk-1.4.0.jar, CollectionFactory.class
package com.hp.hpl.jena.util
CollectionFactory.CollectionFactory ( )
CollectionFactory.createHashedMap ( ) [static] :  Map
CollectionFactory.createHashedMap ( int size ) [static] :  Map
CollectionFactory.createHashedMap ( Map toCopy ) [static] :  Map
CollectionFactory.createHashedSet ( ) [static] :  Set
CollectionFactory.createHashedSet ( Collection toCopy ) [static] :  Set

cdk-1.4.0.jar, ColorByType.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.ColorByType.BasicAtomGenerator.ColorByType ( )
BasicAtomGenerator.ColorByType.getDefault ( ) :  Boolean
BasicAtomGenerator.ColorByType.getDefault ( ) :  Object

cdk-1.4.0.jar, ColoredTree.class
package signature
ColoredTree.accept ( ColoredTreeVisitor visitor ) :  void
ColoredTree.ColoredTree ( String rootLabel )
ColoredTree.getHeight ( ) :  int
ColoredTree.getRoot ( ) :  ColoredTree.Node
ColoredTree.makeNode ( String label, ColoredTree.Node parent, int currentHeight, int color ) :  ColoredTree.Node
ColoredTree.makeNode ( String label, ColoredTree.Node parent, int currentHeight, int color, String edgeSymbol ) :  ColoredTree.Node
ColoredTree.numberOfColors ( ) :  int
ColoredTree.toString ( ) :  String
ColoredTree.updateHeight ( int height ) :  void

cdk-1.4.0.jar, ColoredTreePanel.class
package signature.display
ColoredTreePanel.clear ( ) :  void
ColoredTreePanel.ColoredTreePanel ( ColoredTree tree, int width, int height )
ColoredTreePanel.ColoredTreePanel ( int width, int height )
ColoredTreePanel.paint ( Graphics g ) :  void
ColoredTreePanel.setDrawKey ( boolean drawKey ) :  void
ColoredTreePanel.setTree ( ColoredTree tree ) :  void

cdk-1.4.0.jar, ColoredTreeVisitor.class
package signature
ColoredTreeVisitor.visit ( ColoredTree.Node p1 ) [abstract] :  void

cdk-1.4.0.jar, ColorHash.class
package org.openscience.cdk.renderer
RendererModel.ColorHash.getDefault ( ) :  Map
RendererModel.ColorHash.getDefault ( ) :  Object
RendererModel.ColorHash.RendererModel.ColorHash ( )

cdk-1.4.0.jar, Command.class
package com.hp.hpl.jena.shared
Command.execute ( ) [abstract] :  Object

cdk-1.4.0.jar, CommandLine.class
package jena.cmdline
CommandLine.add ( ArgDecl arg ) :  CommandLine
CommandLine.add ( boolean hasValue, String argName ) :  CommandLine
CommandLine.add ( String argName, boolean hasValue ) :  CommandLine
CommandLine.allowItemIndirect ( ) :  boolean
CommandLine.args ( ) :  Iterator
CommandLine.CommandLine ( )
CommandLine.contains ( ArgDecl argDecl ) :  boolean
CommandLine.contains ( String s ) :  boolean
CommandLine.endProcessing ( String argStr ) :  boolean
CommandLine.getArg ( ArgDecl argDecl ) :  Arg
CommandLine.getArg ( String s ) :  Arg
CommandLine.getIndirectionMarker ( ) :  String
CommandLine.getItem ( int i ) :  String
CommandLine.getItem ( int i, boolean withIndirect ) :  String
CommandLine.getValue ( ArgDecl argDecl ) :  String
CommandLine.getValue ( String argName ) :  String
CommandLine.getValues ( ArgDecl argDecl ) :  List
CommandLine.getValues ( String argName ) :  List
CommandLine.handleUnrecognizedArg ( String argStr ) :  void
CommandLine.hasArg ( ArgDecl argDecl ) :  boolean
CommandLine.hasArg ( String argName ) :  boolean
CommandLine.hasArgs ( ) :  boolean
CommandLine.hasItems ( ) :  boolean
CommandLine.ignoreArgument ( String argStr ) :  boolean
CommandLine.isIgnoreIndirectionMarker ( ) :  boolean
CommandLine.isIndirectItem ( int i ) :  boolean
CommandLine.numArgs ( ) :  int
CommandLine.numItems ( ) :  int
CommandLine.process ( String[ ] argv ) :  void
CommandLine.pushItem ( String s ) :  void
CommandLine.setAllowItemIndirect ( boolean allowItemIndirect ) :  void
CommandLine.setHook ( ArgHandler argHandler ) :  void
CommandLine.setIgnoreIndirectionMarker ( boolean ignoreIndirectionMarker ) :  void
CommandLine.setIndirectionMarker ( String indirectionMarker ) :  void
CommandLine.setUsage ( String usageMessage ) :  void
CommandLine.trace ( ) :  ArgHandler
package org.apache.commons.cli
CommandLine.getArgList ( ) :  List
CommandLine.getArgs ( ) :  String[ ]
CommandLine.getOptionObject ( char opt ) :  Object
CommandLine.getOptionObject ( String opt ) :  Object
CommandLine.getOptions ( ) :  Option[ ]
CommandLine.getOptionValue ( char opt ) :  String
CommandLine.getOptionValue ( char opt, String defaultValue ) :  String
CommandLine.getOptionValue ( String opt ) :  String
CommandLine.getOptionValue ( String opt, String defaultValue ) :  String
CommandLine.getOptionValues ( char opt ) :  String[ ]
CommandLine.getOptionValues ( String opt ) :  String[ ]
CommandLine.hasOption ( char opt ) :  boolean
CommandLine.hasOption ( String opt ) :  boolean
CommandLine.iterator ( ) :  Iterator

cdk-1.4.0.jar, CommandLineParser.class
package org.apache.commons.cli
CommandLineParser.parse ( Options p1, String[ ] p2 ) [abstract] :  CommandLine
CommandLineParser.parse ( Options p1, String[ ] p2, boolean p3 ) [abstract] :  CommandLine

cdk-1.4.0.jar, CompactAtom.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.CompactAtom.BasicAtomGenerator.CompactAtom ( )
BasicAtomGenerator.CompactAtom.getDefault ( ) :  Boolean
BasicAtomGenerator.CompactAtom.getDefault ( ) :  Object

cdk-1.4.0.jar, CompactByteArray.class
package com.ibm.icu.util
CompactByteArray.clone ( ) :  Object
CompactByteArray.compact ( ) :  void
CompactByteArray.compact ( boolean exhaustive ) :  void
CompactByteArray.CompactByteArray ( )
CompactByteArray.CompactByteArray ( byte defaultValue )
CompactByteArray.CompactByteArray ( char[ ] indexArray, byte[ ] newValues )
CompactByteArray.CompactByteArray ( String indexArray, String valueArray )
CompactByteArray.elementAt ( char index ) :  byte
CompactByteArray.equals ( Object obj ) :  boolean
CompactByteArray.getIndexArray ( ) :  char[ ]
CompactByteArray.getValueArray ( ) :  byte[ ]
CompactByteArray.hashCode ( ) :  int
CompactByteArray.setElementAt ( char index, byte value ) :  void
CompactByteArray.setElementAt ( char start, char end, byte value ) :  void

cdk-1.4.0.jar, CompactCharArray.class
package com.ibm.icu.util
CompactCharArray.clone ( ) :  Object
CompactCharArray.compact ( ) :  void
CompactCharArray.compact ( boolean exhaustive ) :  void
CompactCharArray.CompactCharArray ( )
CompactCharArray.CompactCharArray ( char defaultValue )
CompactCharArray.CompactCharArray ( char[ ] indexArray, char[ ] newValues )
CompactCharArray.CompactCharArray ( String indexArray, String valueArray )
CompactCharArray.elementAt ( char index ) :  char
CompactCharArray.equals ( Object obj ) :  boolean
CompactCharArray.getIndexArray ( ) :  char[ ]
CompactCharArray.getValueArray ( ) :  char[ ]
CompactCharArray.hashCode ( ) :  int
CompactCharArray.setElementAt ( char index, char value ) :  void
CompactCharArray.setElementAt ( char start, char end, char value ) :  void

cdk-1.4.0.jar, CompactShape.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.CompactShape.BasicAtomGenerator.CompactShape ( )
BasicAtomGenerator.CompactShape.getDefault ( ) :  BasicAtomGenerator.Shape
BasicAtomGenerator.CompactShape.getDefault ( ) :  Object

cdk-1.4.0.jar, ComplementClass.class
package com.hp.hpl.jena.ontology
ComplementClass.getOperand ( ) [abstract] :  OntClass
ComplementClass.setOperand ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, Complex.class
package org.openscience.cdk.math
Complex.add ( Complex c ) :  void
Complex.Complex ( Complex c )
Complex.Complex ( double real, double imag )
Complex.div ( Complex c ) :  void
Complex.getImaginaryPart ( ) :  double
Complex.getRealPart ( ) :  double
Complex.mul ( Complex c ) :  void
Complex.setImaginaryPart ( double imag ) :  void
Complex.setRealPart ( double real ) :  void
Complex.sub ( Complex c ) :  void
Complex.toString ( ) :  String

cdk-1.4.0.jar, ComposedCharIter.class
package com.ibm.icu.text
ComposedCharIter.ComposedCharIter ( ) *DEPRECATED*
ComposedCharIter.ComposedCharIter ( boolean compat, int options ) *DEPRECATED*
ComposedCharIter.decomposition ( ) :  String *DEPRECATED*
ComposedCharIter.hasNext ( ) :  boolean *DEPRECATED*
ComposedCharIter.next ( ) :  char *DEPRECATED*

cdk-1.4.0.jar, CompositionBase.class
package com.hp.hpl.jena.graph.compose
CompositionBase.butNot ( ClosableIterator a, ClosableIterator b ) [static] :  ClosableIterator
CompositionBase.CompositionBase ( )
CompositionBase.ifIn ( ClosableIterator i ) [static] :  Filter
CompositionBase.ifIn ( Graph g ) [static] :  Filter
CompositionBase.recording ( ClosableIterator i, Set seen ) [static] :  ExtendedIterator
CompositionBase.reject ( ClosableIterator i ) [static] :  Filter
CompositionBase.rejecting ( ExtendedIterator i, Graph seen ) [static] :  ExtendedIterator
CompositionBase.rejecting ( ExtendedIterator i, Set seen ) [static] :  ExtendedIterator

cdk-1.4.0.jar, ConcatenatedIterator.class
package com.hp.hpl.jena.util.iterator
ConcatenatedIterator.ConcatenatedIterator ( Iterator iter0, Iterator iter1 )
ConcatenatedIterator.hasDefaultValue ( ) :  boolean
ConcatenatedIterator.hasNext ( ) :  boolean
ConcatenatedIterator.next ( ) :  Object
ConcatenatedIterator.remove ( ) :  void
ConcatenatedIterator.setDefaultValue ( Object defaultValue ) :  void

cdk-1.4.0.jar, ConfigException.class
package com.hp.hpl.jena.shared
ConfigException.ConfigException ( )
ConfigException.ConfigException ( String message )
ConfigException.ConfigException ( String message, Throwable cause )
ConfigException.ConfigException ( Throwable cause )

cdk-1.4.0.jar, ConfigManager.class
package net.sf.jnati.deploy.artefact
ConfigManager.getConfig ( String id, String version ) [static] :  Configuration
ConfigManager.getDefaultConfig ( ) [static] :  Configuration

cdk-1.4.0.jar, Configuration.class
package net.sf.jnati.config
Configuration.Configuration ( )
Configuration.Configuration ( Configuration parentConfig, Map params )
Configuration.Configuration ( Map params )
Configuration.getProperty ( String key ) :  String
Configuration.loadConfiguration ( InputStream in ) :  void
Configuration.loadDefaults ( InputStream in ) :  void
Configuration.setConfiguration ( Map config ) :  void
Configuration.setDefaults ( Map defaults ) :  void

cdk-1.4.0.jar, ConnectionAssembler.class
package com.hp.hpl.jena.assembler.assemblers
ConnectionAssembler.ConnectionAssembler ( )
ConnectionAssembler.ConnectionAssembler ( Resource init )
ConnectionAssembler.createConnection ( String subject, String dbURL, String dbType, String dbUser, String dbPassword ) :  ConnectionDescription
ConnectionAssembler.get ( Resource root, String label, String ifAbsent ) :  String
ConnectionAssembler.getPassword ( Resource root ) :  String
ConnectionAssembler.getType ( Resource root ) :  String
ConnectionAssembler.getURL ( Resource root ) :  String
ConnectionAssembler.getUser ( Resource root ) :  String
ConnectionAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, ConnectionDescription.class
package com.hp.hpl.jena.assembler
ConnectionDescription.ConnectionDescription ( String subject, String dbURL, String dbUser, String dbPassword, String dbType )
ConnectionDescription.create ( String subject, String dbURL, String dbUser, String dbPassword, String dbType ) [static] :  ConnectionDescription
ConnectionDescription.getConnection ( ) :  IDBConnection
ConnectionDescription.toString ( ) :  String

cdk-1.4.0.jar, Constant.class
package com.hp.hpl.jena.graph.query
Expression.Constant.Expression.Constant ( )
Expression.Constant.getValue ( ) [abstract] :  Object
Expression.Constant.isConstant ( ) :  boolean

cdk-1.4.0.jar, ConstraintStage.class
package com.hp.hpl.jena.graph.query
ConstraintStage.ConstraintStage ( Mapping map, ExpressionSet constraint )
ConstraintStage.deliver ( Pipe L ) :  Pipe

cdk-1.4.0.jar, Container.class
package com.hp.hpl.jena.rdf.model
Container.add ( boolean p1 ) [abstract] :  Container
Container.add ( char p1 ) [abstract] :  Container
Container.add ( double p1 ) [abstract] :  Container
Container.add ( float p1 ) [abstract] :  Container
Container.add ( long p1 ) [abstract] :  Container
Container.add ( Object p1 ) [abstract] :  Container
Container.add ( RDFNode p1 ) [abstract] :  Container
Container.add ( String p1 ) [abstract] :  Container
Container.add ( String p1, String p2 ) [abstract] :  Container
Container.contains ( boolean p1 ) [abstract] :  boolean
Container.contains ( char p1 ) [abstract] :  boolean
Container.contains ( double p1 ) [abstract] :  boolean
Container.contains ( float p1 ) [abstract] :  boolean
Container.contains ( long p1 ) [abstract] :  boolean
Container.contains ( Object p1 ) [abstract] :  boolean
Container.contains ( RDFNode p1 ) [abstract] :  boolean
Container.contains ( String p1 ) [abstract] :  boolean
Container.contains ( String p1, String p2 ) [abstract] :  boolean
Container.isAlt ( ) [abstract] :  boolean
Container.isBag ( ) [abstract] :  boolean
Container.isSeq ( ) [abstract] :  boolean
Container.iterator ( ) [abstract] :  NodeIterator
Container.remove ( Statement p1 ) [abstract] :  Container
Container.size ( ) [abstract] :  int

cdk-1.4.0.jar, Content.class
package com.hp.hpl.jena.assembler
Content.Content ( )
Content.Content ( List contents )
Content.fill ( Model m ) :  Model
Content.isEmpty ( ) :  boolean

cdk-1.4.0.jar, ContentAssembler.class
package com.hp.hpl.jena.assembler.assemblers
ContentAssembler.addExternalContents ( List contents, FileManager fm, Resource root ) :  void
ContentAssembler.addLiteralContent ( List contents, Resource root ) [static] :  void
ContentAssembler.ContentAssembler ( )
ContentAssembler.ContentAssembler ( FileManager fm )
ContentAssembler.getFileManager ( ) :  Object
ContentAssembler.loadContent ( List contents, Assembler a, Resource root ) :  List
ContentAssembler.newModelContent ( Model m ) [static] :  Content
ContentAssembler.objectAsContent ( FileManager fm, Statement s ) :  Content
ContentAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object
ContentAssembler.parseAsN3 ( String value ) [static] :  Model

cdk-1.4.0.jar, ConversionException.class
package com.hp.hpl.jena.ontology
ConversionException.ConversionException ( String msg )

cdk-1.4.0.jar, Convertor.class
package org.openscience.cdk.libio.jena
Convertor.Convertor ( )
Convertor.model2Molecule ( Model model, IChemObjectBuilder builder ) [static] :  IMolecule
Convertor.molecule2Model ( IMolecule molecule ) [static] :  Model
Convertor.order2Resource ( IBond.Order order ) [static] :  Resource
Convertor.resource2Order ( Resource rdfOrder ) [static] :  IBond.Order

cdk-1.4.0.jar, CopticCalendar.class
package com.ibm.icu.util
CopticCalendar.CopticCalendar ( ) *DEPRECATED*
CopticCalendar.CopticCalendar ( Date date ) *DEPRECATED*
CopticCalendar.CopticCalendar ( int year, int month, int date ) *DEPRECATED*
CopticCalendar.CopticCalendar ( int year, int month, int date, int hour, int minute, int second ) *DEPRECATED*
CopticCalendar.CopticCalendar ( Locale aLocale ) *DEPRECATED*
CopticCalendar.CopticCalendar ( TimeZone zone ) *DEPRECATED*
CopticCalendar.CopticCalendar ( TimeZone zone, Locale aLocale ) *DEPRECATED*
CopticCalendar.CopticCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
CopticCalendar.CopticCalendar ( ULocale locale ) *DEPRECATED*
CopticCalendar.copticToJD ( long year, int month, int date ) [static] :  int *DEPRECATED*
CopticCalendar.getDateFromJD ( int julianDay ) [static] :  Integer[ ]
CopticCalendar.getType ( ) :  String

cdk-1.4.0.jar, CountLiteralValues.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
CountLiteralValues.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
CountLiteralValues.CountLiteralValues ( )
CountLiteralValues.getArgLength ( ) :  int
CountLiteralValues.getName ( ) :  String

cdk-1.4.0.jar, CubicTo.class
package org.openscience.cdk.renderer.elements.path
CubicTo.CubicTo ( Point2d cp1, Point2d cp2, Point2d ep )
CubicTo.points ( ) :  float[ ]

cdk-1.4.0.jar, Currency.class
package com.ibm.icu.util
Currency.Currency ( String theISOCode ) *DEPRECATED*
Currency.equals ( Object rhs ) :  boolean
Currency.getAvailableLocales ( ) [static] :  Locale[ ]
Currency.getAvailableULocales ( ) [static] :  ULocale[ ]
Currency.getCurrencyCode ( ) :  String
Currency.getDefaultFractionDigits ( ) :  int
Currency.getInstance ( Locale locale ) [static] :  Currency
Currency.getInstance ( String theISOCode ) [static] :  Currency
Currency.getInstance ( ULocale locale ) [static] :  Currency *DEPRECATED*
Currency.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
Currency.getName ( Locale locale, int nameStyle, boolean[ ] isChoiceFormat ) :  String *DEPRECATED*
Currency.getName ( ULocale locale, int nameStyle, boolean[ ] isChoiceFormat ) :  String *DEPRECATED*
Currency.getRoundingIncrement ( ) :  double
Currency.getSymbol ( ) :  String *DEPRECATED*
Currency.getSymbol ( Locale loc ) :  String *DEPRECATED*
Currency.getSymbol ( ULocale uloc ) :  String *DEPRECATED*
Currency.hashCode ( ) :  int
Currency.parse ( ULocale locale, String text, ParsePosition pos ) [static] :  String
Currency.registerInstance ( Currency currency, ULocale locale ) [static] :  Object *DEPRECATED*
Currency.toString ( ) :  String
Currency.unregister ( Object registryKey ) [static] :  boolean

cdk-1.4.0.jar, CurrencyAmount.class
package com.ibm.icu.util
CurrencyAmount.CurrencyAmount ( double number, Currency currency ) *DEPRECATED*
CurrencyAmount.CurrencyAmount ( Number number, Currency currency ) *DEPRECATED*
CurrencyAmount.getCurrency ( ) :  Currency *DEPRECATED*

cdk-1.4.0.jar, DAG.class
package signature
DAG.accept ( DAGVisitor visitor ) :  void
DAG.addLayer ( List layer ) :  void
DAG.addRelation ( DAG.Node childNode, DAG.Node parentNode ) :  void
DAG.checkInvariantChange ( int[ ] a, int[ ] b ) :  boolean
DAG.colorFor ( int vertexIndex ) :  int
DAG.computeVertexInvariants ( ) :  void
DAG.copyInvariants ( ) :  Invariants
DAG.createOrbit ( int[ ] parents ) :  List
DAG.DAG ( int rootVertexIndex, int graphVertexCount )
DAG.getInvariantPairs ( int[ ] parents ) :  List
DAG.getOccurrences ( ) :  int[ ]
DAG.getParentsInFinalString ( ) :  int[ ]
DAG.getRoot ( ) :  DAG.Node
DAG.getRootLayer ( ) :  List
DAG.initializeWithIntLabels ( int[ ] vertexLabels ) :  void
DAG.initializeWithStringLabels ( String[ ] vertexLabels ) :  void
DAG.iterator ( ) :  Iterator
DAG.makeNode ( int vertexIndex, int layer ) :  DAG.Node
DAG.makeNodeInLayer ( int vertexIndex, int layer ) :  DAG.Node
DAG.occurences ( int vertexIndex ) :  int
DAG.setColor ( int vertexIndex, int color ) :  void
DAG.setInvariants ( Invariants invariants ) :  void
DAG.toString ( ) :  String
DAG.updateLayer ( List layer, DAG.Direction direction ) :  void
DAG.updateNodeInvariants ( DAG.Direction direction ) :  void
DAG.updateVertexInvariants ( ) :  void

cdk-1.4.0.jar, DAGVisitor.class
package signature
DAGVisitor.visit ( DAG.Node p1 ) [abstract] :  void

cdk-1.4.0.jar, DAML_OIL.class
package com.hp.hpl.jena.vocabulary
DAML_OIL.cardinality ( ) :  Property
DAML_OIL.cardinalityQ ( ) :  Property
DAML_OIL.Class ( ) :  Resource
DAML_OIL.comment ( ) :  Property
DAML_OIL.complementOf ( ) :  Property
DAML_OIL.Datatype ( ) :  Resource
DAML_OIL.DatatypeProperty ( ) :  Resource
DAML_OIL.differentIndividualFrom ( ) :  Property
DAML_OIL.disjointUnionOf ( ) :  Property
DAML_OIL.disjointWith ( ) :  Property
DAML_OIL.domain ( ) :  Property
DAML_OIL.equivalentTo ( ) :  Property
DAML_OIL.first ( ) :  Property
DAML_OIL.getInstance ( ) [static] :  DAMLVocabulary
DAML_OIL.getNamespace ( ) :  String
DAML_OIL.hasClass ( ) :  Property
DAML_OIL.hasClassQ ( ) :  Property
DAML_OIL.hasValue ( ) :  Property
DAML_OIL.imports ( ) :  Property
DAML_OIL.intersectionOf ( ) :  Property
DAML_OIL.inverseOf ( ) :  Property
DAML_OIL.isDefinedBy ( ) :  Property
DAML_OIL.item ( ) :  Property
DAML_OIL.label ( ) :  Property
DAML_OIL.List ( ) :  Resource
DAML_OIL.Literal ( ) :  Resource
DAML_OIL.maxCardinality ( ) :  Property
DAML_OIL.maxCardinalityQ ( ) :  Property
DAML_OIL.minCardinality ( ) :  Property
DAML_OIL.minCardinalityQ ( ) :  Property
DAML_OIL.NAMESPACE_DAML ( ) :  Resource
DAML_OIL.nil ( ) :  Resource
DAML_OIL.Nothing ( ) :  Resource
DAML_OIL.ObjectProperty ( ) :  Resource
DAML_OIL.oneOf ( ) :  Property
DAML_OIL.onProperty ( ) :  Property
DAML_OIL.Ontology ( ) :  Resource
DAML_OIL.Property ( ) :  Resource
DAML_OIL.range ( ) :  Property
DAML_OIL.rest ( ) :  Property
DAML_OIL.Restriction ( ) :  Resource
DAML_OIL.sameClassAs ( ) :  Property
DAML_OIL.sameIndividualAs ( ) :  Property
DAML_OIL.samePropertyAs ( ) :  Property
DAML_OIL.seeAlso ( ) :  Property
DAML_OIL.subClassOf ( ) :  Property
DAML_OIL.subPropertyOf ( ) :  Property
DAML_OIL.Thing ( ) :  Resource
DAML_OIL.toClass ( ) :  Property
DAML_OIL.TransitiveProperty ( ) :  Resource
DAML_OIL.type ( ) :  Property
DAML_OIL.UnambiguousProperty ( ) :  Resource
DAML_OIL.unionOf ( ) :  Property
DAML_OIL.UniqueProperty ( ) :  Resource
DAML_OIL.value ( ) :  Property
DAML_OIL.versionInfo ( ) :  Property

cdk-1.4.0.jar, DAMLCollection.class
package com.hp.hpl.jena.rdf.arp.states
DAMLCollection.abort ( ) :  void
DAMLCollection.DAMLCollection ( WantsObjectFrameI s, AbsXMLContext x )
DAMLCollection.startElement ( String x0, String x1, String x2, Attributes x3 ) :  FrameI

cdk-1.4.0.jar, DAMLMicroReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
DAMLMicroReasoner.DAMLMicroReasoner ( ReasonerFactory parent )
DAMLMicroReasoner.getGraphCapabilities ( ) :  Capabilities
DAMLMicroReasoner.loadRules ( ) [static] :  List

cdk-1.4.0.jar, DAMLMicroReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
DAMLMicroReasonerFactory.create ( Resource configuration ) :  Reasoner
DAMLMicroReasonerFactory.DAMLMicroReasonerFactory ( )
DAMLMicroReasonerFactory.getCapabilities ( ) :  Model
DAMLMicroReasonerFactory.getURI ( ) :  String
DAMLMicroReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, DAMLVocabulary.class
package com.hp.hpl.jena.vocabulary
DAMLVocabulary.cardinality ( ) [abstract] :  Property
DAMLVocabulary.cardinalityQ ( ) [abstract] :  Property
DAMLVocabulary.Class ( ) [abstract] :  Resource
DAMLVocabulary.comment ( ) [abstract] :  Property
DAMLVocabulary.complementOf ( ) [abstract] :  Property
DAMLVocabulary.Datatype ( ) [abstract] :  Resource
DAMLVocabulary.DatatypeProperty ( ) [abstract] :  Resource
DAMLVocabulary.differentIndividualFrom ( ) [abstract] :  Property
DAMLVocabulary.disjointUnionOf ( ) [abstract] :  Property
DAMLVocabulary.disjointWith ( ) [abstract] :  Property
DAMLVocabulary.domain ( ) [abstract] :  Property
DAMLVocabulary.equivalentTo ( ) [abstract] :  Property
DAMLVocabulary.first ( ) [abstract] :  Property
DAMLVocabulary.hasClass ( ) [abstract] :  Property
DAMLVocabulary.hasClassQ ( ) [abstract] :  Property
DAMLVocabulary.hasValue ( ) [abstract] :  Property
DAMLVocabulary.imports ( ) [abstract] :  Property
DAMLVocabulary.intersectionOf ( ) [abstract] :  Property
DAMLVocabulary.inverseOf ( ) [abstract] :  Property
DAMLVocabulary.isDefinedBy ( ) [abstract] :  Property
DAMLVocabulary.item ( ) [abstract] :  Property
DAMLVocabulary.label ( ) [abstract] :  Property
DAMLVocabulary.List ( ) [abstract] :  Resource
DAMLVocabulary.Literal ( ) [abstract] :  Resource
DAMLVocabulary.maxCardinality ( ) [abstract] :  Property
DAMLVocabulary.maxCardinalityQ ( ) [abstract] :  Property
DAMLVocabulary.minCardinality ( ) [abstract] :  Property
DAMLVocabulary.minCardinalityQ ( ) [abstract] :  Property
DAMLVocabulary.NAMESPACE_DAML ( ) [abstract] :  Resource
DAMLVocabulary.nil ( ) [abstract] :  Resource
DAMLVocabulary.Nothing ( ) [abstract] :  Resource
DAMLVocabulary.ObjectProperty ( ) [abstract] :  Resource
DAMLVocabulary.oneOf ( ) [abstract] :  Property
DAMLVocabulary.onProperty ( ) [abstract] :  Property
DAMLVocabulary.Ontology ( ) [abstract] :  Resource
DAMLVocabulary.Property ( ) [abstract] :  Resource
DAMLVocabulary.range ( ) [abstract] :  Property
DAMLVocabulary.rest ( ) [abstract] :  Property
DAMLVocabulary.Restriction ( ) [abstract] :  Resource
DAMLVocabulary.sameClassAs ( ) [abstract] :  Property
DAMLVocabulary.sameIndividualAs ( ) [abstract] :  Property
DAMLVocabulary.samePropertyAs ( ) [abstract] :  Property
DAMLVocabulary.seeAlso ( ) [abstract] :  Property
DAMLVocabulary.subClassOf ( ) [abstract] :  Property
DAMLVocabulary.subPropertyOf ( ) [abstract] :  Property
DAMLVocabulary.Thing ( ) [abstract] :  Resource
DAMLVocabulary.toClass ( ) [abstract] :  Property
DAMLVocabulary.TransitiveProperty ( ) [abstract] :  Resource
DAMLVocabulary.type ( ) [abstract] :  Property
DAMLVocabulary.UnambiguousProperty ( ) [abstract] :  Resource
DAMLVocabulary.unionOf ( ) [abstract] :  Property
DAMLVocabulary.UniqueProperty ( ) [abstract] :  Resource
DAMLVocabulary.value ( ) [abstract] :  Property
DAMLVocabulary.versionInfo ( ) [abstract] :  Property

cdk-1.4.0.jar, DataRange.class
package com.hp.hpl.jena.ontology
DataRange.addOneOf ( Iterator p1 ) [abstract] :  void
DataRange.addOneOf ( Literal p1 ) [abstract] :  void
DataRange.getOneOf ( ) [abstract] :  RDFList
DataRange.hasOneOf ( Literal p1 ) [abstract] :  boolean
DataRange.listOneOf ( ) [abstract] :  ExtendedIterator
DataRange.removeOneOf ( Literal p1 ) [abstract] :  void
DataRange.setOneOf ( RDFList p1 ) [abstract] :  void

cdk-1.4.0.jar, DatatypeFormatException.class
package com.hp.hpl.jena.datatypes
DatatypeFormatException.DatatypeFormatException ( )
DatatypeFormatException.DatatypeFormatException ( String lexicalForm, RDFDatatype dtype, String msg )
DatatypeFormatException.DatatypeFormatException ( String msg )

cdk-1.4.0.jar, DateFormat.class
package com.ibm.icu.text
DateFormat.clone ( ) :  Object
DateFormat.DateFormat ( )
DateFormat.equals ( Object obj ) :  boolean
DateFormat.format ( Calendar p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
DateFormat.format ( Date date ) :  String
DateFormat.format ( Date date, StringBuffer toAppendTo, FieldPosition fieldPosition ) :  StringBuffer
DateFormat.format ( Object obj, StringBuffer toAppendTo, FieldPosition fieldPosition ) :  StringBuffer
DateFormat.getAvailableLocales ( ) [static] :  Locale[ ]
DateFormat.getAvailableULocales ( ) [static] :  ULocale[ ] *DEPRECATED*
DateFormat.getCalendar ( ) :  Calendar
DateFormat.getDateInstance ( ) [static] :  DateFormat
DateFormat.getDateInstance ( Calendar cal, int dateStyle ) [static] :  DateFormat
DateFormat.getDateInstance ( Calendar cal, int dateStyle, Locale locale ) [static] :  DateFormat
DateFormat.getDateInstance ( Calendar cal, int dateStyle, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getDateInstance ( int style ) [static] :  DateFormat
DateFormat.getDateInstance ( int style, Locale aLocale ) [static] :  DateFormat
DateFormat.getDateInstance ( int style, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getDateTimeInstance ( ) [static] :  DateFormat
DateFormat.getDateTimeInstance ( Calendar cal, int dateStyle, int timeStyle ) [static] :  DateFormat
DateFormat.getDateTimeInstance ( Calendar cal, int dateStyle, int timeStyle, Locale locale ) [static] :  DateFormat
DateFormat.getDateTimeInstance ( Calendar cal, int dateStyle, int timeStyle, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getDateTimeInstance ( int dateStyle, int timeStyle ) [static] :  DateFormat
DateFormat.getDateTimeInstance ( int dateStyle, int timeStyle, Locale aLocale ) [static] :  DateFormat
DateFormat.getDateTimeInstance ( int dateStyle, int timeStyle, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getInstance ( ) [static] :  DateFormat
DateFormat.getInstance ( Calendar cal ) [static] :  DateFormat
DateFormat.getInstance ( Calendar cal, Locale locale ) [static] :  DateFormat
DateFormat.getInstance ( Calendar cal, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getNumberFormat ( ) :  NumberFormat
DateFormat.getTimeInstance ( ) [static] :  DateFormat
DateFormat.getTimeInstance ( Calendar cal, int timeStyle ) [static] :  DateFormat
DateFormat.getTimeInstance ( Calendar cal, int timeStyle, Locale locale ) [static] :  DateFormat
DateFormat.getTimeInstance ( Calendar cal, int timeStyle, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getTimeInstance ( int style ) [static] :  DateFormat
DateFormat.getTimeInstance ( int style, Locale aLocale ) [static] :  DateFormat
DateFormat.getTimeInstance ( int style, ULocale locale ) [static] :  DateFormat *DEPRECATED*
DateFormat.getTimeZone ( ) :  TimeZone
DateFormat.hashCode ( ) :  int
DateFormat.isLenient ( ) :  boolean
DateFormat.parse ( String p1, Calendar p2, ParsePosition p3 ) [abstract] :  void
DateFormat.parse ( String text ) :  Date
DateFormat.parse ( String text, ParsePosition pos ) :  Date
DateFormat.parseObject ( String source, ParsePosition pos ) :  Object
DateFormat.setCalendar ( Calendar newCalendar ) :  void
DateFormat.setLenient ( boolean lenient ) :  void
DateFormat.setNumberFormat ( NumberFormat newNumberFormat ) :  void
DateFormat.setTimeZone ( TimeZone zone ) :  void

cdk-1.4.0.jar, DateFormatSymbols.class
package com.ibm.icu.text
DateFormatSymbols.clone ( ) :  Object
DateFormatSymbols.DateFormatSymbols ( )
DateFormatSymbols.DateFormatSymbols ( Calendar cal, Locale locale )
DateFormatSymbols.DateFormatSymbols ( Calendar cal, ULocale locale ) *DEPRECATED*
DateFormatSymbols.DateFormatSymbols ( Class calendarClass, Locale locale )
DateFormatSymbols.DateFormatSymbols ( Class calendarClass, ULocale locale ) *DEPRECATED*
DateFormatSymbols.DateFormatSymbols ( Locale locale )
DateFormatSymbols.DateFormatSymbols ( ResourceBundle bundle, Locale locale )
DateFormatSymbols.DateFormatSymbols ( ResourceBundle bundle, ULocale locale ) *DEPRECATED*
DateFormatSymbols.DateFormatSymbols ( ULocale locale ) *DEPRECATED*
DateFormatSymbols.equals ( Object obj ) :  boolean
DateFormatSymbols.getAmPmStrings ( ) :  String[ ]
DateFormatSymbols.getDateFormatBundle ( Calendar cal, Locale locale ) [static] :  ResourceBundle
DateFormatSymbols.getDateFormatBundle ( Calendar cal, ULocale locale ) [static] :  ResourceBundle *DEPRECATED*
DateFormatSymbols.getDateFormatBundle ( Class calendarClass, Locale locale ) [static] :  ResourceBundle
DateFormatSymbols.getDateFormatBundle ( Class calendarClass, ULocale locale ) [static] :  ResourceBundle *DEPRECATED*
DateFormatSymbols.getEraNames ( ) :  String[ ] *DEPRECATED*
DateFormatSymbols.getEras ( ) :  String[ ]
DateFormatSymbols.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
DateFormatSymbols.getLocalPatternChars ( ) :  String
DateFormatSymbols.getMonths ( ) :  String[ ] *DEPRECATED*
DateFormatSymbols.getMonths ( int context, int width ) :  String[ ] *DEPRECATED*
DateFormatSymbols.getShortMonths ( ) :  String[ ]
DateFormatSymbols.getShortWeekdays ( ) :  String[ ]
DateFormatSymbols.getWeekdays ( ) :  String[ ]
DateFormatSymbols.getWeekdays ( int context, int width ) :  String[ ] *DEPRECATED*
DateFormatSymbols.getZoneStrings ( ) :  String[ ][ ]
DateFormatSymbols.hashCode ( ) :  int
DateFormatSymbols.initializeData ( ULocale desiredLocale, CalendarData calData ) :  void *DEPRECATED*
DateFormatSymbols.initializeData ( ULocale desiredLocale, String type ) :  void *DEPRECATED*
DateFormatSymbols.setAmPmStrings ( String[ ] newAmpms ) :  void
DateFormatSymbols.setEras ( String[ ] newEras ) :  void
DateFormatSymbols.setLocalPatternChars ( String newLocalPatternChars ) :  void
DateFormatSymbols.setMonths ( String[ ] newMonths ) :  void
DateFormatSymbols.setShortMonths ( String[ ] newShortMonths ) :  void
DateFormatSymbols.setShortWeekdays ( String[ ] newShortWeekdays ) :  void
DateFormatSymbols.setWeekdays ( String[ ] newWeekdays ) :  void
DateFormatSymbols.setZoneStrings ( String[ ][ ] newZoneStrings ) :  void

cdk-1.4.0.jar, DateRule.class
package com.ibm.icu.util
DateRule.firstAfter ( Date p1 ) [abstract] :  Date *DEPRECATED*
DateRule.firstBetween ( Date p1, Date p2 ) [abstract] :  Date *DEPRECATED*
DateRule.isBetween ( Date p1, Date p2 ) [abstract] :  boolean *DEPRECATED*
DateRule.isOn ( Date p1 ) [abstract] :  boolean *DEPRECATED*

cdk-1.4.0.jar, DB.class
package com.hp.hpl.jena.vocabulary
DB.DB ( )
DB.getURI ( ) [static] :  String

cdk-1.4.0.jar, DBcmd.class
package jena.util
DBcmd.closeConnection ( ) :  void
DBcmd.closeModel ( ) :  void
DBcmd.DBcmd ( String n, boolean posArgs )
DBcmd.exec ( ) :  void
DBcmd.exec0 ( ) [abstract] :  void
DBcmd.exec1 ( String p1 ) [abstract] :  boolean
DBcmd.getCommandLine ( ) :  CommandLine
DBcmd.getConnection ( ) :  IDBConnection
DBcmd.getRDBModel ( ) :  ModelRDB
DBcmd.init ( String[ ] args ) :  void
DBcmd.setUsage ( String a ) :  void
DBcmd.setUsage ( String[ ] a ) :  void
DBcmd.usage ( ) :  void

cdk-1.4.0.jar, DBConnection.class
package com.hp.hpl.jena.db
DBConnection.cleanDB ( ) :  void
DBConnection.close ( ) :  void
DBConnection.containsDefaultModel ( ) :  boolean
DBConnection.containsModel ( String name ) :  boolean
DBConnection.DBConnection ( Connection connection, String databaseType )
DBConnection.DBConnection ( String url, String user, String password, String databaseType )
DBConnection.getAllModelNames ( ) :  ExtendedIterator
DBConnection.getConnection ( ) :  Connection
DBConnection.getDatabaseProperties ( ) :  Model
DBConnection.getDatabaseType ( ) :  String
DBConnection.getDefaultModelProperties ( ) :  Model
DBConnection.getDriver ( ) :  IRDBDriver
DBConnection.isFormatOK ( ) :  boolean
DBConnection.setDatabaseProperties ( Model dbProperties ) :  void
DBConnection.setDatabaseType ( String databaseType ) :  void
DBConnection.setDriver ( IRDBDriver driver ) :  void

cdk-1.4.0.jar, dbcreate.class
package jena
dbcreate.dbcreate ( )
dbcreate.exec0 ( ) :  void
dbcreate.exec1 ( String arg ) :  boolean
dbcreate.main ( String[ ] args ) [static] :  void

cdk-1.4.0.jar, dbdump.class
package jena
dbdump.dbdump ( )
dbdump.exec0 ( ) :  void
dbdump.exec1 ( String arg ) :  boolean
dbdump.main ( String[ ] args ) [static] :  void

cdk-1.4.0.jar, dblist.class
package jena
dblist.dblist ( )
dblist.exec0 ( ) :  void
dblist.exec1 ( String arg ) :  boolean
dblist.main ( String[ ] args ) [static] :  void

cdk-1.4.0.jar, dbload.class
package jena
dbload.dbload ( )
dbload.exec0 ( ) :  void
dbload.exec1 ( String arg ) :  boolean
dbload.main ( String[ ] args ) [static] :  void

cdk-1.4.0.jar, dbquery.class
package jena
dbquery.dbquery ( )
dbquery.doQuery ( Query query, QueryExecution qe, ResultsFormat outputFormat ) :  void
dbquery.exec0 ( ) :  void
dbquery.exec1 ( String arg ) :  boolean
dbquery.main ( String[ ] argv ) [static] :  void
dbquery.main2 ( String[ ] argv ) [static] :  void

cdk-1.4.0.jar, dbremove.class
package jena
dbremove.dbremove ( )
dbremove.exec0 ( ) :  void
dbremove.exec1 ( String arg ) :  boolean
dbremove.main ( String[ ] args ) [static] :  void

cdk-1.4.0.jar, DC.class
package com.hp.hpl.jena.vocabulary
DC.DC ( )

cdk-1.4.0.jar, DC_10.class
package com.hp.hpl.jena.vocabulary
DC_10.DC_10 ( )
DC_10.getURI ( ) [static] :  String

cdk-1.4.0.jar, DC_11.class
package com.hp.hpl.jena.vocabulary
DC_11.DC_11 ( )
DC_11.getURI ( ) [static] :  String

cdk-1.4.0.jar, DCTerms.class
package com.hp.hpl.jena.vocabulary
DCTerms.DCTerms ( )
DCTerms.getURI ( ) [static] :  String

cdk-1.4.0.jar, DCTypes.class
package com.hp.hpl.jena.vocabulary
DCTypes.DCTypes ( )
DCTypes.getURI ( ) [static] :  String

cdk-1.4.0.jar, DebugAminoAcid.class
package org.openscience.cdk.debug
DebugAminoAcid.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugAminoAcid.addStereoElement ( IStereoElement parity ) :  void
DebugAminoAcid.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugAtom.class
package org.openscience.cdk.debug
DebugAtom.getImplicitHydrogenCount ( ) :  Integer
DebugAtom.setImplicitHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.4.0.jar, DebugAtomContainer.class
package org.openscience.cdk.debug
DebugAtomContainer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugAtomContainer.addStereoElement ( IStereoElement parity ) :  void
DebugAtomContainer.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugBioPolymer.class
package org.openscience.cdk.debug
DebugBioPolymer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugBioPolymer.addStereoElement ( IStereoElement parity ) :  void
DebugBioPolymer.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugBond.class
package org.openscience.cdk.debug
DebugBond.DebugBond ( IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo )
DebugBond.getStereo ( ) :  IBond.Stereo
DebugBond.setStereo ( IBond.Stereo stereo ) :  void

cdk-1.4.0.jar, DebugChemObjectBuilder.class
package org.openscience.cdk.debug
DebugChemObjectBuilder.getInstance ( ) [static] :  IChemObjectBuilder
DebugChemObjectBuilder.newInstance ( Class clazz, Object[ ] params ) :  ICDKObject

cdk-1.4.0.jar, DebugCrystal.class
package org.openscience.cdk.debug
DebugCrystal.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugCrystal.addStereoElement ( IStereoElement parity ) :  void
DebugCrystal.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugFragmentAtom.class
package org.openscience.cdk.debug
DebugFragmentAtom.getImplicitHydrogenCount ( ) :  Integer
DebugFragmentAtom.setImplicitHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.4.0.jar, DebugMolecule.class
package org.openscience.cdk.debug
DebugMolecule.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugMolecule.addStereoElement ( IStereoElement parity ) :  void
DebugMolecule.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugMonomer.class
package org.openscience.cdk.debug
DebugMonomer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugMonomer.addStereoElement ( IStereoElement parity ) :  void
DebugMonomer.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugPolymer.class
package org.openscience.cdk.debug
DebugPolymer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugPolymer.addStereoElement ( IStereoElement parity ) :  void
DebugPolymer.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugPseudoAtom.class
package org.openscience.cdk.debug
DebugPseudoAtom.getImplicitHydrogenCount ( ) :  Integer
DebugPseudoAtom.setImplicitHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.4.0.jar, DebugRing.class
package org.openscience.cdk.debug
DebugRing.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugRing.addStereoElement ( IStereoElement parity ) :  void
DebugRing.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DebugStrand.class
package org.openscience.cdk.debug
DebugStrand.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugStrand.addStereoElement ( IStereoElement parity ) :  void
DebugStrand.stereoElements ( ) :  Iterable

cdk-1.4.0.jar, DecimalFormat.class
package com.ibm.icu.text
DecimalFormat.applyLocalizedPattern ( String pattern ) :  void
DecimalFormat.applyPattern ( String pattern ) :  void
DecimalFormat.areSignificantDigitsUsed ( ) :  boolean *DEPRECATED*
DecimalFormat.clone ( ) :  Object
DecimalFormat.DecimalFormat ( )
DecimalFormat.DecimalFormat ( String pattern )
DecimalFormat.DecimalFormat ( String pattern, DecimalFormatSymbols symbols )
DecimalFormat.equals ( Object obj ) :  boolean
DecimalFormat.format ( BigDecimal number, StringBuffer result, FieldPosition fieldPosition ) :  StringBuffer
DecimalFormat.format ( BigDecimal number, StringBuffer result, FieldPosition fieldPosition ) :  StringBuffer
DecimalFormat.format ( BigInteger number, StringBuffer result, FieldPosition fieldPosition ) :  StringBuffer
DecimalFormat.format ( double number, StringBuffer result, FieldPosition fieldPosition ) :  StringBuffer
DecimalFormat.format ( long number, StringBuffer result, FieldPosition fieldPosition ) :  StringBuffer
DecimalFormat.getDecimalFormatSymbols ( ) :  DecimalFormatSymbols
DecimalFormat.getEffectiveCurrency ( ) :  Currency
DecimalFormat.getFormatWidth ( ) :  int
DecimalFormat.getGroupingSize ( ) :  int
DecimalFormat.getMaximumSignificantDigits ( ) :  int *DEPRECATED*
DecimalFormat.getMinimumExponentDigits ( ) :  byte
DecimalFormat.getMinimumSignificantDigits ( ) :  int *DEPRECATED*
DecimalFormat.getMultiplier ( ) :  int
DecimalFormat.getNegativePrefix ( ) :  String
DecimalFormat.getNegativeSuffix ( ) :  String
DecimalFormat.getPadCharacter ( ) :  char
DecimalFormat.getPadPosition ( ) :  int
DecimalFormat.getPositivePrefix ( ) :  String
DecimalFormat.getPositiveSuffix ( ) :  String
DecimalFormat.getRoundingIncrement ( ) :  BigDecimal
DecimalFormat.getRoundingMode ( ) :  int
DecimalFormat.getSecondaryGroupingSize ( ) :  int
DecimalFormat.hashCode ( ) :  int
DecimalFormat.isDecimalSeparatorAlwaysShown ( ) :  boolean
DecimalFormat.isExponentSignAlwaysShown ( ) :  boolean
DecimalFormat.isScientificNotation ( ) :  boolean
DecimalFormat.parse ( String text, ParsePosition parsePosition ) :  Number
DecimalFormat.setCurrency ( Currency theCurrency ) :  void
DecimalFormat.setDecimalFormatSymbols ( DecimalFormatSymbols newSymbols ) :  void
DecimalFormat.setDecimalSeparatorAlwaysShown ( boolean newValue ) :  void
DecimalFormat.setExponentSignAlwaysShown ( boolean expSignAlways ) :  void
DecimalFormat.setFormatWidth ( int width ) :  void
DecimalFormat.setGroupingSize ( int newValue ) :  void
DecimalFormat.setMaximumFractionDigits ( int newValue ) :  void
DecimalFormat.setMaximumIntegerDigits ( int newValue ) :  void
DecimalFormat.setMaximumSignificantDigits ( int max ) :  void *DEPRECATED*
DecimalFormat.setMinimumExponentDigits ( byte minExpDig ) :  void
DecimalFormat.setMinimumFractionDigits ( int newValue ) :  void
DecimalFormat.setMinimumIntegerDigits ( int newValue ) :  void
DecimalFormat.setMinimumSignificantDigits ( int min ) :  void *DEPRECATED*
DecimalFormat.setMultiplier ( int newValue ) :  void
DecimalFormat.setNegativePrefix ( String newValue ) :  void
DecimalFormat.setNegativeSuffix ( String newValue ) :  void
DecimalFormat.setPadCharacter ( char padChar ) :  void
DecimalFormat.setPadPosition ( int padPos ) :  void
DecimalFormat.setPositivePrefix ( String newValue ) :  void
DecimalFormat.setPositiveSuffix ( String newValue ) :  void
DecimalFormat.setRoundingIncrement ( BigDecimal newValue ) :  void
DecimalFormat.setRoundingIncrement ( double newValue ) :  void
DecimalFormat.setRoundingMode ( int roundingMode ) :  void
DecimalFormat.setScientificNotation ( boolean useScientific ) :  void
DecimalFormat.setSecondaryGroupingSize ( int newValue ) :  void
DecimalFormat.setSignificantDigitsUsed ( boolean useSignificantDigits ) :  void *DEPRECATED*
DecimalFormat.toLocalizedPattern ( ) :  String
DecimalFormat.toPattern ( ) :  String

cdk-1.4.0.jar, DecimalFormatSymbols.class
package com.ibm.icu.text
DecimalFormatSymbols.clone ( ) :  Object
DecimalFormatSymbols.DecimalFormatSymbols ( )
DecimalFormatSymbols.DecimalFormatSymbols ( Locale locale )
DecimalFormatSymbols.DecimalFormatSymbols ( ULocale locale ) *DEPRECATED*
DecimalFormatSymbols.equals ( Object obj ) :  boolean
DecimalFormatSymbols.getCurrency ( ) :  Currency *DEPRECATED*
DecimalFormatSymbols.getCurrencySymbol ( ) :  String
DecimalFormatSymbols.getDecimalSeparator ( ) :  char
DecimalFormatSymbols.getDigit ( ) :  char
DecimalFormatSymbols.getExponentSeparator ( ) :  String
DecimalFormatSymbols.getGroupingSeparator ( ) :  char
DecimalFormatSymbols.getInfinity ( ) :  String
DecimalFormatSymbols.getInternationalCurrencySymbol ( ) :  String
DecimalFormatSymbols.getLocale ( ) :  Locale
DecimalFormatSymbols.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
DecimalFormatSymbols.getMinusSign ( ) :  char
DecimalFormatSymbols.getMonetaryDecimalSeparator ( ) :  char
DecimalFormatSymbols.getNaN ( ) :  String
DecimalFormatSymbols.getPadEscape ( ) :  char
DecimalFormatSymbols.getPatternSeparator ( ) :  char
DecimalFormatSymbols.getPercent ( ) :  char
DecimalFormatSymbols.getPerMill ( ) :  char
DecimalFormatSymbols.getPlusSign ( ) :  char
DecimalFormatSymbols.getSignificantDigit ( ) :  char *DEPRECATED*
DecimalFormatSymbols.getULocale ( ) :  ULocale *DEPRECATED*
DecimalFormatSymbols.getZeroDigit ( ) :  char
DecimalFormatSymbols.hashCode ( ) :  int
DecimalFormatSymbols.setCurrency ( Currency currency ) :  void *DEPRECATED*
DecimalFormatSymbols.setCurrencySymbol ( String currency ) :  void
DecimalFormatSymbols.setDecimalSeparator ( char decimalSeparator ) :  void
DecimalFormatSymbols.setDigit ( char digit ) :  void
DecimalFormatSymbols.setExponentSeparator ( String exp ) :  void
DecimalFormatSymbols.setGroupingSeparator ( char groupingSeparator ) :  void
DecimalFormatSymbols.setInfinity ( String infinity ) :  void
DecimalFormatSymbols.setInternationalCurrencySymbol ( String currency ) :  void
DecimalFormatSymbols.setMinusSign ( char minusSign ) :  void
DecimalFormatSymbols.setMonetaryDecimalSeparator ( char sep ) :  void
DecimalFormatSymbols.setNaN ( String NaN ) :  void
DecimalFormatSymbols.setPadEscape ( char c ) :  void
DecimalFormatSymbols.setPatternSeparator ( char patternSeparator ) :  void
DecimalFormatSymbols.setPercent ( char percent ) :  void
DecimalFormatSymbols.setPerMill ( char perMill ) :  void
DecimalFormatSymbols.setPlusSign ( char plus ) :  void
DecimalFormatSymbols.setSignificantDigit ( char sigDigit ) :  void *DEPRECATED*
DecimalFormatSymbols.setZeroDigit ( char zeroDigit ) :  void

cdk-1.4.0.jar, DeduceBondSystemTool.class
package org.openscience.cdk.smiles
DeduceBondSystemTool.DeduceBondSystemTool ( AllRingsFinder ringFinder )

cdk-1.4.0.jar, DefaultBondColor.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.DefaultBondColor.BasicBondGenerator.DefaultBondColor ( )
BasicBondGenerator.DefaultBondColor.getDefault ( ) :  Color
BasicBondGenerator.DefaultBondColor.getDefault ( ) :  Object

cdk-1.4.0.jar, DefaultBondMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultBondMatcher.DefaultBondMatcher ( )
DefaultBondMatcher.DefaultBondMatcher ( IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds )
DefaultBondMatcher.DefaultBondMatcher ( IQueryBond queryBond )
DefaultBondMatcher.isBondMatchFlag ( ) :  boolean
DefaultBondMatcher.matches ( IAtomContainer targetContainer, IBond targetBond ) :  boolean
DefaultBondMatcher.setBondMatchFlag ( boolean shouldMatchBonds ) :  void

cdk-1.4.0.jar, DefaultChemObjectBuilder.class
package org.openscience.cdk
DefaultChemObjectBuilder.getInstance ( ) [static] :  IChemObjectBuilder
DefaultChemObjectBuilder.newInstance ( Class clazz, Object[ ] params ) :  ICDKObject

cdk-1.4.0.jar, DefaultChemObjectReader.class
package org.openscience.cdk.io
DefaultChemObjectReader.handleError ( String message ) :  void
DefaultChemObjectReader.handleError ( String message, Exception exception ) :  void
DefaultChemObjectReader.handleError ( String message, int row, int colStart, int colEnd ) :  void
DefaultChemObjectReader.handleError ( String message, int row, int colStart, int colEnd, Exception exception ) :  void
DefaultChemObjectReader.setErrorHandler ( IChemObjectReaderErrorHandler handler ) :  void

cdk-1.4.0.jar, DefaultIteratingChemObjectReader.class
package org.openscience.cdk.io.iterator
DefaultIteratingChemObjectReader.handleError ( String message ) :  void
DefaultIteratingChemObjectReader.handleError ( String message, Exception exception ) :  void
DefaultIteratingChemObjectReader.handleError ( String message, int row, int colStart, int colEnd ) :  void
DefaultIteratingChemObjectReader.handleError ( String message, int row, int colStart, int colEnd, Exception exception ) :  void
DefaultIteratingChemObjectReader.setErrorHandler ( IChemObjectReaderErrorHandler handler ) :  void

cdk-1.4.0.jar, DefaultMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultMatcher.DefaultMatcher ( )
DefaultMatcher.isAtomMatch ( AtomMatcher atomMatcher1, AtomMatcher atomMatcher2, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds ) [static] :  boolean
DefaultMatcher.isBondMatch ( BondMatcher bondMatcher, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds ) [static] :  boolean

cdk-1.4.0.jar, DefaultMCSPlusAtomMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultMCSPlusAtomMatcher.DefaultMCSPlusAtomMatcher ( )
DefaultMCSPlusAtomMatcher.DefaultMCSPlusAtomMatcher ( IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds )
DefaultMCSPlusAtomMatcher.DefaultMCSPlusAtomMatcher ( IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds )
DefaultMCSPlusAtomMatcher.DefaultMCSPlusAtomMatcher ( IQueryAtom smartQueryAtom, IQueryAtomContainer container )
DefaultMCSPlusAtomMatcher.isBondMatchFlag ( ) :  boolean
DefaultMCSPlusAtomMatcher.matches ( IAtomContainer targetContainer, IAtom targetAtom ) :  boolean
DefaultMCSPlusAtomMatcher.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
DefaultMCSPlusAtomMatcher.setMaximumNeighbors ( int maximum ) :  void
DefaultMCSPlusAtomMatcher.setSymbol ( String symbol ) :  void

cdk-1.4.0.jar, DefaultModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
DefaultModelAssembler.DefaultModelAssembler ( )
DefaultModelAssembler.open ( Assembler a, Resource root, Mode mode ) :  Object
DefaultModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode irrelevant ) :  Model

cdk-1.4.0.jar, DefaultReadHook.class
package com.hp.hpl.jena.ontology
OntDocumentManager.DefaultReadHook.afterRead ( Model model, String source, OntDocumentManager odm ) :  void
OntDocumentManager.DefaultReadHook.beforeRead ( Model model, String source, OntDocumentManager odm ) :  String
OntDocumentManager.DefaultReadHook.OntDocumentManager.DefaultReadHook ( )

cdk-1.4.0.jar, DefaultRGraphAtomMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultRGraphAtomMatcher.DefaultRGraphAtomMatcher ( )
DefaultRGraphAtomMatcher.DefaultRGraphAtomMatcher ( IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds )
DefaultRGraphAtomMatcher.DefaultRGraphAtomMatcher ( IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds )
DefaultRGraphAtomMatcher.isBondMatchFlag ( ) :  boolean
DefaultRGraphAtomMatcher.matches ( IAtomContainer targetContainer, IAtom targetAtom ) :  boolean
DefaultRGraphAtomMatcher.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
DefaultRGraphAtomMatcher.setMaximumNeighbors ( int maximum ) :  void
DefaultRGraphAtomMatcher.setSymbol ( String symbol ) :  void

cdk-1.4.0.jar, DefaultVFAtomMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultVFAtomMatcher.DefaultVFAtomMatcher ( )
DefaultVFAtomMatcher.DefaultVFAtomMatcher ( IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds )
DefaultVFAtomMatcher.DefaultVFAtomMatcher ( IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds )
DefaultVFAtomMatcher.DefaultVFAtomMatcher ( IQueryAtom smartQueryAtom, IQueryAtomContainer container )
DefaultVFAtomMatcher.isBondMatchFlag ( ) :  boolean
DefaultVFAtomMatcher.matches ( TargetProperties targetContainer, IAtom targetAtom ) :  boolean
DefaultVFAtomMatcher.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
DefaultVFAtomMatcher.setMaximumNeighbors ( int maximum ) :  void
DefaultVFAtomMatcher.setSymbol ( String symbol ) :  void

cdk-1.4.0.jar, DefaultVFBondMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
DefaultVFBondMatcher.DefaultVFBondMatcher ( )
DefaultVFBondMatcher.DefaultVFBondMatcher ( IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds )
DefaultVFBondMatcher.DefaultVFBondMatcher ( IQueryBond queryBond )
DefaultVFBondMatcher.isBondMatchFlag ( ) :  boolean
DefaultVFBondMatcher.matches ( TargetProperties targetConatiner, IBond targetBond ) :  boolean
DefaultVFBondMatcher.setBondMatchFlag ( boolean shouldMatchBonds ) :  void

cdk-1.4.0.jar, DeleteDeniedException.class
package com.hp.hpl.jena.shared
DeleteDeniedException.DeleteDeniedException ( String message )
DeleteDeniedException.DeleteDeniedException ( String message, Triple triple )

cdk-1.4.0.jar, Delta.class
package com.hp.hpl.jena.graph.compose
Delta.close ( ) :  void
Delta.Delta ( Graph base )
Delta.getAdditions ( ) :  Graph
Delta.getDeletions ( ) :  Graph
Delta.graphBaseFind ( TripleMatch tm ) :  ExtendedIterator
Delta.graphBaseSize ( ) :  int
Delta.performAdd ( Triple t ) :  void
Delta.performDelete ( Triple t ) :  void

cdk-1.4.0.jar, Derivation.class
package com.hp.hpl.jena.reasoner
Derivation.printTrace ( PrintWriter p1, boolean p2 ) [abstract] :  void
Derivation.toString ( ) [abstract] :  String

cdk-1.4.0.jar, DictionaryBasedBreakIterator.class
package com.ibm.icu.text
DictionaryBasedBreakIterator.DictionaryBasedBreakIterator ( String description, InputStream dictionaryStream )
DictionaryBasedBreakIterator.first ( ) :  int
DictionaryBasedBreakIterator.following ( int offset ) :  int
DictionaryBasedBreakIterator.handleNext ( ) :  int
DictionaryBasedBreakIterator.last ( ) :  int
DictionaryBasedBreakIterator.lookupCategory ( char c ) :  int
DictionaryBasedBreakIterator.makeBuilder ( ) :  RuleBasedBreakIterator_Old.Builder
DictionaryBasedBreakIterator.preceding ( int offset ) :  int
DictionaryBasedBreakIterator.previous ( ) :  int
DictionaryBasedBreakIterator.setText ( CharacterIterator newText ) :  void
DictionaryBasedBreakIterator.writeTablesToFile ( FileOutputStream file, boolean littleEndian ) :  void

cdk-1.4.0.jar, Difference.class
package com.hp.hpl.jena.graph.compose
Difference.Difference ( Graph L, Graph R )
Difference.graphBaseFind ( TripleMatch t ) :  ExtendedIterator
Difference.performAdd ( Triple t ) :  void
Difference.performDelete ( Triple t ) :  void
package com.hp.hpl.jena.reasoner.rulesys.builtins
Difference.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Difference.Difference ( )
Difference.getArgLength ( ) :  int
Difference.getName ( ) :  String

cdk-1.4.0.jar, Direction.class
package org.openscience.cdk.renderer.elements
WedgeLineElement.Direction.valueOf ( String name ) [static] :  WedgeLineElement.Direction
WedgeLineElement.Direction.values ( ) [static] :  WedgeLineElement.Direction[ ]
package signature
DAG.Direction.valueOf ( String name ) [static] :  DAG.Direction
DAG.Direction.values ( ) [static] :  DAG.Direction[ ]

cdk-1.4.0.jar, DisjointSet.class
package com.hp.hpl.jena.ontology
OntTools.DisjointSet.find ( ) :  OntTools.DisjointSet
OntTools.DisjointSet.getAncestor ( ) :  OntTools.DisjointSet
OntTools.DisjointSet.getNode ( ) :  Resource
OntTools.DisjointSet.getParent ( ) :  OntTools.DisjointSet
OntTools.DisjointSet.getRank ( ) :  int
OntTools.DisjointSet.incrementRank ( ) :  void
OntTools.DisjointSet.isBlack ( ) :  boolean
OntTools.DisjointSet.OntTools.DisjointSet ( Resource node )
OntTools.DisjointSet.setAncestor ( OntTools.DisjointSet anc ) :  void
OntTools.DisjointSet.setBlack ( ) :  void
OntTools.DisjointSet.setParent ( OntTools.DisjointSet parent ) :  void
OntTools.DisjointSet.setUsed ( ) :  void
OntTools.DisjointSet.toShortString ( ) :  String
OntTools.DisjointSet.toString ( ) :  String
OntTools.DisjointSet.union ( OntTools.DisjointSet y ) :  void
OntTools.DisjointSet.used ( ) :  boolean

cdk-1.4.0.jar, DisjointUnion.class
package com.hp.hpl.jena.graph.compose
DisjointUnion.DisjointUnion ( Graph L, Graph R )
DisjointUnion.graphBaseContains ( Triple t ) :  boolean
DisjointUnion.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
DisjointUnion.performAdd ( Triple t ) :  void
DisjointUnion.performDelete ( Triple t ) :  void

cdk-1.4.0.jar, DisplayableColoredTree.class
package signature.display
DisplayableColoredTree.DisplayableColoredTree ( ColoredTree tree, int width, int height )
DisplayableColoredTree.DisplayableColoredTree ( int width, int height )
DisplayableColoredTree.makeFromColoredTree ( ColoredTree tree ) :  void
DisplayableColoredTree.paint ( Graphics g ) :  void
DisplayableColoredTree.paint ( Graphics g, DisplayableColoredTree.DrawNode node ) :  void
DisplayableColoredTree.paintKey ( Graphics g ) :  void
DisplayableColoredTree.setDrawKey ( boolean drawKey ) :  void

cdk-1.4.0.jar, DocumentManagerAssembler.class
package com.hp.hpl.jena.assembler.assemblers
DocumentManagerAssembler.createDocumentManager ( ) :  OntDocumentManager
DocumentManagerAssembler.DocumentManagerAssembler ( )
DocumentManagerAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, DoesNotExistException.class
package com.hp.hpl.jena.shared
DoesNotExistException.DoesNotExistException ( String name )

cdk-1.4.0.jar, DoesNotReifyException.class
package com.hp.hpl.jena.rdf.model
DoesNotReifyException.DoesNotReifyException ( Node n )

cdk-1.4.0.jar, DOM2Model.class
package com.hp.hpl.jena.rdf.arp
DOM2Model.createD2M ( String base, Model m ) [static] :  DOM2Model
DOM2Model.createD2M ( String base, Model m, String lang ) [static] :  DOM2Model
DOM2Model.load ( Node document ) :  void

cdk-1.4.0.jar, Domain.class
package com.hp.hpl.jena.graph.query
Domain.copy ( ) :  Domain
Domain.Domain ( int size )
Domain.Domain ( Node[ ] value )
Domain.equals ( Object x ) :  boolean
Domain.get ( int i ) :  Node
Domain.get ( int x0 ) :  Object
Domain.getElement ( int i ) :  Node
Domain.setElement ( int i, Node x ) :  void
Domain.size ( ) :  int
Domain.toString ( ) :  String

cdk-1.4.0.jar, DrawNode.class
package signature.display
DisplayableColoredTree.DrawNode.countLeaves ( ) :  int
DisplayableColoredTree.DrawNode.DisplayableColoredTree.DrawNode ( DisplayableColoredTree label, String parent, DisplayableColoredTree.DrawNode d, int color, int edgeLabel, String p6 )
DisplayableColoredTree.DrawNode.DisplayableColoredTree.DrawNode ( DisplayableColoredTree label, String parent, DisplayableColoredTree.DrawNode d, int color, int p5 )
DisplayableColoredTree.DrawNode.isLeaf ( ) :  boolean
DisplayableColoredTree.DrawNode.toString ( ) :  String

cdk-1.4.0.jar, Drop.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Drop.Drop ( )
Drop.getName ( ) :  String
Drop.headAction ( Node[ ] args, int length, RuleContext context ) :  void
Drop.isMonotonic ( ) :  boolean

cdk-1.4.0.jar, Dyadic.class
package com.hp.hpl.jena.graph.compose
Dyadic.close ( ) :  void
Dyadic.dependsOn ( Graph other ) :  boolean
Dyadic.Dyadic ( Graph L, Graph R )
Dyadic.getL ( ) :  Object
Dyadic.getR ( ) :  Object
Dyadic.union ( Graph X ) :  Union
package com.hp.hpl.jena.graph.query
Dyadic.and ( Expression L, Expression R ) [static] :  Expression
Dyadic.argCount ( ) :  int
Dyadic.Dyadic ( Expression L, String F, Expression R )
Dyadic.evalBool ( Object l, Object r ) :  boolean
Dyadic.evalObject ( Object l, Object r ) :  Object
Dyadic.getArg ( int i ) :  Expression
Dyadic.getFun ( ) :  String
Dyadic.prepare ( VariableIndexes vi ) :  Valuator
Dyadic.toString ( ) :  String

cdk-1.4.0.jar, DyadicLiteral.class
package com.hp.hpl.jena.graph.query
Rewrite.DyadicLiteral.evalBool ( Object l, Object r ) :  boolean
Rewrite.DyadicLiteral.evalBool ( String p1, String p2 ) [abstract] :  boolean
Rewrite.DyadicLiteral.nodeAsString ( Object x ) :  String
Rewrite.DyadicLiteral.Rewrite.DyadicLiteral ( Expression L, String F, String R )

cdk-1.4.0.jar, EarlyBindingIterator.class
package com.hp.hpl.jena.util.iterator
EarlyBindingIterator.EarlyBindingIterator ( Iterator it )

cdk-1.4.0.jar, EasterHoliday.class
package com.ibm.icu.util
EasterHoliday.EasterHoliday ( int daysAfter, boolean orthodox, String name ) *DEPRECATED*
EasterHoliday.EasterHoliday ( int daysAfter, String name ) *DEPRECATED*
EasterHoliday.EasterHoliday ( String name ) *DEPRECATED*

cdk-1.4.0.jar, Edge.class
package signature.simple
SimpleGraph.Edge.compareTo ( Object p1 ) :  int
SimpleGraph.Edge.compareTo ( SimpleGraph.Edge other ) :  int
SimpleGraph.Edge.SimpleGraph.Edge ( SimpleGraph a, int b, int p3 )
SimpleGraph.Edge.toString ( ) :  String

cdk-1.4.0.jar, EdgeBuilder.class
package org.openscience.cdk.smsd.algorithm.vflib.builder
EdgeBuilder.EdgeBuilder ( NodeBuilder source, NodeBuilder target, VFBondMatcher matcher )
EdgeBuilder.getBondMatcher ( ) :  VFBondMatcher
EdgeBuilder.getSource ( ) :  INode
EdgeBuilder.getTarget ( ) :  INode

cdk-1.4.0.jar, Element.class
package com.hp.hpl.jena.graph.query
Element.asNodeMatch ( Domain p1 ) [abstract] :  Node
Element.Element ( )
Element.Element ( int index )
Element.getIndex ( ) :  int
Element.match ( Domain p1, Node p2 ) [abstract] :  boolean
Element.toString ( ) :  String
package com.ibm.icu.util
RangeValueIterator.Element.RangeValueIterator.Element ( )
ValueIterator.Element.ValueIterator.Element ( )
package org.openscience.cdk
Element.Element ( String symbol, Integer atomicNumber )

cdk-1.4.0.jar, ElementGroup.class
package org.openscience.cdk.renderer.elements
ElementGroup.accept ( IRenderingVisitor v ) :  void
ElementGroup.add ( IRenderingElement element ) :  void
ElementGroup.ElementGroup ( )
ElementGroup.iterator ( ) :  Iterator
ElementGroup.visitChildren ( IRenderingVisitor visitor ) :  void

cdk-1.4.0.jar, EmptyListException.class
package com.hp.hpl.jena.rdf.model
EmptyListException.EmptyListException ( )
EmptyListException.EmptyListException ( String msg )

cdk-1.4.0.jar, EmptyListUpdateException.class
package com.hp.hpl.jena.rdf.model
EmptyListUpdateException.EmptyListUpdateException ( )
EmptyListUpdateException.EmptyListUpdateException ( String message )

cdk-1.4.0.jar, EndOfLine.class
package com.hp.hpl.jena.graph.query.regexptrees
EndOfLine.EndOfLine ( )
EndOfLine.equals ( Object x ) :  boolean
EndOfLine.hashCode ( ) :  int
EndOfLine.toString ( ) :  String

cdk-1.4.0.jar, EnhancedNodeCache.class
package com.hp.hpl.jena.util.cache
EnhancedNodeCache.clear ( ) :  void
EnhancedNodeCache.EnhancedNodeCache ( String name, int size )
EnhancedNodeCache.get ( Object key ) :  Object
EnhancedNodeCache.getEnabled ( ) :  boolean
EnhancedNodeCache.getGets ( ) :  long
EnhancedNodeCache.getHits ( ) :  long
EnhancedNodeCache.getPuts ( ) :  long
EnhancedNodeCache.hashNode ( Node n ) :  int
EnhancedNodeCache.put ( Object key, Object value ) :  void
EnhancedNodeCache.setEnabled ( boolean enabled ) :  boolean

cdk-1.4.0.jar, EnhGraph.class
package com.hp.hpl.jena.enhanced
EnhGraph.asGraph ( ) :  Graph
EnhGraph.EnhGraph ( Graph g, Personality p )
EnhGraph.equals ( Object o ) :  boolean
EnhGraph.getNodeAs ( Node n, Class interf ) :  RDFNode
EnhGraph.getNodeCacheControl ( ) :  CacheControl
EnhGraph.getPersonality ( ) :  Personality
EnhGraph.hashCode ( ) :  int
EnhGraph.isIsomorphicWith ( EnhGraph eg ) :  boolean
EnhGraph.setNodeCache ( Cache cc ) :  void

cdk-1.4.0.jar, EnhNode.class
package com.hp.hpl.jena.enhanced
EnhNode.as ( Class t ) :  RDFNode
EnhNode.asNode ( ) :  Node
EnhNode.canAs ( Class t ) :  boolean
EnhNode.canSupport ( Class t ) :  boolean
EnhNode.convertTo ( Class t ) :  RDFNode
EnhNode.convertTo ( Class x0 ) :  Object
EnhNode.EnhNode ( Node n, EnhGraph g )
EnhNode.equals ( Object o ) :  boolean
EnhNode.getGraph ( ) :  EnhGraph
EnhNode.getPersonality ( ) :  Personality
EnhNode.hashCode ( ) :  int
EnhNode.isAnon ( ) :  boolean
EnhNode.isLiteral ( ) :  boolean
EnhNode.isResource ( ) :  boolean
EnhNode.isURIResource ( ) :  boolean
EnhNode.isValid ( ) :  boolean
EnhNode.viewAs ( Class t ) :  RDFNode

cdk-1.4.0.jar, Entry.class
package com.hp.hpl.jena.util
OneToManyMap.Entry.equals ( Object x ) :  boolean
OneToManyMap.Entry.getKey ( ) :  Object
OneToManyMap.Entry.getValue ( ) :  Object
OneToManyMap.Entry.hashCode ( ) :  int
OneToManyMap.Entry.setValue ( Object value ) :  Object

cdk-1.4.0.jar, EnumeratedClass.class
package com.hp.hpl.jena.ontology
EnumeratedClass.addOneOf ( Iterator p1 ) [abstract] :  void
EnumeratedClass.addOneOf ( Resource p1 ) [abstract] :  void
EnumeratedClass.getOneOf ( ) [abstract] :  RDFList
EnumeratedClass.hasOneOf ( Resource p1 ) [abstract] :  boolean
EnumeratedClass.listOneOf ( ) [abstract] :  ExtendedIterator
EnumeratedClass.removeOneOf ( Resource p1 ) [abstract] :  void
EnumeratedClass.setOneOf ( RDFList p1 ) [abstract] :  void

cdk-1.4.0.jar, Equal.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Equal.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Equal.Equal ( )
Equal.getArgLength ( ) :  int
Equal.getName ( ) :  String

cdk-1.4.0.jar, EthiopicCalendar.class
package com.ibm.icu.util
EthiopicCalendar.EthiopicCalendar ( ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( Date date ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( int year, int month, int date ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( int year, int month, int date, int hour, int minute, int second ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( Locale aLocale ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( TimeZone zone ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( TimeZone zone, Locale aLocale ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
EthiopicCalendar.EthiopicCalendar ( ULocale locale ) *DEPRECATED*
EthiopicCalendar.EthiopicToJD ( long year, int month, int date ) [static] :  int *DEPRECATED*
EthiopicCalendar.getDateFromJD ( int julianDay ) [static] :  Integer[ ]
EthiopicCalendar.getType ( ) :  String
EthiopicCalendar.isAmeteAlemEra ( ) :  boolean *DEPRECATED*
EthiopicCalendar.setAmeteAlemEra ( boolean onOff ) :  void *DEPRECATED*

cdk-1.4.0.jar, ExactMapping.class
package org.openscience.cdk.smsd.algorithm.mcsplus
ExactMapping.ExactMapping ( )
ExactMapping.extractMapping ( List _mappings, List comp_graph_nodes, List clique_List_org ) [static] :  List

cdk-1.4.0.jar, ExhaustiveFragmenter.class
package org.openscience.cdk.fragment
ExhaustiveFragmenter.ExhaustiveFragmenter ( )
ExhaustiveFragmenter.ExhaustiveFragmenter ( int minFragSize )
ExhaustiveFragmenter.generateFragments ( IAtomContainer atomContainer ) :  void
ExhaustiveFragmenter.getFragments ( ) :  String[ ]
ExhaustiveFragmenter.getFragmentsAsContainers ( ) :  IAtomContainer[ ]
ExhaustiveFragmenter.setMinimumFragmentSize ( int minFragSize ) :  void

cdk-1.4.0.jar, ExpandingAssemblerGroup.class
package com.hp.hpl.jena.assembler.assemblers
AssemblerGroup.ExpandingAssemblerGroup.assemblerFor ( Resource type ) :  Assembler
AssemblerGroup.ExpandingAssemblerGroup.AssemblerGroup.ExpandingAssemblerGroup ( )
AssemblerGroup.ExpandingAssemblerGroup.implementsTypes ( ) :  Set
AssemblerGroup.ExpandingAssemblerGroup.implementWith ( Resource type, Assembler a ) :  AssemblerGroup
AssemblerGroup.ExpandingAssemblerGroup.loadClasses ( Model model ) :  void
AssemblerGroup.ExpandingAssemblerGroup.open ( Assembler a, Resource suppliedRoot, Mode mode ) :  Object

cdk-1.4.0.jar, Expression.class
package com.hp.hpl.jena.graph.query
Expression.argCount ( ) [abstract] :  int
Expression.getArg ( int p1 ) [abstract] :  Expression
Expression.getFun ( ) [abstract] :  String
Expression.getName ( ) [abstract] :  String
Expression.getValue ( ) [abstract] :  Object
Expression.isApply ( ) [abstract] :  boolean
Expression.isConstant ( ) [abstract] :  boolean
Expression.isVariable ( ) [abstract] :  boolean
Expression.prepare ( VariableIndexes p1 ) [abstract] :  Valuator

cdk-1.4.0.jar, ExpressionSet.class
package com.hp.hpl.jena.graph.query
ExpressionSet.add ( Expression e ) :  ExpressionSet
ExpressionSet.ExpressionSet ( )
ExpressionSet.isComplex ( ) :  boolean
ExpressionSet.iterator ( ) :  Iterator
ExpressionSet.prepare ( VariableIndexes vi ) :  ValuatorSet
ExpressionSet.toString ( ) :  String

cdk-1.4.0.jar, ExtAtomContainerManipulator.class
package org.openscience.cdk.smsd.tools
ExtAtomContainerManipulator.aromatizeMolecule ( IAtomContainer mol ) [static] :  void
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens ( IAtomContainer atomContainer ) [static] :  IAtomContainer
ExtAtomContainerManipulator.ExtAtomContainerManipulator ( )
ExtAtomContainerManipulator.getExplicitHydrogenCount ( IAtomContainer atomContainer, IAtom atom ) [static] :  int
ExtAtomContainerManipulator.getHydrogenCount ( IAtomContainer atomContainer, IAtom atom ) [static] :  int
ExtAtomContainerManipulator.getImplicitHydrogenCount ( IAtom atom ) [static] :  int
ExtAtomContainerManipulator.makeDeepCopy ( IAtomContainer container ) [static] :  IAtomContainer
ExtAtomContainerManipulator.makeDeepCopy ( IMolecule container ) [static] :  IMolecule
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms ( IAtomContainer container ) [static] :  void
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID ( IAtomContainer atomContainer ) [static] :  IMolecule

cdk-1.4.0.jar, ExtendedHandler.class
package com.hp.hpl.jena.rdf.arp
ExtendedHandler.discardNodesWithNodeID ( ) [abstract] :  boolean
ExtendedHandler.endBNodeScope ( AResource p1 ) [abstract] :  void
ExtendedHandler.endRDF ( ) [abstract] :  void
ExtendedHandler.startRDF ( ) [abstract] :  void

cdk-1.4.0.jar, ExtendedIterator.class
package com.hp.hpl.jena.util.iterator
ExtendedIterator.andThen ( Iterator p1 ) [abstract] :  ExtendedIterator
ExtendedIterator.filterDrop ( Filter p1 ) [abstract] :  ExtendedIterator
ExtendedIterator.filterKeep ( Filter p1 ) [abstract] :  ExtendedIterator
ExtendedIterator.mapWith ( Map1 p1 ) [abstract] :  ExtendedIterator
ExtendedIterator.removeNext ( ) [abstract] :  Object
ExtendedIterator.toList ( ) [abstract] :  List
ExtendedIterator.toSet ( ) [abstract] :  Set

cdk-1.4.0.jar, ExternalHighlightColor.class
package org.openscience.cdk.renderer
RendererModel.ExternalHighlightColor.getDefault ( ) :  Color
RendererModel.ExternalHighlightColor.getDefault ( ) :  Object
RendererModel.ExternalHighlightColor.RendererModel.ExternalHighlightColor ( )

cdk-1.4.0.jar, Extraction.class
package com.hp.hpl.jena.graph
GraphExtract.Extraction.extractInto ( Node root ) :  void

cdk-1.4.0.jar, Factory.class
package com.hp.hpl.jena.graph
Factory.createDefaultGraph ( ) [static] :  Graph
Factory.createDefaultGraph ( ReificationStyle style ) [static] :  Graph
Factory.createGraphMem ( ) [static] :  Graph
Factory.createGraphMem ( ReificationStyle style ) [static] :  Graph
Factory.createGraphMemWithTransactionHandler ( TransactionHandler th ) [static] :  Graph
package com.hp.hpl.jena.shared
PrefixMapping.Factory.create ( ) [static] :  PrefixMapping
PrefixMapping.Factory.PrefixMapping.Factory ( )
package com.ibm.icu.text
Transliterator.Factory.getInstance ( String p1 ) [abstract] :  Transliterator

cdk-1.4.0.jar, FasterPatternStage.class
package com.hp.hpl.jena.mem.faster
FasterPatternStage.FasterPatternStage ( Graph graph, Mapping map, ExpressionSet constraints, Triple[ ] triples )

cdk-1.4.0.jar, FasterTripleStore.class
package com.hp.hpl.jena.mem.faster
FasterTripleStore.containsApplyer ( ProcessedTriple pt ) :  Applyer
FasterTripleStore.createApplyer ( ProcessedTriple pt ) :  Applyer
FasterTripleStore.FasterTripleStore ( Graph parent )
FasterTripleStore.getObjects ( ) :  NodeToTriplesMapFaster
FasterTripleStore.getPredicates ( ) :  NodeToTriplesMapFaster
FasterTripleStore.getSubjects ( ) :  NodeToTriplesMapFaster
FasterTripleStore.varSvarOApplyer ( QueryTriple pt ) :  Applyer

cdk-1.4.0.jar, FatalParsingErrorException.class
package com.hp.hpl.jena.rdf.arp
FatalParsingErrorException.FatalParsingErrorException ( )

cdk-1.4.0.jar, FBRuleInfGraph.class
package com.hp.hpl.jena.reasoner.rulesys
FBRuleInfGraph.accept ( Object tin ) :  boolean
FBRuleInfGraph.addBRule ( Rule brule ) :  void
FBRuleInfGraph.addBRules ( List rules ) :  void
FBRuleInfGraph.addDeduction ( Triple t ) :  void
FBRuleInfGraph.addPreprocessingHook ( RulePreprocessHook hook ) :  void
FBRuleInfGraph.addRuleDuringPrepare ( Rule rule ) :  void
FBRuleInfGraph.checkLiteral ( Node prop, Triple triple ) :  ValidityReport.Report
FBRuleInfGraph.close ( ) :  void
FBRuleInfGraph.deleteBRule ( Rule brule ) :  void
FBRuleInfGraph.FBRuleInfGraph ( Reasoner reasoner, Graph schema )
FBRuleInfGraph.FBRuleInfGraph ( Reasoner reasoner, List rules, Graph schema )
FBRuleInfGraph.FBRuleInfGraph ( Reasoner reasoner, List rules, Graph schema, Graph data )
FBRuleInfGraph.FBRuleInfGraph ( Reasoner reasoner, List rules, Graph schema, ReificationStyle style )
FBRuleInfGraph.find ( TriplePattern pattern ) :  ExtendedIterator
FBRuleInfGraph.findDataMatches ( Node subject, Node predicate, Node object ) :  ExtendedIterator
FBRuleInfGraph.findDataMatches ( TriplePattern pattern ) :  ExtendedIterator
FBRuleInfGraph.findFull ( TriplePattern pattern ) :  ExtendedIterator
FBRuleInfGraph.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
FBRuleInfGraph.getBRules ( ) :  List
FBRuleInfGraph.getDTRange ( ) :  HashMap
FBRuleInfGraph.getNRulesFired ( ) :  long
FBRuleInfGraph.getRules ( ) :  List
FBRuleInfGraph.getTemp ( Node instance, Node prop, Node pclass ) :  Node
FBRuleInfGraph.graphBaseFind ( Node subject, Node property, Node object ) :  ExtendedIterator
FBRuleInfGraph.hideNode ( Node n ) :  void
FBRuleInfGraph.instantiateRuleEngine ( List rules ) :  void
FBRuleInfGraph.performAdd ( Triple t ) :  void
FBRuleInfGraph.performDatatypeRangeValidation ( StandardValidityReport report ) :  void
FBRuleInfGraph.performDelete ( Triple t ) :  void
FBRuleInfGraph.preloadDeductions ( Graph preloadIn ) :  boolean
FBRuleInfGraph.prepare ( ) :  void
FBRuleInfGraph.printLPProfile ( ) :  void
FBRuleInfGraph.processBuiltin ( ClauseEntry clause, Rule rule, BindingEnvironment env ) :  boolean
FBRuleInfGraph.rebind ( ) :  void
FBRuleInfGraph.rebindAll ( ) :  void
FBRuleInfGraph.reset ( ) :  void
FBRuleInfGraph.resetLPProfile ( boolean enable ) :  void
FBRuleInfGraph.setDatatypeRangeValidation ( boolean on ) :  void
FBRuleInfGraph.setDerivationLogging ( boolean recordDerivations ) :  void
FBRuleInfGraph.setFunctorFiltering ( boolean param ) :  void
FBRuleInfGraph.setTabled ( Node predicate ) :  void
FBRuleInfGraph.setTraceOn ( boolean state ) :  void
FBRuleInfGraph.setUseTGCCache ( ) :  void
FBRuleInfGraph.validate ( ) :  ValidityReport

cdk-1.4.0.jar, FBRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
FBRuleReasoner.addDescription ( Model configSpec, Resource base ) :  void
FBRuleReasoner.addRules ( List rules ) :  FBRuleReasoner
FBRuleReasoner.bind ( Graph data ) :  InfGraph
FBRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
FBRuleReasoner.bindSchema ( Model tbox ) :  Reasoner
FBRuleReasoner.doSetParameter ( Property parameter, Object value ) :  boolean
FBRuleReasoner.doSetRDFNodeParameter ( Property parameter, RDFNode value ) :  boolean
FBRuleReasoner.doSetResourceParameter ( Property parameter, Resource value ) :  boolean
FBRuleReasoner.FBRuleReasoner ( List rules )
FBRuleReasoner.FBRuleReasoner ( List rules, Graph schemaGraph, ReasonerFactory factory )
FBRuleReasoner.FBRuleReasoner ( List rules, ReasonerFactory factory )
FBRuleReasoner.FBRuleReasoner ( ReasonerFactory factory )
FBRuleReasoner.FBRuleReasoner ( ReasonerFactory factory, Resource configuration )
FBRuleReasoner.getBoundSchema ( ) :  Graph
FBRuleReasoner.getGraphCapabilities ( ) :  Capabilities
FBRuleReasoner.getPreload ( ) :  InfGraph
FBRuleReasoner.getReasonerCapabilities ( ) :  Model
FBRuleReasoner.getRules ( ) :  List
FBRuleReasoner.isTraceOn ( ) :  boolean
FBRuleReasoner.loadConfiguration ( Resource configuration ) :  void
FBRuleReasoner.loadRules ( String fileName ) [static] :  List
FBRuleReasoner.setDerivationLogging ( boolean logOn ) :  void
FBRuleReasoner.setParameter ( Property parameter, Object value ) :  void
FBRuleReasoner.setRules ( List rules ) :  void
FBRuleReasoner.setTraceOn ( boolean state ) :  void
FBRuleReasoner.supportsProperty ( Property property ) :  boolean
FBRuleReasoner.tablePredicate ( Node predicate ) :  void

cdk-1.4.0.jar, FGraph.class
package com.hp.hpl.jena.reasoner
FGraph.contains ( TriplePattern pattern ) :  boolean
FGraph.FGraph ( Graph graph )
FGraph.find ( TriplePattern pattern ) :  ExtendedIterator
FGraph.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
FGraph.getGraph ( ) :  Graph

cdk-1.4.0.jar, Field.class
package com.hp.hpl.jena.graph
Triple.Field.filterOn ( Node p1 ) [abstract] :  Filter
Triple.Field.filterOn ( Triple t ) :  Filter
Triple.Field.getField ( Triple p1 ) [abstract] :  Node
Triple.Field.Triple.Field ( )

cdk-1.4.0.jar, FileManager.class
package com.hp.hpl.jena.util
FileManager.addCacheModel ( String uri, Model m ) :  void
FileManager.addLocator ( Locator loc ) :  void
FileManager.addLocatorClassLoader ( ClassLoader cLoad ) :  void
FileManager.addLocatorFile ( ) :  void
FileManager.addLocatorFile ( String dir ) :  void
FileManager.addLocatorURL ( ) :  void
FileManager.addLocatorZip ( String zfn ) :  void
FileManager.FileManager ( )
FileManager.FileManager ( FileManager filemanager )
FileManager.FileManager ( LocationMapper _mapper )
FileManager.get ( ) [static] :  FileManager
FileManager.getCachingModels ( ) :  boolean
FileManager.getFromCache ( String filenameOrURI ) :  Model
FileManager.getLocationMapper ( ) :  LocationMapper
FileManager.hasCachedModel ( String filenameOrURI ) :  boolean
FileManager.loadModel ( String filenameOrURI ) :  Model
FileManager.loadModel ( String filenameOrURI, String baseURI, String rdfSyntax ) :  Model
FileManager.loadModel ( String filenameOrURI, String rdfSyntax ) :  Model
FileManager.locators ( ) :  Iterator
FileManager.makeGlobal ( ) [static] :  FileManager
FileManager.mapURI ( String filenameOrURI ) :  String
FileManager.open ( String filenameOrURI ) :  InputStream
FileManager.openNoMap ( String filenameOrURI ) :  InputStream
FileManager.openNoMapOrNull ( String filenameOrURI ) :  TypedStream
FileManager.readModel ( Model model, String filenameOrURI ) :  Model
FileManager.readModel ( Model model, String filenameOrURI, String baseURI, String syntax ) :  Model
FileManager.readModel ( Model model, String filenameOrURI, String rdfSyntax ) :  Model
FileManager.readWholeFileAsUTF8 ( InputStream in ) :  String
FileManager.readWholeFileAsUTF8 ( String filename ) :  String
FileManager.remap ( String filenameOrURI ) :  String *DEPRECATED*
FileManager.remove ( Locator loc ) :  void
FileManager.removeCacheModel ( String uri ) :  void
FileManager.resetCache ( ) :  void
FileManager.setGlobalFileManager ( FileManager globalFileManager ) [static] :  void
FileManager.setLocationMapper ( LocationMapper _mapper ) :  void
FileManager.setMapper ( LocationMapper _mapper ) :  void *DEPRECATED*
FileManager.setModelCaching ( boolean state ) :  void
FileManager.setStdLocators ( FileManager fMgr ) [static] :  void

cdk-1.4.0.jar, FileManagerAssembler.class
package com.hp.hpl.jena.assembler.assemblers
FileManagerAssembler.FileManagerAssembler ( )
FileManagerAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, FileModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
FileModelAssembler.createFileModel ( File fullName, String lang, boolean create, boolean strict, ReificationStyle style ) :  Model
FileModelAssembler.FileModelAssembler ( )
FileModelAssembler.getFileName ( Resource root ) :  File
FileModelAssembler.getLanguage ( Resource root, File fullName ) :  String
FileModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode mode ) :  Model

cdk-1.4.0.jar, FileUtils.class
package com.hp.hpl.jena.util
FileUtils.asBufferedUTF8 ( InputStream in ) [static] :  BufferedReader
FileUtils.asPrintWriterUTF8 ( OutputStream out ) [static] :  PrintWriter
FileUtils.asUTF8 ( InputStream in ) [static] :  Reader
FileUtils.asUTF8 ( OutputStream out ) [static] :  Writer
FileUtils.decodeFileName ( String s ) [static] :  String
FileUtils.encodeFileName ( String s ) [static] :  String *DEPRECATED*
FileUtils.FileUtils ( )
FileUtils.getBasename ( String filename ) [static] :  String
FileUtils.getDirname ( String filename ) [static] :  String
FileUtils.getFilenameExt ( String filename ) [static] :  String
FileUtils.getScheme ( String uri ) [static] :  String
FileUtils.getScratchDirectory ( String prefix ) [static] :  File
FileUtils.getTempDirectory ( ) [static] :  String
FileUtils.guessLang ( String name, String otherwise ) [static] :  String
FileUtils.guessLang ( String urlStr ) [static] :  String
FileUtils.isFile ( String name ) [static] :  boolean
FileUtils.isURI ( String name ) [static] :  boolean
FileUtils.openResourceFile ( String filename ) [static] :  BufferedReader
FileUtils.openResourceFileAsStream ( String filename ) [static] :  InputStream
FileUtils.readerFromURL ( String urlStr ) [static] :  BufferedReader
FileUtils.readWholeFileAsUTF8 ( InputStream in ) [static] :  String
FileUtils.readWholeFileAsUTF8 ( String filename ) [static] :  String
FileUtils.tempFileName ( String prefix, String suffix ) [static] :  File
FileUtils.toFilename ( String filenameOrURI ) [static] :  String
FileUtils.toURL ( String filename ) [static] :  String

cdk-1.4.0.jar, Filter.class
package com.hp.hpl.jena.util.iterator
Filter.accept ( Object p1 ) [abstract] :  boolean
Filter.and ( Filter other ) :  Filter
Filter.any ( ) [static] :  Filter
Filter.Filter ( )
Filter.filterKeep ( Iterator it ) :  ExtendedIterator
Filter.isAny ( ) :  boolean

cdk-1.4.0.jar, FilterDropIterator.class
package com.hp.hpl.jena.util.iterator
FilterDropIterator.accept ( Object x ) :  boolean
FilterDropIterator.FilterDropIterator ( Filter f, Iterator it )

cdk-1.4.0.jar, FilterIterator.class
package com.hp.hpl.jena.util.iterator
FilterIterator.accept ( Object x ) :  boolean
FilterIterator.FilterIterator ( Filter fl, Iterator e )
FilterIterator.hasNext ( ) :  boolean
FilterIterator.next ( ) :  Object
FilterIterator.remove ( ) :  void

cdk-1.4.0.jar, FilterKeepIterator.class
package com.hp.hpl.jena.util.iterator
FilterKeepIterator.accept ( Object x ) :  boolean
FilterKeepIterator.FilterKeepIterator ( Filter f, Iterator it )

cdk-1.4.0.jar, FinalMappings.class
package org.openscience.cdk.smsd.helper
FinalMappings.add ( Map mapping ) :  void
FinalMappings.clear ( ) :  void
FinalMappings.FinalMappings ( )
FinalMappings.getFinalMapping ( ) :  List
FinalMappings.getInstance ( ) [static] :  FinalMappings
FinalMappings.getIterator ( ) :  Iterator
FinalMappings.getSize ( ) :  int
FinalMappings.set ( List list ) :  void

cdk-1.4.0.jar, Finder.class
package com.hp.hpl.jena.reasoner
Finder.contains ( TriplePattern p1 ) [abstract] :  boolean
Finder.find ( TriplePattern p1 ) [abstract] :  ExtendedIterator
Finder.findWithContinuation ( TriplePattern p1, Finder p2 ) [abstract] :  ExtendedIterator

cdk-1.4.0.jar, FinderUtil.class
package com.hp.hpl.jena.reasoner
FinderUtil.cascade ( Finder first, Finder second ) [static] :  Finder
FinderUtil.cascade ( Finder first, Finder second, Finder third ) [static] :  Finder
FinderUtil.cascade ( Finder first, Finder second, Finder third, Finder fourth ) [static] :  Finder
FinderUtil.FinderUtil ( )

cdk-1.4.0.jar, FindTriples.class
package com.hp.hpl.jena.graph.query
StageElement.FindTriples.run ( Domain current ) :  void
StageElement.FindTriples.StageElement.FindTriples ( Stage stage, Matcher matcher, Applyer finder, StageElement next )

cdk-1.4.0.jar, Finished.class
package com.hp.hpl.jena.graph.query
BufferPipe.Finished.BufferPipe.Finished ( )
BufferPipe.Finished.BufferPipe.Finished ( Exception e )
BufferPipe.Finished.getCause ( ) :  RuntimeException

cdk-1.4.0.jar, FitToScreen.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.FitToScreen.BasicSceneGenerator.FitToScreen ( )
BasicSceneGenerator.FitToScreen.getDefault ( ) :  Boolean
BasicSceneGenerator.FitToScreen.getDefault ( ) :  Object

cdk-1.4.0.jar, Fixed.class
package com.hp.hpl.jena.graph.query
Expression.Fixed.Expression.Fixed ( Object value )
Expression.Fixed.getValue ( ) :  Object
Expression.Fixed.prepare ( VariableIndexes vi ) :  Valuator
Expression.Fixed.toString ( ) :  String
Fixed.asNodeMatch ( Domain d ) :  Node
Fixed.Fixed ( Node x )
Fixed.match ( Domain d, Node x ) :  boolean
Fixed.toString ( ) :  String
QueryNode.Fixed.finder ( Domain d ) :  Node
QueryNode.Fixed.matchOrBind ( Domain d, Node x ) :  boolean
QueryNode.Fixed.QueryNode.Fixed ( Node n )
QueryNode.Fixed.toString ( ) :  String

cdk-1.4.0.jar, FixedValuator.class
package com.hp.hpl.jena.graph.query
FixedValuator.evalBool ( IndexValues iv ) :  boolean
FixedValuator.evalObject ( IndexValues iv ) :  Object
FixedValuator.FixedValuator ( Object value )

cdk-1.4.0.jar, FMFDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
FMFDescriptor.calculate ( IAtomContainer container ) :  DescriptorValue
FMFDescriptor.FMFDescriptor ( )
FMFDescriptor.getDescriptorNames ( ) :  String[ ]
FMFDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
FMFDescriptor.getParameterNames ( ) :  String[ ]
FMFDescriptor.getParameters ( ) :  Object[ ]
FMFDescriptor.getParameterType ( String name ) :  Object
FMFDescriptor.getSpecification ( ) :  DescriptorSpecification
FMFDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.0.jar, FontName.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.FontName.BasicSceneGenerator.FontName ( )
BasicSceneGenerator.FontName.getDefault ( ) :  Object
BasicSceneGenerator.FontName.getDefault ( ) :  String

cdk-1.4.0.jar, FontStyle.class
package org.openscience.cdk.renderer.font
IFontManager.FontStyle.valueOf ( String name ) [static] :  IFontManager.FontStyle
IFontManager.FontStyle.values ( ) [static] :  IFontManager.FontStyle[ ]

cdk-1.4.0.jar, ForegroundColor.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.ForegroundColor.BasicSceneGenerator.ForegroundColor ( )
BasicSceneGenerator.ForegroundColor.getDefault ( ) :  Color
BasicSceneGenerator.ForegroundColor.getDefault ( ) :  Object

cdk-1.4.0.jar, FormatException.class
package com.hp.hpl.jena.shared.uuid
JenaUUID.FormatException.JenaUUID.FormatException ( )
JenaUUID.FormatException.JenaUUID.FormatException ( String msg )

cdk-1.4.0.jar, ForwardRuleInfGraphI.class
package com.hp.hpl.jena.reasoner.rulesys
ForwardRuleInfGraphI.addBRule ( Rule p1 ) [abstract] :  void
ForwardRuleInfGraphI.addDeduction ( Triple p1 ) [abstract] :  void
ForwardRuleInfGraphI.deleteBRule ( Rule p1 ) [abstract] :  void
ForwardRuleInfGraphI.findDataMatches ( Node p1, Node p2, Node p3 ) [abstract] :  ExtendedIterator
ForwardRuleInfGraphI.getCurrentDeductionsGraph ( ) [abstract] :  Graph
ForwardRuleInfGraphI.getDeductionsGraph ( ) [abstract] :  Graph
ForwardRuleInfGraphI.logDerivation ( Triple p1, Derivation p2 ) [abstract] :  void
ForwardRuleInfGraphI.shouldLogDerivations ( ) [abstract] :  boolean
ForwardRuleInfGraphI.shouldTrace ( ) [abstract] :  boolean

cdk-1.4.0.jar, FourierGridBasis.class
package org.openscience.cdk.math.qm
FourierGridBasis.calcI ( int i, int j, int k, int l ) :  double
FourierGridBasis.calcJ ( int i, int j ) :  double
FourierGridBasis.calcS ( int i, int j ) :  double
FourierGridBasis.calcV ( int i, int j ) :  double
FourierGridBasis.FourierGridBasis ( int N, double minx, double maxx, IFunction potential )
FourierGridBasis.getMaxX ( ) :  double
FourierGridBasis.getMaxY ( ) :  double
FourierGridBasis.getMaxZ ( ) :  double
FourierGridBasis.getMinX ( ) :  double
FourierGridBasis.getMinY ( ) :  double
FourierGridBasis.getMinZ ( ) :  double
FourierGridBasis.getSize ( ) :  int
FourierGridBasis.getValue ( int index, double x, double y, double z ) :  double
FourierGridBasis.getValues ( int index, Matrix m ) :  Vector

cdk-1.4.0.jar, FragmentUtils.class
package org.openscience.cdk.fragment
FragmentUtils.FragmentUtils ( )
FragmentUtils.makeAtomContainer ( IAtom atom, List parts, IAtom excludedAtom ) [static] :  IAtomContainer
FragmentUtils.splitMolecule ( IAtomContainer atomContainer, IBond bond ) [static] :  List
FragmentUtils.traverse ( IAtomContainer atomContainer, IAtom atom, List bondList ) [static] :  List

cdk-1.4.0.jar, Frame.class
package com.hp.hpl.jena.assembler.assemblers
AssemblerGroup.Frame.AssemblerGroup.Frame ( Resource root, Resource type, Class assembler )
AssemblerGroup.Frame.equals ( Object other ) :  boolean
AssemblerGroup.Frame.same ( AssemblerGroup.Frame other ) :  boolean
AssemblerGroup.Frame.toString ( ) :  String
package com.hp.hpl.jena.rdf.arp.states
Frame.abort ( ) :  void
Frame.afterChild ( ) :  void
Frame.characters ( char[ ] ch, int start, int length ) :  void
Frame.comment ( char[ ] ch, int start, int length ) :  void
Frame.endElement ( ) :  void
Frame.Frame ( FrameI p, AbsXMLContext x )
Frame.Frame ( FrameI p, AttributeLexer ap )
Frame.Frame ( XMLHandler a, AbsXMLContext x )
Frame.getParent ( ) :  FrameI
Frame.processingInstruction ( String target, String data ) :  void
Frame.rdfStartElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
Frame.warning ( int i, String msg ) :  void

cdk-1.4.0.jar, FrameI.class
package com.hp.hpl.jena.rdf.arp.states
FrameI.abort ( ) [abstract] :  void
FrameI.afterChild ( ) [abstract] :  void
FrameI.characters ( char[ ] p1, int p2, int p3 ) [abstract] :  void
FrameI.comment ( char[ ] p1, int p2, int p3 ) [abstract] :  void
FrameI.endElement ( ) [abstract] :  void
FrameI.getParent ( ) [abstract] :  FrameI
FrameI.getXMLContext ( ) [abstract] :  AbsXMLContext
FrameI.getXMLHandler ( ) [abstract] :  XMLHandler
FrameI.processingInstruction ( String p1, String p2 ) [abstract] :  void
FrameI.startElement ( String p1, String p2, String p3, Attributes p4 ) [abstract] :  FrameI

cdk-1.4.0.jar, FrontsNode.class
package com.hp.hpl.jena.graph
FrontsNode.asNode ( ) [abstract] :  Node

cdk-1.4.0.jar, FrontsTriple.class
package com.hp.hpl.jena.graph
FrontsTriple.asTriple ( ) [abstract] :  Triple

cdk-1.4.0.jar, Functor.class
package com.hp.hpl.jena.reasoner.rulesys
Functor.equals ( Object obj ) :  boolean
Functor.evalAsBodyClause ( RuleContext context ) :  boolean
Functor.Functor ( String name, List args )
Functor.Functor ( String name, List args, BuiltinRegistry registry )
Functor.Functor ( String name, Node[ ] args )
Functor.getArgLength ( ) :  int
Functor.getArgs ( ) :  Node[ ]
Functor.getBoundArgs ( BindingEnvironment env ) :  Node[ ]
Functor.getImplementor ( ) :  Builtin
Functor.getName ( ) :  String
Functor.hashCode ( ) :  int
Functor.isFunctor ( Node n ) [static] :  boolean
Functor.isGround ( ) :  boolean
Functor.isGround ( BindingEnvironment env ) :  boolean
Functor.makeFunctorNode ( Functor f ) [static] :  Node
Functor.makeFunctorNode ( String name, Node[ ] args ) [static] :  Node
Functor.safeEvalAsBodyClause ( RuleContext context ) :  boolean
Functor.sameAs ( Object o ) :  boolean
Functor.setImplementor ( Builtin implementor ) :  void
Functor.toString ( ) :  String

cdk-1.4.0.jar, FunctorDatatype.class
package com.hp.hpl.jena.reasoner.rulesys
Functor.FunctorDatatype.Functor.FunctorDatatype ( )

cdk-1.4.0.jar, GaussiansBasis.class
package org.openscience.cdk.math.qm
GaussiansBasis.calcD ( double normi, double normj, double alphai, double alphaj, Vector ri, Vector rj ) :  double
GaussiansBasis.calcG ( int n, double t, double alphai, double alphaj, double xi, double xj, double xN ) :  double
GaussiansBasis.calcG ( int n, int m, double u, double alphai, double alphaj, double alphak, double alphal, double xi, double xj, double xk, double xl ) :  double
GaussiansBasis.calcI ( int i, int j, int k, int l ) :  double
GaussiansBasis.calcI ( int ni, int nj, int nk, int nl, double u, double alphai, double alphaj, double alphak, double alphal, double xi, double xj, double xk, double xl ) :  double
GaussiansBasis.calcJ ( int i, int j ) :  double
GaussiansBasis.calcJ ( int ni, int nj, double alphai, double alphaj, double xi, double xj ) :  double
GaussiansBasis.calcS ( int i, int j ) :  double
GaussiansBasis.calcV ( int i, int j ) :  double
GaussiansBasis.calcV ( int i, int j, Vector rN, double Z ) :  double
GaussiansBasis.GaussiansBasis ( )
GaussiansBasis.GaussiansBasis ( int[ ] nx, int[ ] ny, int[ ] nz, double[ ] alpha, Vector[ ] r, IAtom[ ] atoms )
GaussiansBasis.getMaxX ( ) :  double
GaussiansBasis.getMaxY ( ) :  double
GaussiansBasis.getMaxZ ( ) :  double
GaussiansBasis.getMinX ( ) :  double
GaussiansBasis.getMinY ( ) :  double
GaussiansBasis.getMinZ ( ) :  double
GaussiansBasis.getPosition ( int index ) :  Vector
GaussiansBasis.getSize ( ) :  int
GaussiansBasis.getValue ( int index, double x, double y, double z ) :  double
GaussiansBasis.getValues ( int index, Matrix m ) :  Vector
GaussiansBasis.setBasis ( int[ ] nx, int[ ] ny, int[ ] nz, double[ ] alpha, Vector[ ] r, IAtom[ ] atoms ) :  void

cdk-1.4.0.jar, GE.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
GE.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
GE.GE ( )
GE.getArgLength ( ) :  int
GE.getName ( ) :  String

cdk-1.4.0.jar, GeneralPath.class
package org.openscience.cdk.renderer.elements
GeneralPath.accept ( IRenderingVisitor v ) :  void
GeneralPath.GeneralPath ( List elements, Color color )

cdk-1.4.0.jar, GenerateCompatibilityGraph.class
package org.openscience.cdk.smsd.algorithm.mcsplus
GenerateCompatibilityGraph.clear ( ) :  void
GenerateCompatibilityGraph.clearCEgdes ( ) :  void
GenerateCompatibilityGraph.clearCompGraphNodes ( ) :  void
GenerateCompatibilityGraph.clearCompGraphNodesCZero ( ) :  void
GenerateCompatibilityGraph.clearDEgdes ( ) :  void
GenerateCompatibilityGraph.compatibilityGraph ( ) :  int
GenerateCompatibilityGraph.compatibilityGraphCEdgeZero ( ) :  int
GenerateCompatibilityGraph.compatibilityGraphNodes ( ) :  int
GenerateCompatibilityGraph.compatibilityGraphNodesIfCEdgeIsZero ( ) :  Integer
GenerateCompatibilityGraph.GenerateCompatibilityGraph ( )
GenerateCompatibilityGraph.GenerateCompatibilityGraph ( IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds )
GenerateCompatibilityGraph.getCEdgesSize ( ) :  int
GenerateCompatibilityGraph.getCEgdes ( ) :  List
GenerateCompatibilityGraph.getCompGraphNodes ( ) :  List
GenerateCompatibilityGraph.getCompGraphNodesCZero ( ) :  List
GenerateCompatibilityGraph.getDEdgesSize ( ) :  int
GenerateCompatibilityGraph.getDEgdes ( ) :  List
GenerateCompatibilityGraph.isMatchBond ( ) :  boolean
GenerateCompatibilityGraph.resetCEdgesSize ( ) :  void
GenerateCompatibilityGraph.resetDEdgesSize ( ) :  void
GenerateCompatibilityGraph.setMatchBond ( boolean shouldMatchBonds ) :  void

cdk-1.4.0.jar, GenericRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
GenericRuleReasoner.addPreprocessingHook ( RulePreprocessHook hook ) :  void
GenericRuleReasoner.bind ( Graph data ) :  InfGraph
GenericRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
GenericRuleReasoner.doSetParameter ( Property parameter, Object value ) :  boolean
GenericRuleReasoner.doSetResourceParameter ( Property parameter, Resource value ) :  boolean
GenericRuleReasoner.GenericRuleReasoner ( List rules )
GenericRuleReasoner.GenericRuleReasoner ( List rules, Graph schemaGraph, ReasonerFactory factory, GenericRuleReasoner.RuleMode mode )
GenericRuleReasoner.GenericRuleReasoner ( List rules, ReasonerFactory factory )
GenericRuleReasoner.GenericRuleReasoner ( ReasonerFactory factory, Resource configuration )
GenericRuleReasoner.getBruleStore ( ) :  LPRuleStore
GenericRuleReasoner.getPreload ( ) :  InfGraph
GenericRuleReasoner.removePreprocessingHook ( RulePreprocessHook hook ) :  void
GenericRuleReasoner.setFunctorFiltering ( boolean param ) :  void
GenericRuleReasoner.setMode ( GenericRuleReasoner.RuleMode mode ) :  void
GenericRuleReasoner.setOWLTranslation ( boolean enableOWLTranslation ) :  void
GenericRuleReasoner.setRules ( List rules ) :  void
GenericRuleReasoner.setTransitiveClosureCaching ( boolean enableTGCCaching ) :  void

cdk-1.4.0.jar, GenericRuleReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
GenericRuleReasonerFactory.create ( Resource configuration ) :  Reasoner
GenericRuleReasonerFactory.GenericRuleReasonerFactory ( )
GenericRuleReasonerFactory.getCapabilities ( ) :  Model
GenericRuleReasonerFactory.getURI ( ) :  String
GenericRuleReasonerFactory.theInstance ( ) [static] :  GenericRuleReasonerFactory

cdk-1.4.0.jar, GeometryTools.class
package org.openscience.cdk.geometry
GeometryTools.getBondLengthAverage ( IReaction reaction ) [static] :  double
GeometryTools.getClosestAtom ( double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore ) [static] :  IAtom
GeometryTools.getClosestAtom ( IAtomContainer atomCon, IAtom atom ) [static] :  IAtom
GeometryTools.getRectangle2D ( IAtomContainer container ) [static] :  Rectangle2D
GeometryTools.has3DCoordinates ( IChemModel chemModel ) [static] :  boolean
GeometryTools.shiftContainer ( IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap ) [static] :  Rectangle2D
GeometryTools.shiftReactionVertical ( IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap ) [static] :  Rectangle2D

cdk-1.4.0.jar, GetTriple.class
package com.hp.hpl.jena.graph
GetTriple.getTriple ( Node p1 ) [abstract] :  Triple

cdk-1.4.0.jar, GnuParser.class
package org.apache.commons.cli
GnuParser.flatten ( Options options, String[ ] arguments, boolean stopAtNonOption ) :  String[ ]
GnuParser.GnuParser ( )

cdk-1.4.0.jar, Graph.class
package com.hp.hpl.jena.graph
Graph.close ( ) [abstract] :  void
Graph.contains ( Node p1, Node p2, Node p3 ) [abstract] :  boolean
Graph.contains ( Triple p1 ) [abstract] :  boolean
Graph.delete ( Triple p1 ) [abstract] :  void
Graph.dependsOn ( Graph p1 ) [abstract] :  boolean
Graph.find ( Node p1, Node p2, Node p3 ) [abstract] :  ExtendedIterator
Graph.find ( TripleMatch p1 ) [abstract] :  ExtendedIterator
Graph.getBulkUpdateHandler ( ) [abstract] :  BulkUpdateHandler
Graph.getCapabilities ( ) [abstract] :  Capabilities
Graph.getEventManager ( ) [abstract] :  GraphEventManager
Graph.getPrefixMapping ( ) [abstract] :  PrefixMapping
Graph.getReifier ( ) [abstract] :  Reifier
Graph.getStatisticsHandler ( ) [abstract] :  GraphStatisticsHandler
Graph.getTransactionHandler ( ) [abstract] :  TransactionHandler
Graph.isClosed ( ) [abstract] :  boolean
Graph.isEmpty ( ) [abstract] :  boolean
Graph.isIsomorphicWith ( Graph p1 ) [abstract] :  boolean
Graph.queryHandler ( ) [abstract] :  QueryHandler
Graph.size ( ) [abstract] :  int

cdk-1.4.0.jar, GraphAdd.class
package com.hp.hpl.jena.graph
GraphAdd.add ( Triple p1 ) [abstract] :  void

cdk-1.4.0.jar, GraphEventManager.class
package com.hp.hpl.jena.graph
GraphEventManager.listening ( ) [abstract] :  boolean
GraphEventManager.notifyAddIterator ( Graph p1, List p2 ) [abstract] :  void
GraphEventManager.notifyDeleteIterator ( Graph p1, List p2 ) [abstract] :  void
GraphEventManager.register ( GraphListener p1 ) [abstract] :  GraphEventManager
GraphEventManager.unregister ( GraphListener p1 ) [abstract] :  GraphEventManager

cdk-1.4.0.jar, GraphEvents.class
package com.hp.hpl.jena.graph
GraphEvents.equals ( Object o ) :  boolean
GraphEvents.getContent ( ) :  Object
GraphEvents.getTitle ( ) :  Object
GraphEvents.GraphEvents ( String title, Object content )
GraphEvents.remove ( Node s, Node p, Node o ) [static] :  GraphEvents
GraphEvents.same ( GraphEvents o ) :  boolean
GraphEvents.toString ( ) :  String

cdk-1.4.0.jar, GraphExtract.class
package com.hp.hpl.jena.graph
GraphExtract.extract ( Node node, Graph graph ) :  Graph
GraphExtract.extractInto ( Graph toUpdate, Node root, Graph extractFrom ) :  Graph
GraphExtract.GraphExtract ( TripleBoundary b )

cdk-1.4.0.jar, GraphListener.class
package com.hp.hpl.jena.graph
GraphListener.notifyAddArray ( Graph p1, Triple[ ] p2 ) [abstract] :  void
GraphListener.notifyAddGraph ( Graph p1, Graph p2 ) [abstract] :  void
GraphListener.notifyAddIterator ( Graph p1, Iterator p2 ) [abstract] :  void
GraphListener.notifyAddList ( Graph p1, List p2 ) [abstract] :  void
GraphListener.notifyAddTriple ( Graph p1, Triple p2 ) [abstract] :  void
GraphListener.notifyDeleteArray ( Graph p1, Triple[ ] p2 ) [abstract] :  void
GraphListener.notifyDeleteGraph ( Graph p1, Graph p2 ) [abstract] :  void
GraphListener.notifyDeleteIterator ( Graph p1, Iterator p2 ) [abstract] :  void
GraphListener.notifyDeleteList ( Graph p1, List p2 ) [abstract] :  void
GraphListener.notifyDeleteTriple ( Graph p1, Triple p2 ) [abstract] :  void
GraphListener.notifyEvent ( Graph p1, Object p2 ) [abstract] :  void

cdk-1.4.0.jar, GraphMaker.class
package com.hp.hpl.jena.graph
GraphMaker.close ( ) [abstract] :  void
GraphMaker.createGraph ( ) [abstract] :  Graph
GraphMaker.createGraph ( String p1 ) [abstract] :  Graph
GraphMaker.createGraph ( String p1, boolean p2 ) [abstract] :  Graph
GraphMaker.getGraph ( ) [abstract] :  Graph
GraphMaker.getReificationStyle ( ) [abstract] :  ReificationStyle
GraphMaker.hasGraph ( String p1 ) [abstract] :  boolean
GraphMaker.listGraphs ( ) [abstract] :  ExtendedIterator
GraphMaker.openGraph ( ) [abstract] :  Graph
GraphMaker.openGraph ( String p1 ) [abstract] :  Graph
GraphMaker.openGraph ( String p1, boolean p2 ) [abstract] :  Graph
GraphMaker.removeGraph ( String p1 ) [abstract] :  void

cdk-1.4.0.jar, GraphMem.class
package com.hp.hpl.jena.mem
GraphMem.clear ( ) :  void
GraphMem.createTripleStore ( ) :  TripleStore
GraphMem.destroy ( ) :  void
GraphMem.forTestingOnly_getStore ( ) :  GraphTripleStore
GraphMem.graphBaseContains ( Triple t ) :  boolean
GraphMem.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
GraphMem.graphBaseSize ( ) :  int
GraphMem.GraphMem ( )
GraphMem.GraphMem ( ReificationStyle style )
GraphMem.performAdd ( Triple t ) :  void
GraphMem.performDelete ( Triple t ) :  void
GraphMem.queryHandler ( ) :  QueryHandler

cdk-1.4.0.jar, GraphMemBase.class
package com.hp.hpl.jena.mem
GraphMemBase.clear ( ) [abstract] :  void
GraphMemBase.close ( ) :  void
GraphMemBase.createTripleStore ( ) [abstract] :  TripleStore
GraphMemBase.destroy ( ) [abstract] :  void
GraphMemBase.getBulkUpdateHandler ( ) :  BulkUpdateHandler
GraphMemBase.GraphMemBase ( ReificationStyle style )
GraphMemBase.isSafeForEquality ( Triple t ) :  boolean
GraphMemBase.openAgain ( ) :  GraphMemBase

cdk-1.4.0.jar, GraphMemBaseQueryHandler.class
package com.hp.hpl.jena.mem
GraphMemBaseQueryHandler.findObjects ( ) :  ExtendedIterator
GraphMemBaseQueryHandler.findPredicates ( ) :  ExtendedIterator
GraphMemBaseQueryHandler.findSubjects ( ) :  ExtendedIterator
GraphMemBaseQueryHandler.GraphMemBaseQueryHandler ( GraphMemBase graph )
GraphMemBaseQueryHandler.objectsFor ( Node s, Node p ) :  ExtendedIterator
GraphMemBaseQueryHandler.predicatesFor ( Node s, Node o ) :  ExtendedIterator
GraphMemBaseQueryHandler.subjectsFor ( Node p, Node o ) :  ExtendedIterator

cdk-1.4.0.jar, GraphMemBulkUpdateHandler.class
package com.hp.hpl.jena.mem
GraphMemBulkUpdateHandler.clearComponents ( ) :  void
GraphMemBulkUpdateHandler.GraphMemBulkUpdateHandler ( GraphWithPerform graph )
GraphMemBulkUpdateHandler.removeAll ( ) :  void

cdk-1.4.0.jar, GraphMemFaster.class
package com.hp.hpl.jena.mem.faster
GraphMemFaster.clear ( ) :  void
GraphMemFaster.createApplyer ( ProcessedTriple pt ) :  Applyer
GraphMemFaster.createStatisticsHandler ( ) :  GraphStatisticsHandler
GraphMemFaster.createTripleStore ( ) :  TripleStore
GraphMemFaster.destroy ( ) :  void
GraphMemFaster.graphBaseContains ( Triple t ) :  boolean
GraphMemFaster.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
GraphMemFaster.graphBaseSize ( ) :  int
GraphMemFaster.GraphMemFaster ( )
GraphMemFaster.GraphMemFaster ( ReificationStyle style )
GraphMemFaster.hasReifications ( ) :  boolean
GraphMemFaster.matchesReification ( QueryTriple pt ) [static] :  boolean
GraphMemFaster.performAdd ( Triple t ) :  void
GraphMemFaster.performDelete ( Triple t ) :  void
GraphMemFaster.queryHandler ( ) :  QueryHandler
GraphMemFaster.withReification ( Applyer plain, QueryTriple pt ) :  Applyer

cdk-1.4.0.jar, GraphMemFasterQueryHandler.class
package com.hp.hpl.jena.mem.faster
GraphMemFasterQueryHandler.patternStage ( Mapping map, ExpressionSet constraints, Triple[ ] t ) :  Stage

cdk-1.4.0.jar, GraphMemFasterStatisticsHandler.class
package com.hp.hpl.jena.mem.faster
GraphMemFaster.GraphMemFasterStatisticsHandler.countInMap ( Node n, NodeToTriplesMapFaster map ) :  long
GraphMemFaster.GraphMemFasterStatisticsHandler.countsInMap ( Node a, NodeToTriplesMapFaster mapA, Node b, NodeToTriplesMapFaster mapB ) :  long
GraphMemFaster.GraphMemFasterStatisticsHandler.getStatistic ( Node S, Node P, Node O ) :  long
GraphMemFaster.GraphMemFasterStatisticsHandler.GraphMemFaster.GraphMemFasterStatisticsHandler ( FasterTripleStore store, Reifier reifier )

cdk-1.4.0.jar, GraphPersonality.class
package com.hp.hpl.jena.enhanced
GraphPersonality.GraphPersonality ( )

cdk-1.4.0.jar, GraphRDB.class
package com.hp.hpl.jena.db
GraphRDB.add ( List triples ) :  void
GraphRDB.checkOpen ( ) :  void
GraphRDB.clear ( ) :  void
GraphRDB.close ( ) :  void
GraphRDB.DBqueryHandler ( ) :  DBQueryHandler
GraphRDB.delete ( List triples ) :  void
GraphRDB.getBulkUpdateHandler ( ) :  BulkUpdateHandler
GraphRDB.getCapabilities ( ) :  Capabilities
GraphRDB.getConnection ( ) :  IDBConnection
GraphRDB.getDoDuplicateCheck ( ) :  boolean
GraphRDB.getDoFastpath ( ) :  boolean
GraphRDB.getNode ( ) :  Node
GraphRDB.getPrefixMapping ( ) :  PrefixMapping
GraphRDB.getPropertyTriples ( ) :  ExtendedIterator
GraphRDB.getQueryFullReified ( ) :  boolean
GraphRDB.getQueryOnlyAsserted ( ) :  boolean
GraphRDB.getQueryOnlyReified ( ) :  boolean
GraphRDB.getReifier ( ) :  Reifier
GraphRDB.getSpecializedGraphs ( ) :  Iterator
GraphRDB.getTransactionHandler ( ) :  TransactionHandler
GraphRDB.graphBaseContains ( Triple t ) :  boolean
GraphRDB.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
GraphRDB.graphBaseSize ( ) :  int
GraphRDB.GraphRDB ( IDBConnection con, String graphID, Graph requestedProperties, int reificationBehaviour, boolean isNew )
GraphRDB.isClosed ( ) :  boolean
GraphRDB.isOpen ( ) :  boolean
GraphRDB.performAdd ( Triple t ) :  void
GraphRDB.performDelete ( Triple t ) :  void
GraphRDB.queryHandler ( ) :  QueryHandler
GraphRDB.reificationBehavior ( ) :  int
GraphRDB.reifierSize ( ) :  int
GraphRDB.reifierTriples ( TripleMatch m ) :  ExtendedIterator
GraphRDB.remove ( ) :  void
GraphRDB.setDoDuplicateCheck ( boolean bool ) :  void
GraphRDB.setDoFastpath ( boolean val ) :  void
GraphRDB.setDoImplicitJoin ( boolean val ) :  void
GraphRDB.setQueryFullReified ( boolean opt ) :  void
GraphRDB.setQueryOnlyAsserted ( boolean opt ) :  void
GraphRDB.setQueryOnlyReified ( boolean opt ) :  void
GraphRDB.styleRDB ( int behaviour ) [static] :  ReificationStyle
GraphRDB.styleRDB ( ReificationStyle style ) [static] :  int

cdk-1.4.0.jar, GraphRendererModel.class
package org.openscience.cdk.renderer
GraphRendererModel.addFunction ( IFunction function ) :  void
GraphRendererModel.addFunction ( IFunction function, Color color ) :  void
GraphRendererModel.getDisplayMode ( ) :  int
GraphRendererModel.getFunction ( int index ) :  IFunction
GraphRendererModel.getFunctionColor ( int index ) :  Color
GraphRendererModel.getFunctionsSize ( ) :  int
GraphRendererModel.getTitle ( ) :  String
GraphRendererModel.getXMax ( ) :  double
GraphRendererModel.getXMin ( ) :  double
GraphRendererModel.getXTitle ( ) :  String
GraphRendererModel.getYMax ( ) :  double
GraphRendererModel.getYMin ( ) :  double
GraphRendererModel.getYTitle ( ) :  String
GraphRendererModel.GraphRendererModel ( )
GraphRendererModel.setDisplayMode ( int mode ) :  void
GraphRendererModel.setTitle ( String string ) :  void
GraphRendererModel.setX ( double xmin, double xmax ) :  void
GraphRendererModel.setXTitle ( String string ) :  void
GraphRendererModel.setY ( double ymin, double ymax ) :  void
GraphRendererModel.setYTitle ( String string ) :  void

cdk-1.4.0.jar, GraphStatisticsHandler.class
package com.hp.hpl.jena.graph
GraphStatisticsHandler.getStatistic ( Node p1, Node p2, Node p3 ) [abstract] :  long

cdk-1.4.0.jar, GraphTripleStore.class
package com.hp.hpl.jena.mem
GraphTripleStore.GraphTripleStore ( Graph parent )

cdk-1.4.0.jar, GraphTripleStoreBase.class
package com.hp.hpl.jena.mem
GraphTripleStoreBase.add ( Triple t ) :  void
GraphTripleStoreBase.clear ( ) :  void
GraphTripleStoreBase.close ( ) :  void
GraphTripleStoreBase.contains ( Triple t ) :  boolean
GraphTripleStoreBase.containsByEquality ( Triple t ) :  boolean
GraphTripleStoreBase.delete ( Triple t ) :  void
GraphTripleStoreBase.find ( TripleMatch tm ) :  ExtendedIterator
GraphTripleStoreBase.GraphTripleStoreBase ( Graph parent, NodeToTriplesMapBase subjects, NodeToTriplesMapBase predicates, NodeToTriplesMapBase objects )
GraphTripleStoreBase.isEmpty ( ) :  boolean
GraphTripleStoreBase.listObjects ( ) :  ExtendedIterator
GraphTripleStoreBase.listPredicates ( ) :  ExtendedIterator
GraphTripleStoreBase.listSubjects ( ) :  ExtendedIterator
GraphTripleStoreBase.size ( ) :  int

cdk-1.4.0.jar, GraphUtil.class
package com.hp.hpl.jena.graph
GraphUtil.findAll ( Graph g ) [static] :  ExtendedIterator

cdk-1.4.0.jar, GreaterThan.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
GreaterThan.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
GreaterThan.getArgLength ( ) :  int
GreaterThan.getName ( ) :  String
GreaterThan.GreaterThan ( )

cdk-1.4.0.jar, GregorianCalendar.class
package com.ibm.icu.util
GregorianCalendar.getActualMaximum ( int field ) :  int
GregorianCalendar.getActualMinimum ( int field ) :  int
GregorianCalendar.getGregorianChange ( ) :  Date
GregorianCalendar.getType ( ) :  String
GregorianCalendar.GregorianCalendar ( )
GregorianCalendar.GregorianCalendar ( int year, int month, int date )
GregorianCalendar.GregorianCalendar ( int year, int month, int date, int hour, int minute )
GregorianCalendar.GregorianCalendar ( int year, int month, int date, int hour, int minute, int second )
GregorianCalendar.GregorianCalendar ( Locale aLocale )
GregorianCalendar.GregorianCalendar ( TimeZone zone )
GregorianCalendar.GregorianCalendar ( TimeZone zone, Locale aLocale )
GregorianCalendar.GregorianCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
GregorianCalendar.GregorianCalendar ( ULocale locale ) *DEPRECATED*
GregorianCalendar.handleComputeFields ( int julianDay ) :  void
GregorianCalendar.handleComputeJulianDay ( int bestField ) :  int
GregorianCalendar.handleComputeMonthStart ( int eyear, int month, boolean useMonth ) :  int
GregorianCalendar.handleGetExtendedYear ( ) :  int
GregorianCalendar.handleGetLimit ( int field, int limitType ) :  int
GregorianCalendar.handleGetMonthLength ( int extendedYear, int month ) :  int
GregorianCalendar.handleGetYearLength ( int eyear ) :  int
GregorianCalendar.hashCode ( ) :  int
GregorianCalendar.isEquivalentTo ( Calendar other ) :  boolean
GregorianCalendar.isLeapYear ( int year ) :  boolean
GregorianCalendar.roll ( int field, int amount ) :  void
GregorianCalendar.setGregorianChange ( Date date ) :  void

cdk-1.4.0.jar, GuardArranger.class
package com.hp.hpl.jena.graph.query
GuardArranger.canEval ( Expression e, int index ) :  boolean
GuardArranger.GuardArranger ( Triple[ ] triples )
GuardArranger.makeBoundVariables ( Triple[ ] triples ) :  Set[ ]
GuardArranger.makeGuards ( Mapping map, ExpressionSet constraints ) :  ValuatorSet[ ]
GuardArranger.makeGuards ( Mapping map, ExpressionSet constraints, int length ) :  ValuatorSet[ ]
GuardArranger.plantWhereFullyBound ( Expression e, Iterator it, Mapping map, ValuatorSet[ ] es ) :  void

cdk-1.4.0.jar, HanserRingFinder.class
package org.openscience.cdk.smsd.ring
HanserRingFinder.findRings ( IAtomContainer molecule ) :  Collection
HanserRingFinder.getRingSet ( IAtomContainer molecule ) :  IRingSet
HanserRingFinder.HanserRingFinder ( )

cdk-1.4.0.jar, HashCommon.class
package com.hp.hpl.jena.mem
HashCommon.findSlot ( Object key ) :  int
HashCommon.getItemForTestingAt ( int i ) :  Object
HashCommon.growCapacityAndThreshold ( ) :  void
HashCommon.HashCommon ( int initialCapacity )
HashCommon.improveHashCode ( int hashCode ) :  int
HashCommon.initialIndexFor ( Object key ) :  int
HashCommon.keyIterator ( ) :  ExtendedIterator
HashCommon.keyIterator ( HashCommon.NotifyEmpty container ) :  ExtendedIterator
HashCommon.moveAssociatedValues ( int here, int scan ) :  void
HashCommon.newKeyArray ( int p1 ) [abstract] :  Object[ ]
HashCommon.nextSize ( int atLeast ) [static] :  int
HashCommon.remove ( Object key ) :  void
HashCommon.removeAssociatedValues ( int here ) :  void
HashCommon.removeFrom ( int here ) :  Object

cdk-1.4.0.jar, HashedBunchMap.class
package com.hp.hpl.jena.mem
HashedBunchMap.clear ( ) :  void
HashedBunchMap.get ( Object key ) :  TripleBunch
HashedBunchMap.grow ( ) :  void
HashedBunchMap.HashedBunchMap ( )
HashedBunchMap.moveAssociatedValues ( int here, int scan ) :  void
HashedBunchMap.newKeyArray ( int size ) :  Object[ ]
HashedBunchMap.put ( Object key, TripleBunch value ) :  void
HashedBunchMap.removeAssociatedValues ( int here ) :  void
HashedBunchMap.size ( ) :  long

cdk-1.4.0.jar, HashedTripleBunch.class
package com.hp.hpl.jena.mem
HashedTripleBunch.add ( Triple t ) :  void
HashedTripleBunch.app ( Domain d, StageElement next, MatchOrBind s ) :  void
HashedTripleBunch.contains ( Triple t ) :  boolean
HashedTripleBunch.containsBySameValueAs ( Triple t ) :  boolean
HashedTripleBunch.currentCapacity ( ) :  int
HashedTripleBunch.findSlotBySameValueAs ( Triple key ) :  int
HashedTripleBunch.grow ( ) :  void
HashedTripleBunch.HashedTripleBunch ( TripleBunch b )
HashedTripleBunch.iterator ( ) :  ExtendedIterator
HashedTripleBunch.iterator ( HashCommon.NotifyEmpty container ) :  ExtendedIterator
HashedTripleBunch.newKeyArray ( int size ) :  Triple[ ]
HashedTripleBunch.newKeyArray ( int x0 ) :  Object[ ]
HashedTripleBunch.remove ( Object x0 ) :  void
HashedTripleBunch.remove ( Triple t ) :  void
HashedTripleBunch.size ( ) :  int

cdk-1.4.0.jar, HasNoModelException.class
package com.hp.hpl.jena.rdf.model
HasNoModelException.HasNoModelException ( Object x )

cdk-1.4.0.jar, HasSubjectFrameI.class
package com.hp.hpl.jena.rdf.arp.states
HasSubjectFrameI.aPredAndObj ( ANode p1, ANode p2 ) [abstract] :  void
HasSubjectFrameI.makeSubjectReificationWith ( ANode p1 ) [abstract] :  void

cdk-1.4.0.jar, HasValueRestriction.class
package com.hp.hpl.jena.ontology
HasValueRestriction.getHasValue ( ) [abstract] :  RDFNode
HasValueRestriction.hasValue ( RDFNode p1 ) [abstract] :  boolean
HasValueRestriction.removeHasValue ( RDFNode p1 ) [abstract] :  void
HasValueRestriction.setHasValue ( RDFNode p1 ) [abstract] :  void

cdk-1.4.0.jar, HebrewCalendar.class
package com.ibm.icu.util
HebrewCalendar.add ( int field, int amount ) :  void
HebrewCalendar.getType ( ) :  String
HebrewCalendar.handleComputeFields ( int julianDay ) :  void
HebrewCalendar.handleComputeMonthStart ( int eyear, int month, boolean useMonth ) :  int
HebrewCalendar.handleGetExtendedYear ( ) :  int
HebrewCalendar.handleGetLimit ( int field, int limitType ) :  int
HebrewCalendar.handleGetMonthLength ( int extendedYear, int month ) :  int
HebrewCalendar.handleGetYearLength ( int eyear ) :  int
HebrewCalendar.HebrewCalendar ( )
HebrewCalendar.HebrewCalendar ( Date date )
HebrewCalendar.HebrewCalendar ( int year, int month, int date )
HebrewCalendar.HebrewCalendar ( int year, int month, int date, int hour, int minute, int second )
HebrewCalendar.HebrewCalendar ( Locale aLocale )
HebrewCalendar.HebrewCalendar ( TimeZone zone )
HebrewCalendar.HebrewCalendar ( TimeZone zone, Locale aLocale )
HebrewCalendar.HebrewCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
HebrewCalendar.HebrewCalendar ( ULocale locale ) *DEPRECATED*
HebrewCalendar.roll ( int field, int amount ) :  void

cdk-1.4.0.jar, HebrewHoliday.class
package com.ibm.icu.util
HebrewHoliday.HebrewHoliday ( int month, int date, int length, String name ) *DEPRECATED*
HebrewHoliday.HebrewHoliday ( int month, int date, String name ) *DEPRECATED*

cdk-1.4.0.jar, HeightTest.class
package signature
HeightTest.completeGraphTest ( ) :  void
HeightTest.HeightTest ( )
HeightTest.main ( String[ ] args ) [static] :  void
HeightTest.makeCompleteGraph ( int n ) :  SimpleGraph
HeightTest.makeTorus ( int width, int height ) :  SimpleGraph
HeightTest.regularGraphTest ( SimpleGraph graph, int diameter ) :  void
HeightTest.torusTest ( ) :  void

cdk-1.4.0.jar, HelpFormatter.class
package org.apache.commons.cli
HelpFormatter.createPadding ( int len ) :  String
HelpFormatter.findWrapPos ( String text, int width, int startPos ) :  int
HelpFormatter.HelpFormatter ( )
HelpFormatter.printHelp ( int width, String cmdLineSyntax, String header, Options options, String footer ) :  void
HelpFormatter.printHelp ( int width, String cmdLineSyntax, String header, Options options, String footer, boolean autoUsage ) :  void
HelpFormatter.printHelp ( PrintWriter pw, int width, String cmdLineSyntax, String header, Options options, int leftPad, int descPad, String footer ) :  void
HelpFormatter.printHelp ( PrintWriter pw, int width, String cmdLineSyntax, String header, Options options, int leftPad, int descPad, String footer, boolean autoUsage ) :  void
HelpFormatter.printHelp ( String cmdLineSyntax, Options options ) :  void
HelpFormatter.printHelp ( String cmdLineSyntax, Options options, boolean autoUsage ) :  void
HelpFormatter.printHelp ( String cmdLineSyntax, String header, Options options, String footer ) :  void
HelpFormatter.printHelp ( String cmdLineSyntax, String header, Options options, String footer, boolean autoUsage ) :  void
HelpFormatter.printOptions ( PrintWriter pw, int width, Options options, int leftPad, int descPad ) :  void
HelpFormatter.printUsage ( PrintWriter pw, int width, String app, Options options ) :  void
HelpFormatter.printUsage ( PrintWriter pw, int width, String cmdLineSyntax ) :  void
HelpFormatter.printWrapped ( PrintWriter pw, int width, int nextLineTabStop, String text ) :  void
HelpFormatter.printWrapped ( PrintWriter pw, int width, String text ) :  void
HelpFormatter.renderOptions ( StringBuffer sb, int width, Options options, int leftPad, int descPad ) :  StringBuffer
HelpFormatter.renderWrappedText ( StringBuffer sb, int width, int nextLineTabStop, String text ) :  StringBuffer
HelpFormatter.rtrim ( String s ) :  String

cdk-1.4.0.jar, Hide.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Hide.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Hide.getName ( ) :  String
Hide.headAction ( Node[ ] args, int length, RuleContext context ) :  void
Hide.Hide ( )

cdk-1.4.0.jar, Holiday.class
package com.ibm.icu.util
Holiday.firstAfter ( Date start ) :  Date *DEPRECATED*
Holiday.firstBetween ( Date start, Date end ) :  Date *DEPRECATED*
Holiday.getDisplayName ( ) :  String *DEPRECATED*
Holiday.getDisplayName ( Locale locale ) :  String *DEPRECATED*
Holiday.getDisplayName ( ULocale locale ) :  String *DEPRECATED*
Holiday.getHolidays ( ) [static] :  Holiday[ ] *DEPRECATED*
Holiday.getHolidays ( Locale locale ) [static] :  Holiday[ ] *DEPRECATED*
Holiday.getHolidays ( ULocale locale ) [static] :  Holiday[ ] *DEPRECATED*
Holiday.getRule ( ) :  DateRule *DEPRECATED*
Holiday.Holiday ( String name, DateRule rule ) *DEPRECATED*
Holiday.isBetween ( Date start, Date end ) :  boolean *DEPRECATED*
Holiday.isOn ( Date date ) :  boolean *DEPRECATED*
Holiday.setRule ( DateRule rule ) :  void *DEPRECATED*

cdk-1.4.0.jar, HybridizationFingerprinter.class
package org.openscience.cdk.fingerprint
HybridizationFingerprinter.findPathes ( IAtomContainer container, int searchDepth ) :  int[ ]
HybridizationFingerprinter.getBondSymbol ( IBond bond ) :  String
HybridizationFingerprinter.getFingerprint ( IAtomContainer container ) :  BitSet
HybridizationFingerprinter.getSearchDepth ( ) :  int
HybridizationFingerprinter.getSize ( ) :  int
HybridizationFingerprinter.HybridizationFingerprinter ( )
HybridizationFingerprinter.HybridizationFingerprinter ( int size )
HybridizationFingerprinter.HybridizationFingerprinter ( int size, int searchDepth )

cdk-1.4.0.jar, HybridizationRatioDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
HybridizationRatioDescriptor.calculate ( IAtomContainer container ) :  DescriptorValue
HybridizationRatioDescriptor.getDescriptorNames ( ) :  String[ ]
HybridizationRatioDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
HybridizationRatioDescriptor.getParameterNames ( ) :  String[ ]
HybridizationRatioDescriptor.getParameters ( ) :  Object[ ]
HybridizationRatioDescriptor.getParameterType ( String name ) :  Object
HybridizationRatioDescriptor.getSpecification ( ) :  DescriptorSpecification
HybridizationRatioDescriptor.HybridizationRatioDescriptor ( )
HybridizationRatioDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.0.jar, IanaLanguageTag.class
package com.hp.hpl.jena.rdf.arp.lang
IanaLanguageTag.find ( LanguageTag t ) [static] :  IanaLanguageTag

cdk-1.4.0.jar, IAtom.class
package org.openscience.cdk.interfaces
IAtom.getImplicitHydrogenCount ( ) [abstract] :  Integer
IAtom.setImplicitHydrogenCount ( Integer p1 ) [abstract] :  void

cdk-1.4.0.jar, IAtomContainer.class
package org.openscience.cdk.interfaces
IAtomContainer.addBond ( int p1, int p2, IBond.Order p3, IBond.Stereo p4 ) [abstract] :  void
IAtomContainer.addStereoElement ( IStereoElement p1 ) [abstract] :  void
IAtomContainer.stereoElements ( ) [abstract] :  Iterable

cdk-1.4.0.jar, IAtomContainerSet.class
package org.openscience.cdk.interfaces
IAtomContainerSet.sortAtomContainers ( Comparator p1 ) [abstract] :  void

cdk-1.4.0.jar, IBasis.class
package org.openscience.cdk.math.qm
IBasis.calcI ( int p1, int p2, int p3, int p4 ) [abstract] :  double
IBasis.calcJ ( int p1, int p2 ) [abstract] :  double
IBasis.calcS ( int p1, int p2 ) [abstract] :  double
IBasis.calcV ( int p1, int p2 ) [abstract] :  double
IBasis.getMaxX ( ) [abstract] :  double
IBasis.getMaxY ( ) [abstract] :  double
IBasis.getMaxZ ( ) [abstract] :  double
IBasis.getMinX ( ) [abstract] :  double
IBasis.getMinY ( ) [abstract] :  double
IBasis.getMinZ ( ) [abstract] :  double
IBasis.getSize ( ) [abstract] :  int
IBasis.getValue ( int p1, double p2, double p3, double p4 ) [abstract] :  double
IBasis.getValues ( int p1, Matrix p2 ) [abstract] :  Vector

cdk-1.4.0.jar, IBond.class
package org.openscience.cdk.interfaces
IBond.getStereo ( ) [abstract] :  IBond.Stereo
IBond.setStereo ( IBond.Stereo p1 ) [abstract] :  void

cdk-1.4.0.jar, ICanonicalMoleculeLabeller.class
package org.openscience.cdk.smsd.labelling
ICanonicalMoleculeLabeller.getCanonicalMolecule ( IAtomContainer p1 ) [abstract] :  IAtomContainer
ICanonicalMoleculeLabeller.getCanonicalPermutation ( IAtomContainer p1 ) [abstract] :  int[ ]

cdk-1.4.0.jar, ICanonicalReactionLabeller.class
package org.openscience.cdk.smsd.labelling
ICanonicalReactionLabeller.getCanonicalReaction ( IReaction p1 ) [abstract] :  IReaction

cdk-1.4.0.jar, ICDKObject.class
package org.openscience.cdk.interfaces
ICDKObject.getBuilder ( ) [abstract] :  IChemObjectBuilder

cdk-1.4.0.jar, IChemObjectBuilder.class
package org.openscience.cdk.interfaces
IChemObjectBuilder.newInstance ( Class p1, Object[ ] p2 ) [abstract] :  ICDKObject

cdk-1.4.0.jar, IChemObjectReader.class
package org.openscience.cdk.io
IChemObjectReader.handleError ( String p1 ) [abstract] :  void
IChemObjectReader.handleError ( String p1, Exception p2 ) [abstract] :  void
IChemObjectReader.handleError ( String p1, int p2, int p3, int p4 ) [abstract] :  void
IChemObjectReader.handleError ( String p1, int p2, int p3, int p4, Exception p5 ) [abstract] :  void
IChemObjectReader.setErrorHandler ( IChemObjectReaderErrorHandler p1 ) [abstract] :  void

cdk-1.4.0.jar, IChemObjectReaderErrorHandler.class
package org.openscience.cdk.io
IChemObjectReaderErrorHandler.handleError ( String p1 ) [abstract] :  void
IChemObjectReaderErrorHandler.handleError ( String p1, Exception p2 ) [abstract] :  void
IChemObjectReaderErrorHandler.handleError ( String p1, int p2, int p3, int p4 ) [abstract] :  void
IChemObjectReaderErrorHandler.handleError ( String p1, int p2, int p3, int p4, Exception p5 ) [abstract] :  void

cdk-1.4.0.jar, IChemObjectSelection.class
package org.openscience.cdk.renderer.selection
IChemObjectSelection.contains ( IChemObject p1 ) [abstract] :  boolean
IChemObjectSelection.elements ( Class p1 ) [abstract] :  Collection
IChemObjectSelection.getConnectedAtomContainer ( ) [abstract] :  IAtomContainer
IChemObjectSelection.isFilled ( ) [abstract] :  boolean
IChemObjectSelection.select ( IChemModel p1 ) [abstract] :  void

cdk-1.4.0.jar, IDBConnection.class
package com.hp.hpl.jena.db
IDBConnection.cleanDB ( ) [abstract] :  void
IDBConnection.close ( ) [abstract] :  void
IDBConnection.containsDefaultModel ( ) [abstract] :  boolean
IDBConnection.containsModel ( String p1 ) [abstract] :  boolean
IDBConnection.getAllModelNames ( ) [abstract] :  ExtendedIterator
IDBConnection.getConnection ( ) [abstract] :  Connection
IDBConnection.getDatabaseProperties ( ) [abstract] :  Model
IDBConnection.getDatabaseType ( ) [abstract] :  String
IDBConnection.getDefaultModelProperties ( ) [abstract] :  Model
IDBConnection.getDriver ( ) [abstract] :  IRDBDriver
IDBConnection.isFormatOK ( ) [abstract] :  boolean
IDBConnection.setDatabaseProperties ( Model p1 ) [abstract] :  void
IDBConnection.setDatabaseType ( String p1 ) [abstract] :  void
IDBConnection.setDriver ( IRDBDriver p1 ) [abstract] :  void

cdk-1.4.0.jar, IDNA.class
package com.ibm.icu.text
IDNA.compare ( String s1, String s2, int options ) [static] :  int
IDNA.compare ( StringBuffer s1, StringBuffer s2, int options ) [static] :  int
IDNA.compare ( UCharacterIterator s1, UCharacterIterator s2, int options ) [static] :  int
IDNA.convertIDNToASCII ( String src, int options ) [static] :  StringBuffer
IDNA.convertIDNToASCII ( StringBuffer src, int options ) [static] :  StringBuffer
IDNA.convertIDNToASCII ( UCharacterIterator src, int options ) [static] :  StringBuffer
IDNA.convertIDNToUnicode ( String src, int options ) [static] :  StringBuffer
IDNA.convertIDNToUnicode ( StringBuffer src, int options ) [static] :  StringBuffer
IDNA.convertIDNToUnicode ( UCharacterIterator src, int options ) [static] :  StringBuffer
IDNA.convertToASCII ( String src, int options ) [static] :  StringBuffer
IDNA.convertToASCII ( StringBuffer src, int options ) [static] :  StringBuffer
IDNA.convertToASCII ( UCharacterIterator src, int options ) [static] :  StringBuffer
IDNA.convertToUnicode ( String src, int options ) [static] :  StringBuffer
IDNA.convertToUnicode ( StringBuffer src, int options ) [static] :  StringBuffer
IDNA.convertToUnicode ( UCharacterIterator src, int options ) [static] :  StringBuffer

cdk-1.4.0.jar, IDrawVisitor.class
package org.openscience.cdk.renderer.visitor
IDrawVisitor.setFontManager ( IFontManager p1 ) [abstract] :  void
IDrawVisitor.setRendererModel ( RendererModel p1 ) [abstract] :  void

cdk-1.4.0.jar, IEdge.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
IEdge.getBondMatcher ( ) [abstract] :  VFBondMatcher
IEdge.getSource ( ) [abstract] :  INode
IEdge.getTarget ( ) [abstract] :  INode

cdk-1.4.0.jar, IFinalMapping.class
package org.openscience.cdk.smsd.interfaces
IFinalMapping.add ( Map p1 ) [abstract] :  void
IFinalMapping.clear ( ) [abstract] :  void
IFinalMapping.getFinalMapping ( ) [abstract] :  List
IFinalMapping.getIterator ( ) [abstract] :  Iterator
IFinalMapping.getSize ( ) [abstract] :  int
IFinalMapping.set ( List p1 ) [abstract] :  void

cdk-1.4.0.jar, IFontManager.class
package org.openscience.cdk.renderer.font
IFontManager.setFontForZoom ( double p1 ) [abstract] :  void
IFontManager.setFontName ( String p1 ) [abstract] :  void
IFontManager.setFontStyle ( IFontManager.FontStyle p1 ) [abstract] :  void

cdk-1.4.0.jar, IFragmenter.class
package org.openscience.cdk.fragment
IFragmenter.generateFragments ( IAtomContainer p1 ) [abstract] :  void
IFragmenter.getFragments ( ) [abstract] :  String[ ]
IFragmenter.getFragmentsAsContainers ( ) [abstract] :  IAtomContainer[ ]

cdk-1.4.0.jar, IFunction.class
package org.openscience.cdk.math
IFunction.getValue ( double p1, double p2, double p3 ) [abstract] :  double
IFunction.getValues ( Matrix p1 ) [abstract] :  Vector

cdk-1.4.0.jar, IGenerator.class
package org.openscience.cdk.renderer.generators
IGenerator.generate ( IChemObject p1, RendererModel p2 ) [abstract] :  IRenderingElement
IGenerator.getParameters ( ) [abstract] :  List

cdk-1.4.0.jar, IGeneratorParameter.class
package org.openscience.cdk.renderer.generators
IGeneratorParameter.getDefault ( ) [abstract] :  Object
IGeneratorParameter.getValue ( ) [abstract] :  Object
IGeneratorParameter.setValue ( Object p1 ) [abstract] :  void

cdk-1.4.0.jar, ILigand.class
package org.openscience.cdk.geometry.cip
ILigand.getAtomContainer ( ) [abstract] :  IAtomContainer
ILigand.getCentralAtom ( ) [abstract] :  IAtom
ILigand.getLigandAtom ( ) [abstract] :  IAtom
ILigand.getVisitedAtoms ( ) [abstract] :  VisitedAtoms
ILigand.isVisited ( IAtom p1 ) [abstract] :  boolean

cdk-1.4.0.jar, IllegalDateTimeFieldException.class
package com.hp.hpl.jena.datatypes.xsd
IllegalDateTimeFieldException.IllegalDateTimeFieldException ( String msg )

cdk-1.4.0.jar, IllegalParameterException.class
package com.hp.hpl.jena.reasoner
IllegalParameterException.IllegalParameterException ( String message )

cdk-1.4.0.jar, IllegalPrefixException.class
package com.hp.hpl.jena.shared
PrefixMapping.IllegalPrefixException.PrefixMapping.IllegalPrefixException ( String prefixName )

cdk-1.4.0.jar, ILoggerFactory.class
package org.slf4j
ILoggerFactory.getLogger ( String p1 ) [abstract] :  Logger

cdk-1.4.0.jar, ILoggingTool.class
package org.openscience.cdk.tools
ILoggingTool.debug ( Object p1 ) [abstract] :  void
ILoggingTool.debug ( Object p1, Object[ ] p2 ) [abstract] :  void
ILoggingTool.dumpClasspath ( ) [abstract] :  void
ILoggingTool.dumpSystemProperties ( ) [abstract] :  void
ILoggingTool.error ( Object p1 ) [abstract] :  void
ILoggingTool.error ( Object p1, Object[ ] p2 ) [abstract] :  void
ILoggingTool.fatal ( Object p1 ) [abstract] :  void
ILoggingTool.info ( Object p1 ) [abstract] :  void
ILoggingTool.info ( Object p1, Object[ ] p2 ) [abstract] :  void
ILoggingTool.isDebugEnabled ( ) [abstract] :  boolean
ILoggingTool.setStackLength ( int p1 ) [abstract] :  void
ILoggingTool.warn ( Object p1 ) [abstract] :  void
ILoggingTool.warn ( Object p1, Object[ ] p2 ) [abstract] :  void

cdk-1.4.0.jar, IMapper.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
IMapper.countMaps ( IAtomContainer p1 ) [abstract] :  int
IMapper.countMaps ( TargetProperties p1 ) [abstract] :  int
IMapper.getFirstMap ( IAtomContainer p1 ) [abstract] :  Map
IMapper.getFirstMap ( TargetProperties p1 ) [abstract] :  Map
IMapper.getMaps ( IAtomContainer p1 ) [abstract] :  List
IMapper.getMaps ( TargetProperties p1 ) [abstract] :  List
IMapper.hasMap ( IAtomContainer p1 ) [abstract] :  boolean
IMapper.hasMap ( TargetProperties p1 ) [abstract] :  boolean

cdk-1.4.0.jar, IMarkerFactory.class
package org.slf4j
IMarkerFactory.detachMarker ( String p1 ) [abstract] :  boolean
IMarkerFactory.exists ( String p1 ) [abstract] :  boolean
IMarkerFactory.getDetachedMarker ( String p1 ) [abstract] :  Marker
IMarkerFactory.getMarker ( String p1 ) [abstract] :  Marker

cdk-1.4.0.jar, IMatrix.class
package org.openscience.cdk.math
IMatrix.add ( IMatrix b ) :  IMatrix
IMatrix.add ( IMatrix b, IMatrix result ) :  void
IMatrix.contraction ( ) :  Complex
IMatrix.duplicate ( ) :  IMatrix
IMatrix.duplicate ( IMatrix result ) :  void
IMatrix.getColumns ( ) :  int
IMatrix.getRows ( ) :  int
IMatrix.getVectorFromColumn ( int index ) :  IVector
IMatrix.getVectorFromDiagonal ( ) :  IVector
IMatrix.getVectorFromRow ( int index ) :  IVector
IMatrix.IMatrix ( int rows, int columns )
IMatrix.IMatrix ( Matrix m )
IMatrix.mul ( Complex a ) :  IMatrix
IMatrix.mul ( Complex a, IMatrix result ) :  void
IMatrix.mul ( IMatrix b ) :  IMatrix
IMatrix.mul ( IMatrix b, IMatrix result ) :  void
IMatrix.mul ( IVector a ) :  IVector
IMatrix.mul ( IVector a, IVector result ) :  void
IMatrix.reshape ( int newrows, int newcolumns ) :  void
IMatrix.similar ( IMatrix U ) :  IMatrix
IMatrix.similar ( IMatrix U, IMatrix result ) :  void
IMatrix.sub ( IMatrix b ) :  IMatrix
IMatrix.sub ( IMatrix b, IMatrix result ) :  void
IMatrix.toString ( ) :  String
IMatrix.transpose ( ) :  IMatrix
IMatrix.transpose ( IMatrix result ) :  void

cdk-1.4.0.jar, IMCSBase.class
package org.openscience.cdk.smsd.interfaces
IMCSBase.getAllAtomMapping ( ) [abstract] :  List
IMCSBase.getAllMapping ( ) [abstract] :  List
IMCSBase.getFirstAtomMapping ( ) [abstract] :  Map
IMCSBase.getFirstMapping ( ) [abstract] :  Map
IMCSBase.set ( IQueryAtomContainer p1, IAtomContainer p2 ) [abstract] :  void
IMCSBase.set ( MolHandler p1, MolHandler p2 ) [abstract] :  void

cdk-1.4.0.jar, Implementation.class
package com.hp.hpl.jena.enhanced
Implementation.canWrap ( Node p1, EnhGraph p2 ) [abstract] :  boolean
Implementation.Implementation ( )
Implementation.wrap ( Node p1, EnhGraph p2 ) [abstract] :  EnhNode

cdk-1.4.0.jar, ImplicitHydrogenLigand.class
package org.openscience.cdk.geometry.cip
ImplicitHydrogenLigand.ImplicitHydrogenLigand ( IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom )

cdk-1.4.0.jar, ImportManager.class
package com.hp.hpl.jena.assembler
ImportManager.clear ( ) :  void
ImportManager.graphFor ( FileManager fm, Set loading, String path ) :  Graph
ImportManager.ImportManager ( )
ImportManager.withImports ( FileManager fm, Model model ) :  Model
ImportManager.withImports ( Model model ) :  Model

cdk-1.4.0.jar, INCHI_BOND_STEREO.class
package net.sf.jniinchi
INCHI_BOND_STEREO.valueOf ( String name ) [static] :  INCHI_BOND_STEREO
INCHI_BOND_STEREO.values ( ) [static] :  INCHI_BOND_STEREO[ ]

cdk-1.4.0.jar, INCHI_BOND_TYPE.class
package net.sf.jniinchi
INCHI_BOND_TYPE.valueOf ( String name ) [static] :  INCHI_BOND_TYPE
INCHI_BOND_TYPE.values ( ) [static] :  INCHI_BOND_TYPE[ ]

cdk-1.4.0.jar, INCHI_KEY.class
package net.sf.jniinchi
INCHI_KEY.valueOf ( String name ) [static] :  INCHI_KEY
INCHI_KEY.values ( ) [static] :  INCHI_KEY[ ]

cdk-1.4.0.jar, INCHI_KEY_STATUS.class
package net.sf.jniinchi
INCHI_KEY_STATUS.valueOf ( String name ) [static] :  INCHI_KEY_STATUS
INCHI_KEY_STATUS.values ( ) [static] :  INCHI_KEY_STATUS[ ]

cdk-1.4.0.jar, INCHI_OPTION.class
package net.sf.jniinchi
INCHI_OPTION.valueOf ( String name ) [static] :  INCHI_OPTION
INCHI_OPTION.valueOfIgnoreCase ( String string ) [static] :  INCHI_OPTION
INCHI_OPTION.values ( ) [static] :  INCHI_OPTION[ ]

cdk-1.4.0.jar, INCHI_PARITY.class
package net.sf.jniinchi
INCHI_PARITY.valueOf ( String name ) [static] :  INCHI_PARITY
INCHI_PARITY.values ( ) [static] :  INCHI_PARITY[ ]

cdk-1.4.0.jar, INCHI_RADICAL.class
package net.sf.jniinchi
INCHI_RADICAL.valueOf ( String name ) [static] :  INCHI_RADICAL
INCHI_RADICAL.values ( ) [static] :  INCHI_RADICAL[ ]

cdk-1.4.0.jar, INCHI_RET.class
package net.sf.jniinchi
INCHI_RET.valueOf ( String name ) [static] :  INCHI_RET
INCHI_RET.values ( ) [static] :  INCHI_RET[ ]

cdk-1.4.0.jar, INCHI_STATUS.class
package net.sf.jniinchi
INCHI_STATUS.getIndx ( ) :  int
INCHI_STATUS.getValue ( int value ) [static] :  INCHI_STATUS
INCHI_STATUS.valueOf ( String name ) [static] :  INCHI_STATUS
INCHI_STATUS.values ( ) [static] :  INCHI_STATUS[ ]

cdk-1.4.0.jar, INCHI_STEREOTYPE.class
package net.sf.jniinchi
INCHI_STEREOTYPE.valueOf ( String name ) [static] :  INCHI_STEREOTYPE
INCHI_STEREOTYPE.values ( ) [static] :  INCHI_STEREOTYPE[ ]

cdk-1.4.0.jar, InChIGeneratorFactory.class
package org.openscience.cdk.inchi
InChIGeneratorFactory.getInstance ( ) [static] :  InChIGeneratorFactory

cdk-1.4.0.jar, InChITautomerGenerator.class
package org.openscience.cdk.tautomers
InChITautomerGenerator.getTautomers ( IAtomContainer inputMolecule, String inchi ) :  List
InChITautomerGenerator.getTautomers ( IAtomContainer molecule ) :  List
InChITautomerGenerator.InChITautomerGenerator ( )

cdk-1.4.0.jar, IncludeQueueEntry.class
package jena
rdfcat.IncludeQueueEntry.rdfcat.IncludeQueueEntry ( rdfcat includeURI, String includeStmt, Statement p3 )

cdk-1.4.0.jar, IndexValues.class
package com.hp.hpl.jena.graph.query
IndexValues.get ( int p1 ) [abstract] :  Object

cdk-1.4.0.jar, Individual.class
package com.hp.hpl.jena.ontology
Individual.addOntClass ( Resource p1 ) [abstract] :  void
Individual.getOntClass ( ) [abstract] :  OntClass
Individual.getOntClass ( boolean p1 ) [abstract] :  OntClass
Individual.hasOntClass ( Resource p1 ) [abstract] :  boolean
Individual.hasOntClass ( Resource p1, boolean p2 ) [abstract] :  boolean
Individual.hasOntClass ( String p1 ) [abstract] :  boolean
Individual.listOntClasses ( boolean p1 ) [abstract] :  ExtendedIterator
Individual.removeOntClass ( Resource p1 ) [abstract] :  void
Individual.setOntClass ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, InfCapabilities.class
package com.hp.hpl.jena.reasoner
BaseInfGraph.InfCapabilities.BaseInfGraph.InfCapabilities ( )
BaseInfGraph.InfCapabilities.deleteAllowed ( boolean every ) :  boolean
BaseInfGraph.InfCapabilities.findContractSafe ( ) :  boolean
BaseInfGraph.InfCapabilities.iteratorRemoveAllowed ( ) :  boolean
BaseInfGraph.InfCapabilities.sizeAccurate ( ) :  boolean

cdk-1.4.0.jar, InfFindSafeCapabilities.class
package com.hp.hpl.jena.reasoner
BaseInfGraph.InfFindSafeCapabilities.BaseInfGraph.InfFindSafeCapabilities ( )
BaseInfGraph.InfFindSafeCapabilities.findContractSafe ( ) :  boolean

cdk-1.4.0.jar, InfGraph.class
package com.hp.hpl.jena.reasoner
InfGraph.find ( Node p1, Node p2, Node p3, Graph p4 ) [abstract] :  ExtendedIterator
InfGraph.getDeductionsGraph ( ) [abstract] :  Graph
InfGraph.getDerivation ( Triple p1 ) [abstract] :  Iterator
InfGraph.getGlobalProperty ( Node p1 ) [abstract] :  Node
InfGraph.getRawGraph ( ) [abstract] :  Graph
InfGraph.getReasoner ( ) [abstract] :  Reasoner
InfGraph.prepare ( ) [abstract] :  void
InfGraph.rebind ( ) [abstract] :  void
InfGraph.rebind ( Graph p1 ) [abstract] :  void
InfGraph.reset ( ) [abstract] :  void
InfGraph.setDerivationLogging ( boolean p1 ) [abstract] :  void
InfGraph.testGlobalProperty ( Node p1 ) [abstract] :  boolean
InfGraph.validate ( ) [abstract] :  ValidityReport

cdk-1.4.0.jar, InfModel.class
package com.hp.hpl.jena.rdf.model
InfModel.getDeductionsModel ( ) [abstract] :  Model
InfModel.getDerivation ( Statement p1 ) [abstract] :  Iterator
InfModel.getRawModel ( ) [abstract] :  Model
InfModel.getReasoner ( ) [abstract] :  Reasoner
InfModel.listStatements ( Resource p1, Property p2, RDFNode p3, Model p4 ) [abstract] :  StmtIterator
InfModel.prepare ( ) [abstract] :  void
InfModel.rebind ( ) [abstract] :  void
InfModel.reset ( ) [abstract] :  void
InfModel.setDerivationLogging ( boolean p1 ) [abstract] :  void
InfModel.validate ( ) [abstract] :  ValidityReport

cdk-1.4.0.jar, InfModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
InfModelAssembler.getBase ( Assembler a, Resource root, Mode mode ) :  Model
InfModelAssembler.getReasoner ( Assembler a, Resource root ) :  Reasoner
InfModelAssembler.getReasonerFactory ( Assembler a, Resource root ) :  ReasonerFactory
InfModelAssembler.InfModelAssembler ( )
InfModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode mode ) :  Model

cdk-1.4.0.jar, InfTransactionHandler.class
package com.hp.hpl.jena.reasoner
BaseInfGraph.InfTransactionHandler.abort ( ) :  void
BaseInfGraph.InfTransactionHandler.BaseInfGraph.InfTransactionHandler ( BaseInfGraph base )
BaseInfGraph.InfTransactionHandler.begin ( ) :  void
BaseInfGraph.InfTransactionHandler.commit ( ) :  void
BaseInfGraph.InfTransactionHandler.getBaseHandler ( ) :  TransactionHandler
BaseInfGraph.InfTransactionHandler.transactionsSupported ( ) :  boolean

cdk-1.4.0.jar, Initialize.class
package com.hp.hpl.jena.iri
ViolationCodes.Initialize.ViolationCodes.Initialize ( )

cdk-1.4.0.jar, InitialStage.class
package com.hp.hpl.jena.graph.query
InitialStage.close ( ) :  void
InitialStage.deliver ( Pipe result ) :  Pipe
InitialStage.InitialStage ( int count )

cdk-1.4.0.jar, InnerXMLLiteral.class
package com.hp.hpl.jena.rdf.arp.states
InnerXMLLiteral.endElement ( ) :  void
InnerXMLLiteral.InnerXMLLiteral ( AbsXMLLiteral f, String rawName, Map ns )

cdk-1.4.0.jar, INode.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
INode.addEdge ( EdgeBuilder p1 ) [abstract] :  void
INode.addNeighbor ( NodeBuilder p1 ) [abstract] :  void
INode.countNeighbors ( ) [abstract] :  int
INode.getAtomMatcher ( ) [abstract] :  VFAtomMatcher
INode.getEdges ( ) [abstract] :  List
INode.neighbors ( ) [abstract] :  Iterable

cdk-1.4.0.jar, Interface.class
package com.hp.hpl.jena.rdf.model
ResourceFactory.Interface.createPlainLiteral ( String p1 ) [abstract] :  Literal
ResourceFactory.Interface.createProperty ( String p1 ) [abstract] :  Property
ResourceFactory.Interface.createProperty ( String p1, String p2 ) [abstract] :  Property
ResourceFactory.Interface.createResource ( ) [abstract] :  Resource
ResourceFactory.Interface.createResource ( String p1 ) [abstract] :  Resource
ResourceFactory.Interface.createStatement ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  Statement
ResourceFactory.Interface.createTypedLiteral ( Object p1 ) [abstract] :  Literal
ResourceFactory.Interface.createTypedLiteral ( String p1, RDFDatatype p2 ) [abstract] :  Literal

cdk-1.4.0.jar, Intersection.class
package com.hp.hpl.jena.graph.compose
Intersection.graphBaseFind ( TripleMatch s ) :  ExtendedIterator
Intersection.Intersection ( Graph L, Graph R )
Intersection.performAdd ( Triple t ) :  void
Intersection.performDelete ( Triple t ) :  void

cdk-1.4.0.jar, InvalidListException.class
package com.hp.hpl.jena.rdf.model
InvalidListException.InvalidListException ( )
InvalidListException.InvalidListException ( String msg )

cdk-1.4.0.jar, InvalidPropertyURIException.class
package com.hp.hpl.jena.shared
InvalidPropertyURIException.InvalidPropertyURIException ( String uri )

cdk-1.4.0.jar, InvariantArray.class
package signature
InvariantArray.compareTo ( InvariantArray o ) :  int
InvariantArray.compareTo ( Object x0 ) :  int
InvariantArray.equals ( int[ ] other ) :  boolean
InvariantArray.equals ( Object o ) :  boolean
InvariantArray.InvariantArray ( int[ ] invariants, int originalIndex )
InvariantArray.toString ( ) :  String

cdk-1.4.0.jar, InvariantInt.class
package signature
InvariantInt.compareTo ( InvariantInt o ) :  int
InvariantInt.compareTo ( Object x0 ) :  int
InvariantInt.InvariantInt ( int invariant, int index )
InvariantInt.toString ( ) :  String

cdk-1.4.0.jar, InvariantIntIntPair.class
package signature
InvariantIntIntPair.compareTo ( InvariantIntIntPair o ) :  int
InvariantIntIntPair.compareTo ( Object x0 ) :  int
InvariantIntIntPair.equals ( int label, int value ) :  boolean
InvariantIntIntPair.equals ( InvariantIntIntPair o ) :  boolean
InvariantIntIntPair.getOriginalIndex ( ) :  int
InvariantIntIntPair.InvariantIntIntPair ( int label, int value, int originalIndex )
InvariantIntIntPair.toString ( ) :  String

cdk-1.4.0.jar, InvariantIntStringPair.class
package signature
InvariantIntStringPair.compareTo ( InvariantIntStringPair o ) :  int
InvariantIntStringPair.compareTo ( Object x0 ) :  int
InvariantIntStringPair.equals ( InvariantIntStringPair o ) :  boolean
InvariantIntStringPair.equals ( String string, int value ) :  boolean
InvariantIntStringPair.getOriginalIndex ( ) :  int
InvariantIntStringPair.InvariantIntStringPair ( String string, int value, int originalIndex )
InvariantIntStringPair.toString ( ) :  String

cdk-1.4.0.jar, InvariantList.class
package signature
InvariantList.add ( int i ) :  void
InvariantList.addAll ( Collection other ) :  void
InvariantList.compareTo ( InvariantList o ) :  int
InvariantList.compareTo ( Object x0 ) :  int
InvariantList.equals ( List other ) :  boolean
InvariantList.equals ( Object o ) :  boolean
InvariantList.InvariantList ( int originalIndex )
InvariantList.toString ( ) :  String

cdk-1.4.0.jar, Invariants.class
package signature
Invariants.clone ( ) :  Object
Invariants.getColor ( int vertexIndex ) :  int
Invariants.getNodeInvariant ( int nodeIndex ) :  int
Invariants.getVertexInvariant ( int vertexIndex ) :  int
Invariants.getVertexInvariantCopy ( ) :  int[ ]
Invariants.getVertexInvariants ( ) :  int[ ]
Invariants.Invariants ( int vertexCount, int nodeCount )
Invariants.setColor ( int vertexIndex, int color ) :  void
Invariants.setNodeInvariant ( int nodeIndex, int value ) :  void
Invariants.setVertexInvariant ( int vertexIndex, int value ) :  void
Invariants.toString ( ) :  String

cdk-1.4.0.jar, InvariantType.class
package signature
AbstractVertexSignature.InvariantType.valueOf ( String p1 ) [static] :  AbstractVertexSignature.InvariantType
AbstractVertexSignature.InvariantType.values ( ) [static] :  AbstractVertexSignature.InvariantType[ ]

cdk-1.4.0.jar, IQuery.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
IQuery.countEdges ( ) [abstract] :  int
IQuery.countNodes ( ) [abstract] :  int
IQuery.edges ( ) [abstract] :  Iterable
IQuery.getAtom ( INode p1 ) [abstract] :  IAtom
IQuery.getEdge ( INode p1, INode p2 ) [abstract] :  IEdge
IQuery.getEdge ( int p1 ) [abstract] :  IEdge
IQuery.getNode ( int p1 ) [abstract] :  INode
IQuery.nodes ( ) [abstract] :  Iterable

cdk-1.4.0.jar, IQueryCompiler.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
IQueryCompiler.compile ( ) [abstract] :  IQuery

cdk-1.4.0.jar, IRenderer.class
package org.openscience.cdk.renderer
IRenderer.calculateDiagramBounds ( IChemObject p1 ) [abstract] :  Rectangle
IRenderer.generateDiagram ( IChemObject p1 ) [abstract] :  IRenderingElement
IRenderer.getGenerators ( ) [abstract] :  List
IRenderer.getRenderer2DModel ( ) [abstract] :  RendererModel
IRenderer.paint ( IChemObject p1, IDrawVisitor p2 ) [abstract] :  Rectangle
IRenderer.paint ( IChemObject p1, IDrawVisitor p2, Rectangle2D p3, boolean p4 ) [abstract] :  void
IRenderer.setScale ( IChemObject p1 ) [abstract] :  void
IRenderer.setup ( IChemObject p1, Rectangle p2 ) [abstract] :  void
IRenderer.setZoom ( double p1 ) [abstract] :  void
IRenderer.shiftDrawCenter ( double p1, double p2 ) [abstract] :  void
IRenderer.toModelCoordinates ( double p1, double p2 ) [abstract] :  Point2d
IRenderer.toScreenCoordinates ( double p1, double p2 ) [abstract] :  Point2d

cdk-1.4.0.jar, IRenderingElement.class
package org.openscience.cdk.renderer.elements
IRenderingElement.accept ( IRenderingVisitor p1 ) [abstract] :  void

cdk-1.4.0.jar, IRenderingVisitor.class
package org.openscience.cdk.renderer.elements
IRenderingVisitor.setTransform ( AffineTransform p1 ) [abstract] :  void
IRenderingVisitor.visit ( IRenderingElement p1 ) [abstract] :  void

cdk-1.4.0.jar, IRGroupQuery.class
package org.openscience.cdk.isomorphism.matchers
IRGroupQuery.areRootAtomsDefined ( ) [abstract] :  boolean
IRGroupQuery.areSubstituentsDefined ( ) [abstract] :  boolean
IRGroupQuery.getAllConfigurations ( ) [abstract] :  List
IRGroupQuery.getAtomContainerCount ( ) [abstract] :  int
IRGroupQuery.getRGroupDefinitions ( ) [abstract] :  Map
IRGroupQuery.getRootAttachmentPoints ( ) [abstract] :  Map
IRGroupQuery.getRootStructure ( ) [abstract] :  IAtomContainer
IRGroupQuery.getSubstituents ( ) [abstract] :  List
IRGroupQuery.setRGroupDefinitions ( Map p1 ) [abstract] :  void
IRGroupQuery.setRootAttachmentPoints ( Map p1 ) [abstract] :  void
IRGroupQuery.setRootStructure ( IAtomContainer p1 ) [abstract] :  void

cdk-1.4.0.jar, IRI.class
package com.hp.hpl.jena.iri
IRI.getASCIIHost ( ) [abstract] :  String
IRI.getAuthority ( ) [abstract] :  String
IRI.getFragment ( ) [abstract] :  String
IRI.getHost ( ) [abstract] :  String
IRI.getPath ( ) [abstract] :  String
IRI.getPort ( ) [abstract] :  int
IRI.getQuery ( ) [abstract] :  String
IRI.getRawAuthority ( ) [abstract] :  String
IRI.getRawFragment ( ) [abstract] :  String
IRI.getRawHost ( ) [abstract] :  String
IRI.getRawPath ( ) [abstract] :  String
IRI.getRawQuery ( ) [abstract] :  String
IRI.getRawUserinfo ( ) [abstract] :  String
IRI.getScheme ( ) [abstract] :  String
IRI.getUserinfo ( ) [abstract] :  String
IRI.hasViolation ( boolean p1 ) [abstract] :  boolean
IRI.IRI ( )
IRI.isAbsolute ( ) [abstract] :  boolean
IRI.isRelative ( ) [abstract] :  boolean
IRI.isRootless ( ) [abstract] :  boolean
IRI.ladderEquals ( IRI p1 ) [abstract] :  int
IRI.ladderEquals ( IRI p1, int p2 ) [abstract] :  boolean
IRI.main ( String[ ] args ) [static] :  void
IRI.normalize ( boolean p1 ) [abstract] :  IRI
IRI.relativize ( IRI p1 ) [abstract] :  IRI
IRI.relativize ( IRI p1, int p2 ) [abstract] :  IRI
IRI.relativize ( String p1 ) [abstract] :  IRI
IRI.relativize ( String p1, int p2 ) [abstract] :  IRI
IRI.resolve ( IRI relative ) :  IRI
IRI.resolve ( String relative ) :  IRI
IRI.toASCIIString ( ) [abstract] :  String
IRI.toDisplayString ( ) [abstract] :  String
IRI.toString ( ) [abstract] :  String
IRI.toURL ( ) [abstract] :  URL
IRI.violations ( boolean p1 ) [abstract] :  Iterator

cdk-1.4.0.jar, IRIException.class
package com.hp.hpl.jena.iri
IRIException.getViolation ( ) [abstract] :  Violation
IRIException.IRIException ( )

cdk-1.4.0.jar, IRIFactory.class
package com.hp.hpl.jena.iri
IRIFactory.allowUnwiseCharacters ( ) :  void
IRIFactory.construct ( String scheme, String authority, String path, String query, String fragment ) :  IRI
IRIFactory.construct ( String scheme, String userInfo, String host, int port, String path, String query, String fragment ) :  IRI
IRIFactory.create ( String scheme, String authority, String path, String query, String fragment ) :  IRI
IRIFactory.create ( String scheme, String userInfo, String host, int port, String path, String query, String fragment ) :  IRI
IRIFactory.dnsViolation ( boolean isError, boolean isWarning ) :  void
IRIFactory.ignoring ( int code ) :  boolean
IRIFactory.IRIFactory ( )
IRIFactory.IRIFactory ( IRIFactory template )
IRIFactory.iriImplementation ( ) [static] :  IRIFactory
IRIFactory.isError ( int code ) :  boolean
IRIFactory.isWarning ( int code ) :  boolean
IRIFactory.jenaImplementation ( ) [static] :  IRIFactory
IRIFactory.mintingViolation ( boolean isError, boolean isWarning ) :  void
IRIFactory.securityViolation ( boolean isError, boolean isWarning ) :  void
IRIFactory.semanticWebImplementation ( ) [static] :  IRIFactory
IRIFactory.setEncoding ( String enc ) :  void
IRIFactory.setIriImplementation ( IRIFactory iriF ) [static] :  void
IRIFactory.setIsError ( int code, boolean set ) :  void
IRIFactory.setIsWarning ( int code, boolean set ) :  void
IRIFactory.setJenaImplementation ( IRIFactory jf ) [static] :  void
IRIFactory.setQueryCharacterRestrictions ( boolean restrict ) :  void
IRIFactory.setSameSchemeRelativeReferences ( String scheme ) :  void
IRIFactory.setSemanticWebImplementation ( IRIFactory sw ) [static] :  void
IRIFactory.setUriImplementation ( IRIFactory uriF ) [static] :  void
IRIFactory.shouldViolation ( boolean isError, boolean isWarning ) :  void
IRIFactory.uriImplementation ( ) [static] :  IRIFactory
IRIFactory.useSchemeSpecificRules ( String scheme, boolean asErrors ) :  void
IRIFactory.useSpecificationIRI ( boolean asErrors ) :  void
IRIFactory.useSpecificationRDF ( boolean asErrors ) :  void
IRIFactory.useSpecificationURI ( boolean asErrors ) :  void
IRIFactory.useSpecificationXLink ( boolean asErrors ) :  void
IRIFactory.useSpecificationXMLSchema ( boolean asErrors ) :  void
IRIFactory.useSpecificationXMLSystemID ( boolean asErrors ) :  void

cdk-1.4.0.jar, IRIFactoryI.class
package com.hp.hpl.jena.iri
IRIFactoryI.construct ( IRI p1 ) [abstract] :  IRI
IRIFactoryI.construct ( String p1 ) [abstract] :  IRI
IRIFactoryI.create ( IRI p1 ) [abstract] :  IRI
IRIFactoryI.create ( String p1 ) [abstract] :  IRI

cdk-1.4.0.jar, IRIResolver.class
package com.hp.hpl.jena.n3
IRIResolver.chooseBaseURI ( ) [static] :  String
IRIResolver.chooseBaseURI ( String baseURI ) [static] :  String
IRIResolver.getBaseIRI ( ) :  String
IRIResolver.IRIResolver ( )
IRIResolver.IRIResolver ( String baseS )
IRIResolver.resolve ( String relStr, String baseStr ) [static] :  String
IRIResolver.resolve ( String relURI ) :  String
IRIResolver.resolveFileURL ( String filename ) [static] :  String
IRIResolver.resolveGlobal ( String str ) [static] :  String
IRIResolver.suppressExceptions ( ) [static] :  void

cdk-1.4.0.jar, IsBNode.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
IsBNode.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
IsBNode.getArgLength ( ) :  int
IsBNode.getName ( ) :  String
IsBNode.IsBNode ( )

cdk-1.4.0.jar, IsDType.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
IsDType.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
IsDType.getArgLength ( ) :  int
IsDType.getName ( ) :  String
IsDType.IsDType ( )
IsDType.isTypeOK ( Node val, Node dt ) [static] :  boolean

cdk-1.4.0.jar, ISequenceSubRule.class
package org.openscience.cdk.geometry.cip.rules
ISequenceSubRule.compare ( Object p1, Object p2 ) [abstract] :  int

cdk-1.4.0.jar, IsFunctor.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
IsFunctor.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
IsFunctor.getArgLength ( ) :  int
IsFunctor.getName ( ) :  String
IsFunctor.IsFunctor ( )

cdk-1.4.0.jar, IslamicCalendar.class
package com.ibm.icu.util
IslamicCalendar.getType ( ) :  String
IslamicCalendar.handleComputeFields ( int julianDay ) :  void
IslamicCalendar.handleComputeMonthStart ( int eyear, int month, boolean useMonth ) :  int
IslamicCalendar.handleGetExtendedYear ( ) :  int
IslamicCalendar.handleGetLimit ( int field, int limitType ) :  int
IslamicCalendar.handleGetMonthLength ( int extendedYear, int month ) :  int
IslamicCalendar.handleGetYearLength ( int extendedYear ) :  int
IslamicCalendar.isCivil ( ) :  boolean
IslamicCalendar.IslamicCalendar ( )
IslamicCalendar.IslamicCalendar ( Date date )
IslamicCalendar.IslamicCalendar ( int year, int month, int date )
IslamicCalendar.IslamicCalendar ( int year, int month, int date, int hour, int minute, int second )
IslamicCalendar.IslamicCalendar ( Locale aLocale )
IslamicCalendar.IslamicCalendar ( TimeZone zone )
IslamicCalendar.IslamicCalendar ( TimeZone zone, Locale aLocale )
IslamicCalendar.IslamicCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
IslamicCalendar.IslamicCalendar ( ULocale locale ) *DEPRECATED*
IslamicCalendar.setCivil ( boolean beCivil ) :  void

cdk-1.4.0.jar, IsLiteral.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
IsLiteral.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
IsLiteral.getArgLength ( ) :  int
IsLiteral.getName ( ) :  String
IsLiteral.IsLiteral ( )

cdk-1.4.0.jar, Iso3166.class
package com.hp.hpl.jena.rdf.arp.lang
Iso3166.find ( String countryId ) [static] :  Iso3166

cdk-1.4.0.jar, Iso639.class
package com.hp.hpl.jena.rdf.arp.lang
Iso639.find ( String lang ) [static] :  Iso639

cdk-1.4.0.jar, Isomorphism.class
package org.openscience.cdk.smsd
Isomorphism.getAllAtomMapping ( ) :  List
Isomorphism.getAllBondMaps ( ) :  List
Isomorphism.getAllMapping ( ) :  List
Isomorphism.getBondInSensitiveTimeOut ( ) :  double
Isomorphism.getBondSensitiveTimeOut ( ) :  double
Isomorphism.getEnergyScore ( int Key ) :  Double
Isomorphism.getEuclideanDistance ( ) :  double
Isomorphism.getFirstAtomMapping ( ) :  Map
Isomorphism.getFirstBondMap ( ) :  Map
Isomorphism.getFirstMapping ( ) :  Map
Isomorphism.getFragmentSize ( int Key ) :  Integer
Isomorphism.getProductMolecule ( ) :  IAtomContainer
Isomorphism.getReactantMolecule ( ) :  IAtomContainer
Isomorphism.getStereoScore ( int Key ) :  Integer
Isomorphism.getTanimotoAtomSimilarity ( ) :  double
Isomorphism.getTanimotoBondSimilarity ( ) :  double
Isomorphism.getTanimotoSimilarity ( ) :  double
Isomorphism.init ( IAtomContainer reactant, IAtomContainer product, boolean removeHydrogen, boolean cleanAndConfigureMolecule ) :  void
Isomorphism.init ( IMolecule reactant, IMolecule product, boolean removeHydrogen, boolean cleanAndConfigureMolecule ) :  void
Isomorphism.init ( IQueryAtomContainer reactant, IAtomContainer product ) :  void
Isomorphism.init ( String sourceMolFileName, String targetMolFileName, boolean removeHydrogen, boolean cleanAndConfigureMolecule ) :  void
Isomorphism.isMatchBonds ( ) :  boolean
Isomorphism.Isomorphism ( Algorithm algorithmType, boolean bondTypeFlag )
Isomorphism.isStereoMisMatch ( ) :  boolean
Isomorphism.isSubgraph ( ) :  boolean
Isomorphism.isTimeOut ( ) :  boolean
Isomorphism.makeBondMapOfAtomMap ( IAtomContainer ac1, IAtomContainer ac2, Map mapping ) [static] :  Map
Isomorphism.makeBondMapsOfAtomMaps ( IAtomContainer ac1, IAtomContainer ac2, List mappings ) [static] :  List
Isomorphism.resetTimeOut ( ) :  void
Isomorphism.setBondInSensitiveTimeOut ( double bondInSensitiveTimeOut ) :  void
Isomorphism.setBondSensitiveTimeOut ( double bondSensitiveTimeOut ) :  void
Isomorphism.setChemFilters ( boolean stereoFilter, boolean fragmentFilter, boolean energyFilter ) :  void
Isomorphism.setMatchBonds ( boolean matchBonds ) :  void

cdk-1.4.0.jar, IsotopeFactory.class
package org.openscience.cdk.config
IsotopeFactory.getIsotope ( String symbol, int massNumber ) :  IIsotope

cdk-1.4.0.jar, IState.class
package org.openscience.cdk.smsd.algorithm.vflib.interfaces
IState.backTrack ( ) [abstract] :  void
IState.getMap ( ) [abstract] :  Map
IState.hasNextCandidate ( ) [abstract] :  boolean
IState.isDead ( ) [abstract] :  boolean
IState.isGoal ( ) [abstract] :  boolean
IState.isMatchFeasible ( Match p1 ) [abstract] :  boolean
IState.nextCandidate ( ) [abstract] :  Match
IState.nextState ( Match p1 ) [abstract] :  IState

cdk-1.4.0.jar, IteratorCollection.class
package com.hp.hpl.jena.util
IteratorCollection.iteratorToList ( Iterator it ) [static] :  List
IteratorCollection.iteratorToSet ( Iterator i ) [static] :  Set

cdk-1.4.0.jar, IteratorIterator.class
package com.hp.hpl.jena.util.iterator
IteratorIterator.hasNext ( ) :  boolean
IteratorIterator.IteratorIterator ( Iterator e )
IteratorIterator.next ( ) :  Object
IteratorIterator.remove ( ) :  void

cdk-1.4.0.jar, ITetrahedralChirality.class
package org.openscience.cdk.interfaces
ITetrahedralChirality.getChiralAtom ( ) [abstract] :  IAtom
ITetrahedralChirality.getLigands ( ) [abstract] :  IAtom[ ]
ITetrahedralChirality.getStereo ( ) [abstract] :  ITetrahedralChirality.Stereo

cdk-1.4.0.jar, IVector.class
package org.openscience.cdk.math
IVector.add ( IVector b ) :  IVector
IVector.add ( IVector b, IVector result ) :  void
IVector.dot ( IVector b ) :  Complex
IVector.duplicate ( ) :  IVector
IVector.duplicate ( IVector result ) :  void
IVector.getSize ( ) :  int
IVector.IVector ( int size )
IVector.mul ( double b ) :  IVector
IVector.mul ( double b, IVector result ) :  void
IVector.reshape ( int newsize ) :  void
IVector.sub ( IVector b ) :  IVector
IVector.sub ( IVector b, IVector result ) :  void
IVector.toString ( ) :  String

cdk-1.4.0.jar, JA.class
package com.hp.hpl.jena.assembler
JA.getSchema ( ) [static] :  Model
JA.getURI ( ) [static] :  String
JA.JA ( )
JA.property ( String localName ) [static] :  Property
JA.resource ( String localName ) [static] :  Resource

cdk-1.4.0.jar, JapaneseCalendar.class
package com.ibm.icu.util
JapaneseCalendar.getType ( ) :  String
JapaneseCalendar.handleComputeFields ( int julianDay ) :  void
JapaneseCalendar.handleGetExtendedYear ( ) :  int
JapaneseCalendar.handleGetLimit ( int field, int limitType ) :  int
JapaneseCalendar.JapaneseCalendar ( )
JapaneseCalendar.JapaneseCalendar ( Date date )
JapaneseCalendar.JapaneseCalendar ( int era, int year, int month, int date )
JapaneseCalendar.JapaneseCalendar ( int year, int month, int date )
JapaneseCalendar.JapaneseCalendar ( int year, int month, int date, int hour, int minute, int second )
JapaneseCalendar.JapaneseCalendar ( Locale aLocale )
JapaneseCalendar.JapaneseCalendar ( TimeZone zone )
JapaneseCalendar.JapaneseCalendar ( TimeZone zone, Locale aLocale )
JapaneseCalendar.JapaneseCalendar ( TimeZone zone, ULocale locale ) *DEPRECATED*
JapaneseCalendar.JapaneseCalendar ( ULocale locale ) *DEPRECATED*

cdk-1.4.0.jar, JavaCharStream.class
package com.hp.hpl.jena.n3.turtle.parser
JavaCharStream.adjustBeginLineColumn ( int newLine, int newCol ) :  void
JavaCharStream.AdjustBuffSize ( ) :  void
JavaCharStream.backup ( int amount ) :  void
JavaCharStream.BeginToken ( ) :  char
JavaCharStream.Done ( ) :  void
JavaCharStream.ExpandBuff ( boolean wrapAround ) :  void
JavaCharStream.FillBuff ( ) :  void
JavaCharStream.getBeginColumn ( ) :  int
JavaCharStream.getBeginLine ( ) :  int
JavaCharStream.getColumn ( ) :  int *DEPRECATED*
JavaCharStream.getEndColumn ( ) :  int
JavaCharStream.getEndLine ( ) :  int
JavaCharStream.GetImage ( ) :  String
JavaCharStream.getLine ( ) :  int *DEPRECATED*
JavaCharStream.GetSuffix ( int len ) :  char[ ]
JavaCharStream.getTabSize ( int i ) :  int
JavaCharStream.JavaCharStream ( InputStream dstream )
JavaCharStream.JavaCharStream ( InputStream dstream, int startline, int startcolumn )
JavaCharStream.JavaCharStream ( InputStream dstream, int startline, int startcolumn, int buffersize )
JavaCharStream.JavaCharStream ( InputStream dstream, String encoding )
JavaCharStream.JavaCharStream ( InputStream dstream, String encoding, int startline, int startcolumn )
JavaCharStream.JavaCharStream ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize )
JavaCharStream.JavaCharStream ( Reader dstream )
JavaCharStream.JavaCharStream ( Reader dstream, int startline, int startcolumn )
JavaCharStream.JavaCharStream ( Reader dstream, int startline, int startcolumn, int buffersize )
JavaCharStream.ReadByte ( ) :  char
JavaCharStream.readChar ( ) :  char
JavaCharStream.ReInit ( InputStream dstream ) :  void
JavaCharStream.ReInit ( InputStream dstream, int startline, int startcolumn ) :  void
JavaCharStream.ReInit ( InputStream dstream, int startline, int startcolumn, int buffersize ) :  void
JavaCharStream.ReInit ( InputStream dstream, String encoding ) :  void
JavaCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn ) :  void
JavaCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize ) :  void
JavaCharStream.ReInit ( Reader dstream ) :  void
JavaCharStream.ReInit ( Reader dstream, int startline, int startcolumn ) :  void
JavaCharStream.ReInit ( Reader dstream, int startline, int startcolumn, int buffersize ) :  void
JavaCharStream.setTabSize ( int i ) :  void
JavaCharStream.UpdateLineColumn ( char c ) :  void

cdk-1.4.0.jar, JenaException.class
package com.hp.hpl.jena.shared
JenaException.JenaException ( )
JenaException.JenaException ( String message )
JenaException.JenaException ( String message, Throwable cause )
JenaException.JenaException ( Throwable cause )

cdk-1.4.0.jar, JenaLockedException.class
package com.hp.hpl.jena.shared
PrefixMapping.JenaLockedException.PrefixMapping.JenaLockedException ( PrefixMapping pm )

cdk-1.4.0.jar, JenaReader.class
package com.hp.hpl.jena.rdf.arp
JenaReader.getOptions ( ) :  ARPOptions
JenaReader.JenaReader ( )
JenaReader.read ( Graph g, InputStream in, String xmlBase ) :  void
JenaReader.read ( Graph g, Reader reader, String xmlBase ) :  void
JenaReader.read ( Model m, InputStream in, String xmlBase ) :  void
JenaReader.read ( Model m, Reader reader, String xmlBase ) :  void
JenaReader.read ( Model m, String url ) :  void
JenaReader.setErrorHandler ( RDFErrorHandler errHandler ) :  RDFErrorHandler
JenaReader.setOptionsWith ( ARPOptions opts ) :  void
JenaReader.setProperty ( String str, Object value ) :  Object

cdk-1.4.0.jar, JenaReaderBase.class
package com.hp.hpl.jena.n3
JenaReaderBase.checkReader ( Reader r ) :  void
JenaReaderBase.JenaReaderBase ( )
JenaReaderBase.read ( Model model, InputStream in, String base ) :  void
JenaReaderBase.read ( Model model, Reader r, String base ) :  void
JenaReaderBase.read ( Model model, String url ) :  void
JenaReaderBase.readWorker ( Model p1, Reader p2, String p3 ) [abstract] :  void
JenaReaderBase.setErrorHandler ( RDFErrorHandler errHandler ) :  RDFErrorHandler
JenaReaderBase.setProperty ( String propName, Object propValue ) :  Object

cdk-1.4.0.jar, JenaRuntime.class
package com.hp.hpl.jena
JenaRuntime.getLineSeparator ( ) [static] :  String
JenaRuntime.getSystemProperty ( String propName ) [static] :  String
JenaRuntime.getSystemProperty ( String propName, String defaultValue ) [static] :  String
JenaRuntime.JenaRuntime ( )
JenaRuntime.runNotUnder ( String featureName ) [static] :  boolean
JenaRuntime.runUnder ( String featureName ) [static] :  boolean
JenaRuntime.setFeature ( String featureName ) [static] :  void

cdk-1.4.0.jar, JenaURIException.class
package com.hp.hpl.jena.n3
JenaURIException.JenaURIException ( Exception e )
JenaURIException.JenaURIException ( String msg )

cdk-1.4.0.jar, JenaUUID.class
package com.hp.hpl.jena.shared.uuid
JenaUUID._getVariant ( long mostSigBits, long leastSigBits ) :  int
JenaUUID._getVersion ( long mostSigBits, long leastSigBits ) :  int
JenaUUID.asString ( ) :  String
JenaUUID.asURI ( ) :  String
JenaUUID.asURN ( ) :  String
JenaUUID.asUUID ( ) :  UUID
JenaUUID.generate ( ) [static] :  JenaUUID
JenaUUID.getFactory ( ) [static] :  UUIDFactory
JenaUUID.getLeastSignificantBits ( ) [abstract] :  long
JenaUUID.getMostSignificantBits ( ) [abstract] :  long
JenaUUID.getVariant ( ) [abstract] :  int
JenaUUID.getVersion ( ) [abstract] :  int
JenaUUID.isNil ( ) :  boolean
JenaUUID.JenaUUID ( )
JenaUUID.nil ( ) [static] :  JenaUUID
JenaUUID.parse ( String s ) [static] :  JenaUUID
JenaUUID.reset ( ) [static] :  void
JenaUUID.setFactory ( UUIDFactory factory ) [static] :  void
JenaUUID.strNil ( ) [static] :  String

cdk-1.4.0.jar, JniInchiAtom.class
package net.sf.jniinchi
JniInchiAtom.JniInchiAtom ( String el )

cdk-1.4.0.jar, JniInchiInputData.class
package net.sf.jniinchi
JniInchiInputData.getErrorMessage ( ) :  String
JniInchiInputData.getInput ( ) :  JniInchiInput
JniInchiInputData.getReturnValue ( ) :  INCHI_RET
JniInchiInputData.JniInchiInputData ( int returnValue, JniInchiInput input, int chiral, String errorMessage )

cdk-1.4.0.jar, JniInchiStructure.class
package net.sf.jniinchi
JniInchiStructure.addAtoms ( JniInchiAtom[ ] atoms ) :  void
JniInchiStructure.addBonds ( JniInchiBond[ ] bonds ) :  void

cdk-1.4.0.jar, JniInchiWrapper.class
package net.sf.jniinchi
JniInchiWrapper.checkInchi ( String inchi, boolean strict ) [static] :  INCHI_STATUS
JniInchiWrapper.checkInchiKey ( String key ) [static] :  INCHI_KEY_STATUS
JniInchiWrapper.getInchiKey ( String inchi ) [static] :  JniInchiOutputKey
JniInchiWrapper.getInputFromAuxInfo ( String auxInfo ) [static] :  JniInchiInputData
JniInchiWrapper.getStdInchi ( JniInchiInput input ) [static] :  JniInchiOutput

cdk-1.4.0.jar, JustBound.class
package com.hp.hpl.jena.graph.query
QueryNode.JustBound.isFrozen ( ) :  boolean
QueryNode.JustBound.match ( Domain d, Node X ) :  boolean
QueryNode.JustBound.matchOrBind ( Domain d, Node x ) :  boolean
QueryNode.JustBound.mustMatch ( ) :  boolean
QueryNode.JustBound.QueryNode.JustBound ( Node n, int index )
QueryNode.JustBound.toString ( ) :  String

cdk-1.4.0.jar, juuid.class
package jena
juuid.exec ( ) :  void
juuid.getCommandName ( ) :  String
juuid.getSummary ( ) :  String
juuid.main ( String[ ] argv ) [static] :  void
juuid.processModulesAndArgs ( ) :  void

cdk-1.4.0.jar, KekuleStructure.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.KekuleStructure.BasicAtomGenerator.KekuleStructure ( )
BasicAtomGenerator.KekuleStructure.getDefault ( ) :  Boolean
BasicAtomGenerator.KekuleStructure.getDefault ( ) :  Object

cdk-1.4.0.jar, LabelContainer.class
package org.openscience.cdk.smsd.helper
LabelContainer.addLabel ( String label ) :  void
LabelContainer.getInstance ( ) [static] :  LabelContainer
LabelContainer.getLabel ( Integer labelID ) :  String
LabelContainer.getLabelID ( String label ) :  Integer
LabelContainer.getSize ( ) :  int
LabelContainer.LabelContainer ( )

cdk-1.4.0.jar, LabelToNodeMap.class
package com.hp.hpl.jena.n3.turtle
LabelToNodeMap.allocNode ( ) :  Node
LabelToNodeMap.asNode ( String label ) :  Node
LabelToNodeMap.clear ( ) :  void
LabelToNodeMap.LabelToNodeMap ( )

cdk-1.4.0.jar, LanguageConsistencyException.class
package com.hp.hpl.jena.ontology
LanguageConsistencyException.LanguageConsistencyException ( String message )

cdk-1.4.0.jar, LanguageTag.class
package com.hp.hpl.jena.rdf.arp.lang
LanguageTag.errorMessage ( ) :  String
LanguageTag.LanguageTag ( String tag )
LanguageTag.tagType ( ) :  int

cdk-1.4.0.jar, LargeMoleculeTest.class
package signature.chemistry
LargeMoleculeTest.addRing ( int atomToAttachTo, int ringSize, Molecule molecule ) :  void
LargeMoleculeTest.buckyballTest ( ) :  void
LargeMoleculeTest.buckyballWithoutMultipleBonds ( ) :  void
LargeMoleculeTest.dodecahedraneTest ( ) :  void
LargeMoleculeTest.drawTrees ( MoleculeQuotientGraph mqg, String directoryPath ) :  void
LargeMoleculeTest.faulonsBuckySignatures ( ) :  void
LargeMoleculeTest.LargeMoleculeTest ( )
LargeMoleculeTest.main ( String[ ] args ) [static] :  void
LargeMoleculeTest.makeChain ( int length ) :  Molecule
LargeMoleculeTest.makeMinimalMultiRing ( int ringCount, int ringSize ) :  Molecule
LargeMoleculeTest.makeTetrakisTriphenylPhosphoranylRhodium ( ) :  Molecule
LargeMoleculeTest.readSigs ( String filename ) :  List
LargeMoleculeTest.readSigs2 ( String filename ) :  List
LargeMoleculeTest.testLongChains ( ) :  void
LargeMoleculeTest.testMinimalMol ( ) :  void
LargeMoleculeTest.ttprTest ( ) :  void

cdk-1.4.0.jar, LateBindingIterator.class
package com.hp.hpl.jena.util.iterator
LateBindingIterator.create ( ) [abstract] :  Iterator
LateBindingIterator.hasNext ( ) :  boolean
LateBindingIterator.LateBindingIterator ( )
LateBindingIterator.next ( ) :  Object
LateBindingIterator.remove ( ) :  void

cdk-1.4.0.jar, LazyIterator.class
package com.hp.hpl.jena.util.iterator
LazyIterator.andThen ( ClosableIterator other ) :  ExtendedIterator
LazyIterator.close ( ) :  void
LazyIterator.create ( ) [abstract] :  ExtendedIterator
LazyIterator.filterDrop ( Filter f ) :  ExtendedIterator
LazyIterator.filterKeep ( Filter f ) :  ExtendedIterator
LazyIterator.hasNext ( ) :  boolean
LazyIterator.LazyIterator ( )
LazyIterator.mapWith ( Map1 map1 ) :  ExtendedIterator
LazyIterator.next ( ) :  Object
LazyIterator.remove ( ) :  void

cdk-1.4.0.jar, LCAIndex.class
package com.hp.hpl.jena.ontology
OntTools.LCAIndex.getLCA ( Resource u, Resource v ) :  Resource
OntTools.LCAIndex.getSet ( Resource r ) :  OntTools.DisjointSet
OntTools.LCAIndex.OntTools.LCAIndex ( )
OntTools.LCAIndex.setLCA ( Resource u, Resource v, Resource lca ) :  void

cdk-1.4.0.jar, LE.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
LE.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
LE.getArgLength ( ) :  int
LE.getName ( ) :  String
LE.LE ( )

cdk-1.4.0.jar, LessThan.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
LessThan.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
LessThan.getArgLength ( ) :  int
LessThan.getName ( ) :  String
LessThan.LessThan ( )

cdk-1.4.0.jar, Ligand.class
package org.openscience.cdk.geometry.cip
Ligand.getAtomContainer ( ) :  IAtomContainer
Ligand.getCentralAtom ( ) :  IAtom
Ligand.getLigandAtom ( ) :  IAtom
Ligand.getVisitedAtoms ( ) :  VisitedAtoms
Ligand.isVisited ( IAtom atom ) :  boolean
Ligand.Ligand ( IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom, IAtom ligandAtom )

cdk-1.4.0.jar, LineElement.class
package org.openscience.cdk.renderer.elements
LineElement.accept ( IRenderingVisitor visitor ) :  void
LineElement.LineElement ( double firstPointX, double firstPointY, double secondPointX, double secondPointY, double width, Color color )

cdk-1.4.0.jar, LineTo.class
package org.openscience.cdk.renderer.elements.path
LineTo.LineTo ( Point2d point )
LineTo.points ( ) :  float[ ]

cdk-1.4.0.jar, LineType.class
package org.openscience.cdk.renderer.elements
LineElement.LineType.count ( ) :  int
LineElement.LineType.valueOf ( String name ) [static] :  LineElement.LineType
LineElement.LineType.values ( ) [static] :  LineElement.LineType[ ]

cdk-1.4.0.jar, LinkedSeq.class
package com.hp.hpl.jena.assembler
ModelExpansion.LinkedSeq.toString ( ) :  String

cdk-1.4.0.jar, ListContains.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListContains.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListContains.getArgLength ( ) :  int
ListContains.getName ( ) :  String
ListContains.ListContains ( )
ListContains.listContains ( Node list, Node element, RuleContext context ) [static] :  boolean

cdk-1.4.0.jar, ListEntry.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListEntry.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListEntry.getArgLength ( ) :  int
ListEntry.getEntry ( Node list, int i, RuleContext context ) [static] :  Node
ListEntry.getName ( ) :  String
ListEntry.ListEntry ( )

cdk-1.4.0.jar, ListEqual.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListEqual.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListEqual.getArgLength ( ) :  int
ListEqual.getName ( ) :  String
ListEqual.ListEqual ( )
ListEqual.listEqual ( Node list1, Node list2, RuleContext context ) [static] :  boolean

cdk-1.4.0.jar, ListIndexException.class
package com.hp.hpl.jena.rdf.model
ListIndexException.ListIndexException ( )
ListIndexException.ListIndexException ( String msg )

cdk-1.4.0.jar, ListLength.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListLength.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListLength.getArgLength ( ) :  int
ListLength.getLength ( Node node, RuleContext context ) [static] :  int
ListLength.getName ( ) :  String
ListLength.ListLength ( )

cdk-1.4.0.jar, ListMapAsObject.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListMapAsObject.getArgLength ( ) :  int
ListMapAsObject.getName ( ) :  String
ListMapAsObject.headAction ( Node[ ] args, int length, RuleContext context ) :  void
ListMapAsObject.ListMapAsObject ( )

cdk-1.4.0.jar, ListMapAsSubject.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListMapAsSubject.getArgLength ( ) :  int
ListMapAsSubject.getName ( ) :  String
ListMapAsSubject.headAction ( Node[ ] args, int length, RuleContext context ) :  void
ListMapAsSubject.ListMapAsSubject ( )

cdk-1.4.0.jar, ListNotContains.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListNotContains.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListNotContains.getArgLength ( ) :  int
ListNotContains.getName ( ) :  String
ListNotContains.ListNotContains ( )

cdk-1.4.0.jar, ListNotEqual.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
ListNotEqual.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
ListNotEqual.getArgLength ( ) :  int
ListNotEqual.getName ( ) :  String
ListNotEqual.ListNotEqual ( )

cdk-1.4.0.jar, Literal.class
package com.hp.hpl.jena.rdf.model
Literal.equals ( Object p1 ) [abstract] :  boolean
Literal.getBoolean ( ) [abstract] :  boolean
Literal.getByte ( ) [abstract] :  byte
Literal.getChar ( ) [abstract] :  char
Literal.getDatatype ( ) [abstract] :  RDFDatatype
Literal.getDatatypeURI ( ) [abstract] :  String
Literal.getDouble ( ) [abstract] :  double
Literal.getFloat ( ) [abstract] :  float
Literal.getInt ( ) [abstract] :  int
Literal.getLanguage ( ) [abstract] :  String
Literal.getLexicalForm ( ) [abstract] :  String
Literal.getLong ( ) [abstract] :  long
Literal.getObject ( ObjectF p1 ) [abstract] :  Object *DEPRECATED*
Literal.getShort ( ) [abstract] :  short
Literal.getString ( ) [abstract] :  String
Literal.getValue ( ) [abstract] :  Object
Literal.isWellFormedXML ( ) [abstract] :  boolean
Literal.sameValueAs ( Literal p1 ) [abstract] :  boolean

cdk-1.4.0.jar, LiteralRequiredException.class
package com.hp.hpl.jena.rdf.model
LiteralRequiredException.LiteralRequiredException ( Node n )
LiteralRequiredException.LiteralRequiredException ( RDFNode n )

cdk-1.4.0.jar, LitTestObj.class
package com.hp.hpl.jena.regression
Regression.LitTestObj.equals ( Object o ) :  boolean
Regression.LitTestObj.hashCode ( ) :  int
Regression.LitTestObj.Regression.LitTestObj ( long l )
Regression.LitTestObj.Regression.LitTestObj ( String s )
Regression.LitTestObj.toString ( ) :  String

cdk-1.4.0.jar, LitTestObjF.class
package com.hp.hpl.jena.regression
Regression.LitTestObjF.createObject ( String s ) :  Object
Regression.LitTestObjF.Regression.LitTestObjF ( )

cdk-1.4.0.jar, LocaleData.class
package com.ibm.icu.util
LocaleData.getDelimiter ( int type ) :  String *DEPRECATED*
LocaleData.getExemplarSet ( int options, int extype ) :  UnicodeSet *DEPRECATED*
LocaleData.getExemplarSet ( ULocale locale, int options ) [static] :  UnicodeSet *DEPRECATED*
LocaleData.getInstance ( ) [static] :  LocaleData *DEPRECATED*
LocaleData.getInstance ( ULocale locale ) [static] :  LocaleData *DEPRECATED*
LocaleData.getMeasurementSystem ( ULocale locale ) [static] :  LocaleData.MeasurementSystem *DEPRECATED*
LocaleData.getNoSubstitute ( ) :  boolean *DEPRECATED*
LocaleData.getPaperSize ( ULocale locale ) [static] :  LocaleData.PaperSize *DEPRECATED*
LocaleData.setNoSubstitute ( boolean setting ) :  void *DEPRECATED*

cdk-1.4.0.jar, LocationAwareLogger.class
package org.slf4j.spi
LocationAwareLogger.log ( Marker p1, String p2, int p3, String p4, Throwable p5 ) [abstract] :  void

cdk-1.4.0.jar, LocationMapper.class
package com.hp.hpl.jena.util
LocationMapper.addAltEntry ( String uri, String alt ) :  void
LocationMapper.addAltPrefix ( String uriPrefix, String altPrefix ) :  void
LocationMapper.altMapping ( String uri ) :  String
LocationMapper.altMapping ( String uri, String otherwise ) :  String
LocationMapper.equals ( Object obj ) :  boolean
LocationMapper.get ( ) [static] :  LocationMapper
LocationMapper.getAltEntry ( String uri ) :  String
LocationMapper.getAltPrefix ( String uriPrefix ) :  String
LocationMapper.hashCode ( ) :  int
LocationMapper.listAltEntries ( ) :  Iterator
LocationMapper.listAltPrefixes ( ) :  Iterator
LocationMapper.LocationMapper ( )
LocationMapper.LocationMapper ( LocationMapper locMapper )
LocationMapper.LocationMapper ( Model model )
LocationMapper.LocationMapper ( String config )
LocationMapper.makeGlobal ( ) [static] :  LocationMapper
LocationMapper.processConfig ( Model m ) :  void
LocationMapper.removeAltEntry ( String uri ) :  void
LocationMapper.removeAltPrefix ( String uriPrefix ) :  void
LocationMapper.setGlobalLocationMapper ( LocationMapper globalLocationMapper ) [static] :  void
LocationMapper.toModel ( ) :  Model
LocationMapper.toModel ( Model model ) :  void
LocationMapper.toString ( ) :  String

cdk-1.4.0.jar, LocationMapperAssembler.class
package com.hp.hpl.jena.assembler.assemblers
LocationMapperAssembler.LocationMapperAssembler ( )
LocationMapperAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, LocationMappingVocab.class
package com.hp.hpl.jena.vocabulary
LocationMappingVocab.getURI ( ) [static] :  String
LocationMappingVocab.LocationMappingVocab ( )

cdk-1.4.0.jar, Locator.class
package com.hp.hpl.jena.util
Locator.getName ( ) [abstract] :  String
Locator.open ( String p1 ) [abstract] :  TypedStream

cdk-1.4.0.jar, LocatorClassLoader.class
package com.hp.hpl.jena.util
LocatorClassLoader.equals ( Object other ) :  boolean
LocatorClassLoader.getName ( ) :  String
LocatorClassLoader.hashCode ( ) :  int
LocatorClassLoader.LocatorClassLoader ( ClassLoader _classLoader )
LocatorClassLoader.open ( String filenameOrURI ) :  TypedStream

cdk-1.4.0.jar, LocatorFile.class
package com.hp.hpl.jena.util
LocatorFile.equals ( Object other ) :  boolean
LocatorFile.exists ( String filenameOrURI ) :  boolean
LocatorFile.getName ( ) :  String
LocatorFile.hashCode ( ) :  int
LocatorFile.LocatorFile ( String dir )
LocatorFile.open ( String filenameOrURI ) :  TypedStream

cdk-1.4.0.jar, LocatorURL.class
package com.hp.hpl.jena.util
LocatorURL.equals ( Object other ) :  boolean
LocatorURL.getName ( ) :  String
LocatorURL.hashCode ( ) :  int
LocatorURL.LocatorURL ( )
LocatorURL.open ( String filenameOrURI ) :  TypedStream

cdk-1.4.0.jar, Lock.class
package com.hp.hpl.jena.shared
Lock.enterCriticalSection ( boolean p1 ) [abstract] :  void
Lock.leaveCriticalSection ( ) [abstract] :  void

cdk-1.4.0.jar, LockMRSW.class
package com.hp.hpl.jena.shared
LockMRSW.enterCriticalSection ( boolean readLockRequested ) :  void
LockMRSW.leaveCriticalSection ( ) :  void
LockMRSW.LockMRSW ( )

cdk-1.4.0.jar, LockMutex.class
package com.hp.hpl.jena.shared
LockMutex.enterCriticalSection ( boolean readLockRequested ) :  void
LockMutex.leaveCriticalSection ( ) :  void
LockMutex.LockMutex ( )

cdk-1.4.0.jar, LockNone.class
package com.hp.hpl.jena.shared
LockNone.enterCriticalSection ( boolean readLockRequested ) :  void
LockNone.leaveCriticalSection ( ) :  void
LockNone.LockNone ( )

cdk-1.4.0.jar, Log.class
package org.apache.commons.logging
Log.debug ( Object p1 ) [abstract] :  void
Log.debug ( Object p1, Throwable p2 ) [abstract] :  void
Log.error ( Object p1 ) [abstract] :  void
Log.error ( Object p1, Throwable p2 ) [abstract] :  void
Log.fatal ( Object p1 ) [abstract] :  void
Log.fatal ( Object p1, Throwable p2 ) [abstract] :  void
Log.info ( Object p1 ) [abstract] :  void
Log.info ( Object p1, Throwable p2 ) [abstract] :  void
Log.isDebugEnabled ( ) [abstract] :  boolean
Log.isErrorEnabled ( ) [abstract] :  boolean
Log.isFatalEnabled ( ) [abstract] :  boolean
Log.isInfoEnabled ( ) [abstract] :  boolean
Log.isTraceEnabled ( ) [abstract] :  boolean
Log.isWarnEnabled ( ) [abstract] :  boolean
Log.trace ( Object p1 ) [abstract] :  void
Log.trace ( Object p1, Throwable p2 ) [abstract] :  void
Log.warn ( Object p1 ) [abstract] :  void
Log.warn ( Object p1, Throwable p2 ) [abstract] :  void

cdk-1.4.0.jar, LogConfigurationException.class
package org.apache.commons.logging
LogConfigurationException.getCause ( ) :  Throwable
LogConfigurationException.LogConfigurationException ( )
LogConfigurationException.LogConfigurationException ( String message )
LogConfigurationException.LogConfigurationException ( String message, Throwable cause )
LogConfigurationException.LogConfigurationException ( Throwable cause )

cdk-1.4.0.jar, LogFactory.class
package org.apache.commons.logging
LogFactory.createFactory ( String factoryClass, ClassLoader classLoader ) [static] :  Object
LogFactory.directGetContextClassLoader ( ) [static] :  ClassLoader
LogFactory.getAttribute ( String p1 ) [abstract] :  Object
LogFactory.getAttributeNames ( ) [abstract] :  String[ ]
LogFactory.getClassLoader ( Class clazz ) [static] :  ClassLoader
LogFactory.getContextClassLoader ( ) [static] :  ClassLoader
LogFactory.getFactory ( ) [static] :  LogFactory
LogFactory.getInstance ( Class p1 ) [abstract] :  Log
LogFactory.getInstance ( String p1 ) [abstract] :  Log
LogFactory.getLog ( Class clazz ) [static] :  Log
LogFactory.getLog ( String name ) [static] :  Log
LogFactory.isDiagnosticsEnabled ( ) [static] :  boolean
LogFactory.LogFactory ( )
LogFactory.logRawDiagnostic ( String msg ) [static] :  void
LogFactory.newFactory ( String factoryClass, ClassLoader classLoader ) [static] :  LogFactory
LogFactory.newFactory ( String factoryClass, ClassLoader classLoader, ClassLoader contextClassLoader ) [static] :  LogFactory
LogFactory.objectId ( Object o ) [static] :  String
LogFactory.release ( ) [abstract] :  void
LogFactory.release ( ClassLoader classLoader ) [static] :  void
LogFactory.releaseAll ( ) [static] :  void
LogFactory.removeAttribute ( String p1 ) [abstract] :  void
LogFactory.setAttribute ( String p1, Object p2 ) [abstract] :  void

cdk-1.4.0.jar, Logger.class
package org.slf4j
Logger.debug ( Marker p1, String p2 ) [abstract] :  void
Logger.debug ( Marker p1, String p2, Object p3 ) [abstract] :  void
Logger.debug ( Marker p1, String p2, Object p3, Object p4 ) [abstract] :  void
Logger.debug ( Marker p1, String p2, Object[ ] p3 ) [abstract] :  void
Logger.debug ( Marker p1, String p2, Throwable p3 ) [abstract] :  void
Logger.debug ( String p1 ) [abstract] :  void
Logger.debug ( String p1, Object p2 ) [abstract] :  void
Logger.debug ( String p1, Object p2, Object p3 ) [abstract] :  void
Logger.debug ( String p1, Object[ ] p2 ) [abstract] :  void
Logger.debug ( String p1, Throwable p2 ) [abstract] :  void
Logger.error ( Marker p1, String p2 ) [abstract] :  void
Logger.error ( Marker p1, String p2, Object p3 ) [abstract] :  void
Logger.error ( Marker p1, String p2, Object p3, Object p4 ) [abstract] :  void
Logger.error ( Marker p1, String p2, Object[ ] p3 ) [abstract] :  void
Logger.error ( Marker p1, String p2, Throwable p3 ) [abstract] :  void
Logger.error ( String p1 ) [abstract] :  void
Logger.error ( String p1, Object p2 ) [abstract] :  void
Logger.error ( String p1, Object p2, Object p3 ) [abstract] :  void
Logger.error ( String p1, Object[ ] p2 ) [abstract] :  void
Logger.error ( String p1, Throwable p2 ) [abstract] :  void
Logger.getName ( ) [abstract] :  String
Logger.info ( Marker p1, String p2 ) [abstract] :  void
Logger.info ( Marker p1, String p2, Object p3 ) [abstract] :  void
Logger.info ( Marker p1, String p2, Object p3, Object p4 ) [abstract] :  void
Logger.info ( Marker p1, String p2, Object[ ] p3 ) [abstract] :  void
Logger.info ( Marker p1, String p2, Throwable p3 ) [abstract] :  void
Logger.info ( String p1 ) [abstract] :  void
Logger.info ( String p1, Object p2 ) [abstract] :  void
Logger.info ( String p1, Object p2, Object p3 ) [abstract] :  void
Logger.info ( String p1, Object[ ] p2 ) [abstract] :  void
Logger.info ( String p1, Throwable p2 ) [abstract] :  void
Logger.isDebugEnabled ( ) [abstract] :  boolean
Logger.isDebugEnabled ( Marker p1 ) [abstract] :  boolean
Logger.isErrorEnabled ( ) [abstract] :  boolean
Logger.isErrorEnabled ( Marker p1 ) [abstract] :  boolean
Logger.isInfoEnabled ( ) [abstract] :  boolean
Logger.isInfoEnabled ( Marker p1 ) [abstract] :  boolean
Logger.isTraceEnabled ( ) [abstract] :  boolean
Logger.isTraceEnabled ( Marker p1 ) [abstract] :  boolean
Logger.isWarnEnabled ( ) [abstract] :  boolean
Logger.isWarnEnabled ( Marker p1 ) [abstract] :  boolean
Logger.trace ( Marker p1, String p2 ) [abstract] :  void
Logger.trace ( Marker p1, String p2, Object p3 ) [abstract] :  void
Logger.trace ( Marker p1, String p2, Object p3, Object p4 ) [abstract] :  void
Logger.trace ( Marker p1, String p2, Object[ ] p3 ) [abstract] :  void
Logger.trace ( Marker p1, String p2, Throwable p3 ) [abstract] :  void
Logger.trace ( String p1 ) [abstract] :  void
Logger.trace ( String p1, Object p2 ) [abstract] :  void
Logger.trace ( String p1, Object p2, Object p3 ) [abstract] :  void
Logger.trace ( String p1, Object[ ] p2 ) [abstract] :  void
Logger.trace ( String p1, Throwable p2 ) [abstract] :  void
Logger.warn ( Marker p1, String p2 ) [abstract] :  void
Logger.warn ( Marker p1, String p2, Object p3 ) [abstract] :  void
Logger.warn ( Marker p1, String p2, Object p3, Object p4 ) [abstract] :  void
Logger.warn ( Marker p1, String p2, Object[ ] p3 ) [abstract] :  void
Logger.warn ( Marker p1, String p2, Throwable p3 ) [abstract] :  void
Logger.warn ( String p1 ) [abstract] :  void
Logger.warn ( String p1, Object p2 ) [abstract] :  void
Logger.warn ( String p1, Object p2, Object p3 ) [abstract] :  void
Logger.warn ( String p1, Object[ ] p2 ) [abstract] :  void
Logger.warn ( String p1, Throwable p2 ) [abstract] :  void

cdk-1.4.0.jar, LoggerFactory.class
package org.slf4j
LoggerFactory.getILoggerFactory ( ) [static] :  ILoggerFactory
LoggerFactory.getLogger ( Class clazz ) [static] :  Logger
LoggerFactory.getLogger ( String name ) [static] :  Logger

cdk-1.4.0.jar, LoggerFactoryBinder.class
package org.slf4j.spi
LoggerFactoryBinder.getLoggerFactory ( ) [abstract] :  ILoggerFactory
LoggerFactoryBinder.getLoggerFactoryClassStr ( ) [abstract] :  String

cdk-1.4.0.jar, LoggingTool.class
package org.openscience.cdk.tools
LoggingTool.create ( Class sourceClass ) [static] :  ILoggingTool
LoggingTool.debug ( Object object, Object[ ] objects ) :  void
LoggingTool.error ( Object object, Object[ ] objects ) :  void
LoggingTool.info ( Object object, Object[ ] objects ) :  void
LoggingTool.warn ( Object object, Object[ ] objects ) :  void

cdk-1.4.0.jar, LoggingToolFactory.class
package org.openscience.cdk.tools
LoggingToolFactory.createLoggingTool ( Class sourceClass ) [static] :  ILoggingTool
LoggingToolFactory.getLoggingToolClass ( ) [static] :  Class
LoggingToolFactory.LoggingToolFactory ( )
LoggingToolFactory.setLoggingToolClass ( Class loggingTool ) [static] :  void

cdk-1.4.0.jar, LogSource.class
package org.apache.commons.logging
LogSource.getInstance ( Class clazz ) [static] :  Log
LogSource.getInstance ( String name ) [static] :  Log
LogSource.getLogNames ( ) [static] :  String[ ]
LogSource.makeNewLogInstance ( String name ) [static] :  Log
LogSource.setLogImplementation ( Class logclass ) [static] :  void
LogSource.setLogImplementation ( String classname ) [static] :  void

cdk-1.4.0.jar, LookingForRDF.class
package com.hp.hpl.jena.rdf.arp.states
LookingForRDF.characters ( char[ ] ch, int start, int length ) :  void
LookingForRDF.LookingForRDF ( FrameI s, AttributeLexer x )
LookingForRDF.LookingForRDF ( XMLHandler s, AbsXMLContext x )
LookingForRDF.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI

cdk-1.4.0.jar, LPBackwardRuleInfGraph.class
package com.hp.hpl.jena.reasoner.rulesys
LPBackwardRuleInfGraph.extractAxioms ( ) :  void
LPBackwardRuleInfGraph.find ( TriplePattern pattern ) :  ExtendedIterator
LPBackwardRuleInfGraph.findDataMatches ( TriplePattern pattern ) :  ExtendedIterator
LPBackwardRuleInfGraph.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
LPBackwardRuleInfGraph.getDerivation ( Triple t ) :  Iterator
LPBackwardRuleInfGraph.getSchemaGraph ( ) :  Graph
LPBackwardRuleInfGraph.getTemp ( Node instance, Node prop, Node pclass ) :  Node
LPBackwardRuleInfGraph.graphBaseFind ( Node subject, Node property, Node object ) :  ExtendedIterator
LPBackwardRuleInfGraph.isTraceOn ( ) :  boolean
LPBackwardRuleInfGraph.logDerivation ( Triple t, Derivation derivation ) :  void
LPBackwardRuleInfGraph.LPBackwardRuleInfGraph ( Reasoner reasoner, LPRuleStore ruleStore, Graph data, Graph schema )
LPBackwardRuleInfGraph.performAdd ( Triple t ) :  void
LPBackwardRuleInfGraph.performDelete ( Triple t ) :  void
LPBackwardRuleInfGraph.prepare ( ) :  void
LPBackwardRuleInfGraph.processBuiltin ( ClauseEntry clause, Rule rule, BindingEnvironment env ) :  boolean
LPBackwardRuleInfGraph.rebind ( ) :  void
LPBackwardRuleInfGraph.rebind ( Graph data ) :  void
LPBackwardRuleInfGraph.reset ( ) :  void
LPBackwardRuleInfGraph.setDerivationLogging ( boolean recordDerivations ) :  void
LPBackwardRuleInfGraph.setTabled ( Node predicate ) :  void
LPBackwardRuleInfGraph.setTraceOn ( boolean state ) :  void
LPBackwardRuleInfGraph.silentAdd ( Triple t ) :  void

cdk-1.4.0.jar, LPBackwardRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
LPBackwardRuleReasoner.addDescription ( Model configSpec, Resource base ) :  void
LPBackwardRuleReasoner.bind ( Graph data ) :  InfGraph
LPBackwardRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
LPBackwardRuleReasoner.bindSchema ( Model tbox ) :  Reasoner
LPBackwardRuleReasoner.getGraphCapabilities ( ) :  Capabilities
LPBackwardRuleReasoner.getReasonerCapabilities ( ) :  Model
LPBackwardRuleReasoner.getRules ( ) :  List
LPBackwardRuleReasoner.LPBackwardRuleReasoner ( List rules )
LPBackwardRuleReasoner.LPBackwardRuleReasoner ( List rules, ReasonerFactory factory )
LPBackwardRuleReasoner.LPBackwardRuleReasoner ( LPBackwardRuleReasoner parent, Graph schemaGraph )
LPBackwardRuleReasoner.setDerivationLogging ( boolean logOn ) :  void
LPBackwardRuleReasoner.setParameter ( Property parameter, Object value ) :  void
LPBackwardRuleReasoner.setTraceOn ( boolean state ) :  void
LPBackwardRuleReasoner.supportsProperty ( Property property ) :  boolean
LPBackwardRuleReasoner.tablePredicate ( Node predicate ) :  void

cdk-1.4.0.jar, MakeInstance.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
MakeInstance.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
MakeInstance.getName ( ) :  String
MakeInstance.MakeInstance ( )

cdk-1.4.0.jar, MakeTemp.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
MakeTemp.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
MakeTemp.getName ( ) :  String
MakeTemp.headAction ( Node[ ] args, RuleContext context ) :  void
MakeTemp.MakeTemp ( )

cdk-1.4.0.jar, MalformedIDNException.class
package com.hp.hpl.jena.iri
MalformedIDNException.MalformedIDNException ( StringPrepParseException e )

cdk-1.4.0.jar, Manifest.class
package com.hp.hpl.jena.util.junit
Manifest.apply ( ManifestItemHandler gen ) :  void
Manifest.getName ( ) :  String
Manifest.includedManifests ( ) :  Iterator
Manifest.Manifest ( String fn )

cdk-1.4.0.jar, ManifestItemHandler.class
package com.hp.hpl.jena.util.junit
ManifestItemHandler.processManifestItem ( Resource p1, Resource p2, String p3, Resource p4, Resource p5 ) [abstract] :  boolean

cdk-1.4.0.jar, MannholdLogPDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
MannholdLogPDescriptor.calculate ( IAtomContainer atomContainer ) :  DescriptorValue
MannholdLogPDescriptor.getDescriptorNames ( ) :  String[ ]
MannholdLogPDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
MannholdLogPDescriptor.getParameterNames ( ) :  String[ ]
MannholdLogPDescriptor.getParameters ( ) :  Object[ ]
MannholdLogPDescriptor.getParameterType ( String name ) :  Object
MannholdLogPDescriptor.getSpecification ( ) :  DescriptorSpecification
MannholdLogPDescriptor.MannholdLogPDescriptor ( )
MannholdLogPDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.0.jar, Map1.class
package com.hp.hpl.jena.util.iterator
Map1.map1 ( Object p1 ) [abstract] :  Object

cdk-1.4.0.jar, Map1Iterator.class
package com.hp.hpl.jena.util.iterator
Map1Iterator.hasNext ( ) :  boolean
Map1Iterator.Map1Iterator ( Map1 map, Iterator base )
Map1Iterator.next ( ) :  Object
Map1Iterator.remove ( ) :  void

cdk-1.4.0.jar, MapFilter.class
package com.hp.hpl.jena.util.iterator
MapFilter.accept ( Object p1 ) [abstract] :  Object

cdk-1.4.0.jar, MapFilterIterator.class
package com.hp.hpl.jena.util.iterator
MapFilterIterator.close ( ) :  void
MapFilterIterator.hasNext ( ) :  boolean
MapFilterIterator.MapFilterIterator ( MapFilter fl, ExtendedIterator e )
MapFilterIterator.next ( ) :  Object
MapFilterIterator.remove ( ) :  void

cdk-1.4.0.jar, MapObjectToContent.class
package com.hp.hpl.jena.assembler.assemblers
AssemblerBase.MapObjectToContent.AssemblerBase.MapObjectToContent ( Assembler a )
AssemblerBase.MapObjectToContent.map1 ( Object x0 ) :  Object
AssemblerBase.MapObjectToContent.map1 ( Statement o ) :  Content

cdk-1.4.0.jar, Mapping.class
package com.hp.hpl.jena.graph.query
Mapping.hasBound ( Node v ) :  boolean
Mapping.indexOf ( Node v ) :  int
Mapping.indexOf ( String name ) :  int
Mapping.lookUp ( Node v ) :  int
Mapping.Mapping ( Node[ ] preDeclare )
Mapping.newIndex ( Node v ) :  int
Mapping.size ( ) :  int
Mapping.toString ( ) :  String

cdk-1.4.0.jar, Margin.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.Margin.BasicSceneGenerator.Margin ( )
BasicSceneGenerator.Margin.getDefault ( ) :  Double
BasicSceneGenerator.Margin.getDefault ( ) :  Object

cdk-1.4.0.jar, Marker.class
package org.slf4j
Marker.add ( Marker p1 ) [abstract] :  void
Marker.contains ( Marker p1 ) [abstract] :  boolean
Marker.contains ( String p1 ) [abstract] :  boolean
Marker.equals ( Object p1 ) [abstract] :  boolean
Marker.getName ( ) [abstract] :  String
Marker.hasChildren ( ) [abstract] :  boolean *DEPRECATED*
Marker.hashCode ( ) [abstract] :  int
Marker.hasReferences ( ) [abstract] :  boolean
Marker.iterator ( ) [abstract] :  Iterator
Marker.remove ( Marker p1 ) [abstract] :  boolean

cdk-1.4.0.jar, MarkerFactory.class
package org.slf4j
MarkerFactory.getDetachedMarker ( String name ) [static] :  Marker
MarkerFactory.getIMarkerFactory ( ) [static] :  IMarkerFactory
MarkerFactory.getMarker ( String name ) [static] :  Marker

cdk-1.4.0.jar, MarkerFactoryBinder.class
package org.slf4j.spi
MarkerFactoryBinder.getMarkerFactory ( ) [abstract] :  IMarkerFactory
MarkerFactoryBinder.getMarkerFactoryClassStr ( ) [abstract] :  String

cdk-1.4.0.jar, MarkerIgnoringBase.class
package org.slf4j.helpers
MarkerIgnoringBase.debug ( Marker marker, String format, Object arg ) :  void
MarkerIgnoringBase.debug ( Marker marker, String format, Object arg1, Object arg2 ) :  void
MarkerIgnoringBase.debug ( Marker marker, String format, Object[ ] argArray ) :  void
MarkerIgnoringBase.debug ( Marker marker, String msg ) :  void
MarkerIgnoringBase.debug ( Marker marker, String msg, Throwable t ) :  void
MarkerIgnoringBase.error ( Marker marker, String format, Object arg ) :  void
MarkerIgnoringBase.error ( Marker marker, String format, Object arg1, Object arg2 ) :  void
MarkerIgnoringBase.error ( Marker marker, String format, Object[ ] argArray ) :  void
MarkerIgnoringBase.error ( Marker marker, String msg ) :  void
MarkerIgnoringBase.error ( Marker marker, String msg, Throwable t ) :  void
MarkerIgnoringBase.info ( Marker marker, String format, Object arg ) :  void
MarkerIgnoringBase.info ( Marker marker, String format, Object arg1, Object arg2 ) :  void
MarkerIgnoringBase.info ( Marker marker, String format, Object[ ] argArray ) :  void
MarkerIgnoringBase.info ( Marker marker, String msg ) :  void
MarkerIgnoringBase.info ( Marker marker, String msg, Throwable t ) :  void
MarkerIgnoringBase.isDebugEnabled ( Marker marker ) :  boolean
MarkerIgnoringBase.isErrorEnabled ( Marker marker ) :  boolean
MarkerIgnoringBase.isInfoEnabled ( Marker marker ) :  boolean
MarkerIgnoringBase.isTraceEnabled ( Marker marker ) :  boolean
MarkerIgnoringBase.isWarnEnabled ( Marker marker ) :  boolean
MarkerIgnoringBase.MarkerIgnoringBase ( )
MarkerIgnoringBase.toString ( ) :  String
MarkerIgnoringBase.trace ( Marker marker, String format, Object arg ) :  void
MarkerIgnoringBase.trace ( Marker marker, String format, Object arg1, Object arg2 ) :  void
MarkerIgnoringBase.trace ( Marker marker, String format, Object[ ] argArray ) :  void
MarkerIgnoringBase.trace ( Marker marker, String msg ) :  void
MarkerIgnoringBase.trace ( Marker marker, String msg, Throwable t ) :  void
MarkerIgnoringBase.warn ( Marker marker, String format, Object arg ) :  void
MarkerIgnoringBase.warn ( Marker marker, String format, Object arg1, Object arg2 ) :  void
MarkerIgnoringBase.warn ( Marker marker, String format, Object[ ] argArray ) :  void
MarkerIgnoringBase.warn ( Marker marker, String msg ) :  void
MarkerIgnoringBase.warn ( Marker marker, String msg, Throwable t ) :  void

cdk-1.4.0.jar, Match.class
package org.openscience.cdk.smsd.algorithm.vflib.map
Match.getQueryNode ( ) :  INode
Match.getTargetAtom ( ) :  IAtom
Match.Match ( INode query, IAtom target )

cdk-1.4.0.jar, Matcher.class
package com.hp.hpl.jena.graph.query
Matcher.match ( Domain p1, Triple p2 ) [abstract] :  boolean
Matcher.Matcher ( )

cdk-1.4.0.jar, MatchOrBind.class
package com.hp.hpl.jena.mem
MatchOrBind.createPO ( ProcessedTriple Q ) [static] :  MatchOrBind
MatchOrBind.createSP ( ProcessedTriple Q ) [static] :  MatchOrBind
MatchOrBind.matches ( Triple p1 ) [abstract] :  boolean
MatchOrBind.MatchOrBind ( )
MatchOrBind.reset ( Domain p1 ) [abstract] :  MatchOrBind

cdk-1.4.0.jar, MathContext.class
package com.ibm.icu.math
MathContext.getDigits ( ) :  int
MathContext.getForm ( ) :  int
MathContext.getLostDigits ( ) :  boolean
MathContext.getRoundingMode ( ) :  int
MathContext.MathContext ( int setdigits )
MathContext.MathContext ( int setdigits, int setform )
MathContext.MathContext ( int setdigits, int setform, boolean setlostdigits )
MathContext.MathContext ( int setdigits, int setform, boolean setlostdigits, int setroundingmode )
MathContext.toString ( ) :  String

cdk-1.4.0.jar, Matrix.class
package org.openscience.cdk.math
Matrix.add ( Matrix b ) :  Matrix
Matrix.contraction ( ) :  double
Matrix.diagonalize ( int nrot ) :  Matrix
Matrix.duplicate ( ) :  Matrix
Matrix.elimination ( Matrix matrix, Vector vector ) [static] :  Vector
Matrix.getColumns ( ) :  int
Matrix.getRows ( ) :  int
Matrix.getVectorFromColumn ( int index ) :  Vector
Matrix.getVectorFromDiagonal ( ) :  Vector
Matrix.getVectorFromRow ( int index ) :  Vector
Matrix.Matrix ( double[ ][ ] array )
Matrix.Matrix ( int rows, int columns )
Matrix.mul ( double a ) :  Matrix
Matrix.mul ( Matrix b ) :  Matrix
Matrix.mul ( Vector a ) :  Vector
Matrix.normalize ( Matrix S ) :  Matrix
Matrix.orthonormalize ( Matrix S ) :  Matrix
Matrix.similar ( Matrix U ) :  Matrix
Matrix.sub ( Matrix b ) :  Matrix
Matrix.toString ( ) :  String
Matrix.transpose ( ) :  Matrix

cdk-1.4.0.jar, Max.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Max.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Max.getArgLength ( ) :  int
Max.getName ( ) :  String
Max.Max ( )

cdk-1.4.0.jar, MaxCardinalityQRestriction.class
package com.hp.hpl.jena.ontology
MaxCardinalityQRestriction.getMaxCardinalityQ ( ) [abstract] :  int
MaxCardinalityQRestriction.hasMaxCardinalityQ ( int p1 ) [abstract] :  boolean
MaxCardinalityQRestriction.removeMaxCardinalityQ ( int p1 ) [abstract] :  void
MaxCardinalityQRestriction.setMaxCardinalityQ ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, MaxCardinalityRestriction.class
package com.hp.hpl.jena.ontology
MaxCardinalityRestriction.getMaxCardinality ( ) [abstract] :  int
MaxCardinalityRestriction.hasMaxCardinality ( int p1 ) [abstract] :  boolean
MaxCardinalityRestriction.removeMaxCardinality ( int p1 ) [abstract] :  void
MaxCardinalityRestriction.setMaxCardinality ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, McGregor.class
package org.openscience.cdk.smsd.algorithm.mcgregor
McGregor.getMappings ( ) :  List
McGregor.getMCSSize ( ) :  int
McGregor.isNewMatrix ( ) :  boolean
McGregor.McGregor ( IAtomContainer source, IAtomContainer target, List _mappings, boolean shouldMatchBonds )
McGregor.McGregor ( IQueryAtomContainer source, IAtomContainer target, List _mappings )
McGregor.setNewMatrix ( boolean newMatrix ) :  void
McGregor.startMcGregorIteration ( int largestMappingSize, List clique_vector, List comp_graph_nodes ) :  void
McGregor.startMcGregorIteration ( int largestMappingSize, Map present_Mapping ) :  void

cdk-1.4.0.jar, McGregorChecks.class
package org.openscience.cdk.smsd.algorithm.mcgregor
McGregorChecks.case1 ( int G1_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4 ) [static] :  boolean
McGregorChecks.case2 ( int G2_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4 ) [static] :  boolean
McGregorChecks.case3 ( int G1_atom, int G3_atom, int G2_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4 ) [static] :  boolean
McGregorChecks.case4 ( int G1_atom, int G2_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4 ) [static] :  boolean
McGregorChecks.cases ( int G1_atom, int G2_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4 ) [static] :  boolean
McGregorChecks.changeCharBonds ( int corresponding_atom, String new_symbol, int neighbor_bondnum, IAtomContainer atomContainer, List c_bond_neighbors ) [static] :  int
McGregorChecks.changeCharBonds ( int corresponding_atom, String new_symbol, int neighbor_bondnum, List i_bond_neighbors, List c_bond_neighbors ) [static] :  int
McGregorChecks.countArcsLeft ( List TEMPMARCS, int neighborBondNumA, int neighborBondNumB ) [static] :  int
McGregorChecks.generateCSetCopy ( int bond_number, List c_set ) [static] :  List
McGregorChecks.generateCTabCopy ( IAtomContainer atomContainer ) [static] :  List
McGregorChecks.isAtomMatch ( String G1A, String G2A, String G1B, String G2B ) [static] :  boolean
McGregorChecks.isFurtherMappingPossible ( IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List i_bond_neighbor_atoms_A, List i_bond_neighbor_atoms_B, List cBondNeighborsA, List cBondNeighborsB, boolean shouldMatchBonds ) [static] :  boolean
McGregorChecks.isMatchFeasible ( IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds ) [static] :  boolean
McGregorChecks.McGregorChecks ( )
McGregorChecks.removeRecurringMappings ( List atom_mapping ) [static] :  List
McGregorChecks.removeRedundantArcs ( int row, int column, List MARCS, McgregorHelper mcGregorHelper ) [static] :  void
McGregorChecks.removeTreeStructure ( BinaryTree cur_struc ) [static] :  int
McGregorChecks.searchCorrespondingAtom ( int mappedAtomsSize, int atomFromOtherMolecule, int molecule, List mapped_atoms_org ) [static] :  int
McGregorChecks.setArcs ( IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List i_bond_neighbor_atoms_A, List i_bond_neighbor_atoms_B, List cBondNeighborsA, List cBondNeighborsB, List modifiedARCS, boolean shouldMatchBonds ) [static] :  List

cdk-1.4.0.jar, McgregorHelper.class
package org.openscience.cdk.smsd.algorithm.mcgregor
McgregorHelper.getcBondNeighborsA ( ) :  List
McgregorHelper.getcBondNeighborsB ( ) :  List
McgregorHelper.getCBondSetA ( ) :  List
McgregorHelper.getCBondSetB ( ) :  List
McgregorHelper.getiBondNeighborAtomsA ( ) :  List
McgregorHelper.getiBondNeighborAtomsB ( ) :  List
McgregorHelper.getIBondSetA ( ) :  List
McgregorHelper.getIBondSetB ( ) :  List
McgregorHelper.getMappedAtomCount ( ) :  int
McgregorHelper.getMappedAtomsOrg ( ) :  List
McgregorHelper.getNeighborBondNumA ( ) :  int
McgregorHelper.getNeighborBondNumB ( ) :  int
McgregorHelper.getSetNumA ( ) :  int
McgregorHelper.isMappingCheckFlag ( ) :  boolean
McgregorHelper.McgregorHelper ( boolean mappingCheckFlag, int mappedAtomCount, List mappedAtomsOrg, int neighborBondNumA, int neighborBondNumB, List iBondNeighborAtomsA, List iBondNeighborAtomsB, List cBondNeighborsA, List cBondNeighborsB, int setNumA, int setNumB, List i_bond_setA, List i_bond_setB, List c_bond_setA, List c_bond_setB )

cdk-1.4.0.jar, MCSPlus.class
package org.openscience.cdk.smsd.algorithm.mcsplus
MCSPlus.getOverlaps ( IAtomContainer ac1, IAtomContainer ac2, boolean shouldMatchBonds ) :  List
MCSPlus.getTimeManager ( ) [static] :  TimeManager
MCSPlus.getTimeout ( ) [static] :  double
MCSPlus.isTimeOut ( ) [static] :  boolean
MCSPlus.MCSPlus ( )
MCSPlus.setTimeManager ( TimeManager aTimeManager ) [static] :  void

cdk-1.4.0.jar, MCSPlusHandler.class
package org.openscience.cdk.smsd.algorithm.mcsplus
MCSPlusHandler.getAllAtomMapping ( ) :  List
MCSPlusHandler.getAllMapping ( ) :  List
MCSPlusHandler.getFirstAtomMapping ( ) :  Map
MCSPlusHandler.getFirstMapping ( ) :  Map
MCSPlusHandler.MCSPlusHandler ( )
MCSPlusHandler.searchMCS ( boolean shouldMatchBonds ) :  void
MCSPlusHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
MCSPlusHandler.set ( MolHandler source, MolHandler target ) :  void

cdk-1.4.0.jar, MDC.class
package org.slf4j
MDC.clear ( ) [static] :  void
MDC.get ( String key ) [static] :  String
MDC.getCopyOfContextMap ( ) [static] :  Map
MDC.getMDCAdapter ( ) [static] :  MDCAdapter
MDC.put ( String key, String val ) [static] :  void
MDC.remove ( String key ) [static] :  void
MDC.setContextMap ( Map contextMap ) [static] :  void

cdk-1.4.0.jar, MDCAdapter.class
package org.slf4j.spi
MDCAdapter.clear ( ) [abstract] :  void
MDCAdapter.get ( String p1 ) [abstract] :  String
MDCAdapter.getCopyOfContextMap ( ) [abstract] :  Map
MDCAdapter.put ( String p1, String p2 ) [abstract] :  void
MDCAdapter.remove ( String p1 ) [abstract] :  void
MDCAdapter.setContextMap ( Map p1 ) [abstract] :  void

cdk-1.4.0.jar, MDLV2000Reader.class
package org.openscience.cdk.io
MDLV2000Reader.getAtomsByLinePosition ( ) :  List

cdk-1.4.0.jar, MDLV2000Writer.class
package org.openscience.cdk.io
MDLV2000Writer.accepts ( Class classObject ) :  boolean
MDLV2000Writer.close ( ) :  void
MDLV2000Writer.customizeJob ( ) :  void
MDLV2000Writer.formatMDLFloat ( float fl ) [static] :  String
MDLV2000Writer.formatMDLInt ( int i, int l ) [static] :  String
MDLV2000Writer.formatMDLString ( String s, int le ) [static] :  String
MDLV2000Writer.getFormat ( ) :  IResourceFormat
MDLV2000Writer.getIOSettings ( ) :  IOSetting[ ]
MDLV2000Writer.MDLV2000Writer ( )
MDLV2000Writer.MDLV2000Writer ( OutputStream output )
MDLV2000Writer.MDLV2000Writer ( Writer out )
MDLV2000Writer.setWriter ( OutputStream output ) :  void
MDLV2000Writer.setWriter ( Writer out ) :  void
MDLV2000Writer.write ( IChemObject object ) :  void
MDLV2000Writer.writeMolecule ( IAtomContainer container ) :  void

cdk-1.4.0.jar, Measure.class
package com.ibm.icu.util
Measure.equals ( Object obj ) :  boolean *DEPRECATED*
Measure.getNumber ( ) :  Number *DEPRECATED*
Measure.getUnit ( ) :  MeasureUnit *DEPRECATED*
Measure.hashCode ( ) :  int *DEPRECATED*
Measure.Measure ( Number number, MeasureUnit unit ) *DEPRECATED*
Measure.toString ( ) :  String *DEPRECATED*

cdk-1.4.0.jar, MeasureFormat.class
package com.ibm.icu.text
MeasureFormat.getCurrencyFormat ( ) [static] :  MeasureFormat *DEPRECATED*
MeasureFormat.getCurrencyFormat ( ULocale locale ) [static] :  MeasureFormat *DEPRECATED*
MeasureFormat.MeasureFormat ( )

cdk-1.4.0.jar, MeasureUnit.class
package com.ibm.icu.util
MeasureUnit.MeasureUnit ( )

cdk-1.4.0.jar, MegaTestSuite.class
package com.hp.hpl.jena.regression
MegaTestSuite.suite ( ) [static] :  TestSuite

cdk-1.4.0.jar, MemoryModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
MemoryModelAssembler.MemoryModelAssembler ( )
MemoryModelAssembler.open ( Assembler a, Resource root, Mode mode ) :  Object
MemoryModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode irrelevant ) :  Model

cdk-1.4.0.jar, MessageFormat.class
package com.ibm.icu.text
MessageFormat.applyPattern ( String pattern ) :  void *DEPRECATED*
MessageFormat.autoQuoteApostrophe ( String pattern ) [static] :  String *DEPRECATED*
MessageFormat.clone ( ) :  Object *DEPRECATED*
MessageFormat.equals ( Object obj ) :  boolean *DEPRECATED*
MessageFormat.format ( Object arguments, StringBuffer result, FieldPosition pos ) :  StringBuffer *DEPRECATED*
MessageFormat.format ( Object[ ] arguments, StringBuffer result, FieldPosition pos ) :  StringBuffer *DEPRECATED*
MessageFormat.format ( String pattern, Object[ ] arguments ) [static] :  String *DEPRECATED*
MessageFormat.getFormats ( ) :  Format[ ] *DEPRECATED*
MessageFormat.getFormatsByArgumentIndex ( ) :  Format[ ] *DEPRECATED*
MessageFormat.getLocale ( ) :  Locale *DEPRECATED*
MessageFormat.getULocale ( ) :  ULocale *DEPRECATED*
MessageFormat.hashCode ( ) :  int *DEPRECATED*
MessageFormat.MessageFormat ( String pattern ) *DEPRECATED*
MessageFormat.MessageFormat ( String pattern, Locale locale ) *DEPRECATED*
MessageFormat.MessageFormat ( String pattern, ULocale locale ) *DEPRECATED*
MessageFormat.parse ( String source ) :  Object[ ] *DEPRECATED*
MessageFormat.parse ( String source, ParsePosition pos ) :  Object[ ] *DEPRECATED*
MessageFormat.parseObject ( String source, ParsePosition pos ) :  Object *DEPRECATED*
MessageFormat.setFormat ( int formatElementIndex, Format newFormat ) :  void *DEPRECATED*
MessageFormat.setFormatByArgumentIndex ( int argumentIndex, Format newFormat ) :  void *DEPRECATED*
MessageFormat.setFormats ( Format[ ] newFormats ) :  void *DEPRECATED*
MessageFormat.setFormatsByArgumentIndex ( Format[ ] newFormats ) :  void *DEPRECATED*
MessageFormat.setLocale ( Locale locale ) :  void *DEPRECATED*
MessageFormat.setLocale ( ULocale locale ) :  void *DEPRECATED*
MessageFormat.toPattern ( ) :  String *DEPRECATED*

cdk-1.4.0.jar, MessageFormatter.class
package org.slf4j.helpers
MessageFormatter.arrayFormat ( String messagePattern, Object[ ] argArray ) [static] :  String
MessageFormatter.format ( String messagePattern, Object arg ) [static] :  String
MessageFormatter.format ( String messagePattern, Object arg1, Object arg2 ) [static] :  String
MessageFormatter.MessageFormatter ( )

cdk-1.4.0.jar, Min.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Min.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Min.getArgLength ( ) :  int
Min.getName ( ) :  String
Min.Min ( )

cdk-1.4.0.jar, MinCardinalityQRestriction.class
package com.hp.hpl.jena.ontology
MinCardinalityQRestriction.getMinCardinalityQ ( ) [abstract] :  int
MinCardinalityQRestriction.hasMinCardinalityQ ( int p1 ) [abstract] :  boolean
MinCardinalityQRestriction.removeMinCardinalityQ ( int p1 ) [abstract] :  void
MinCardinalityQRestriction.setMinCardinalityQ ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, MinCardinalityRestriction.class
package com.hp.hpl.jena.ontology
MinCardinalityRestriction.getMinCardinality ( ) [abstract] :  int
MinCardinalityRestriction.hasMinCardinality ( int p1 ) [abstract] :  boolean
MinCardinalityRestriction.removeMinCardinality ( int p1 ) [abstract] :  void
MinCardinalityRestriction.setMinCardinality ( int p1 ) [abstract] :  void

cdk-1.4.0.jar, MissingArgumentException.class
package org.apache.commons.cli
MissingArgumentException.MissingArgumentException ( String message )

cdk-1.4.0.jar, MissingOptionException.class
package org.apache.commons.cli
MissingOptionException.MissingOptionException ( String message )

cdk-1.4.0.jar, MixedGraphMem.class
package com.hp.hpl.jena.mem
MixedGraphMem.clear ( ) :  void
MixedGraphMem.createTripleStore ( ) :  TripleStore
MixedGraphMem.destroy ( ) :  void
MixedGraphMem.graphBaseContains ( Triple t ) :  boolean
MixedGraphMem.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
MixedGraphMem.graphBaseSize ( ) :  int
MixedGraphMem.isEmpty ( ) :  boolean
MixedGraphMem.MixedGraphMem ( )
MixedGraphMem.MixedGraphMem ( ReificationStyle style )
MixedGraphMem.performAdd ( Triple t ) :  void
MixedGraphMem.performDelete ( Triple t ) :  void

cdk-1.4.0.jar, MixedGraphMemStore.class
package com.hp.hpl.jena.mem
MixedGraphMemStore.add ( Node key, Triple t ) :  boolean
MixedGraphMemStore.add ( Triple t ) :  void
MixedGraphMemStore.clear ( ) :  void
MixedGraphMemStore.contains ( Triple t ) :  boolean
MixedGraphMemStore.isEmpty ( ) :  boolean
MixedGraphMemStore.iterator ( Node key, Triple pattern ) :  ExtendedIterator
MixedGraphMemStore.iterator ( Triple pattern ) :  ExtendedIterator
MixedGraphMemStore.MixedGraphMemStore ( Graph parent )
MixedGraphMemStore.remove ( Node key, Triple t ) :  boolean
MixedGraphMemStore.remove ( Triple t ) :  void
MixedGraphMemStore.size ( ) :  int

cdk-1.4.0.jar, Mode.class
package com.hp.hpl.jena.assembler
Mode.Mode ( boolean mayCreate, boolean mayReuse )
Mode.permitCreateNew ( Resource root, String name ) :  boolean
Mode.permitUseExisting ( Resource root, String name ) :  boolean
package com.ibm.icu.text
Normalizer.Mode.getMask ( ) :  int
Normalizer.Mode.getMinC ( ) :  int
Normalizer.Mode.getNextBoundary ( ) :  Normalizer.IsNextBoundary
Normalizer.Mode.getPrevBoundary ( ) :  Normalizer.IsPrevBoundary
Normalizer.Mode.isNFSkippable ( int c ) :  boolean
Normalizer.Mode.normalize ( char[ ] src, int srcStart, int srcLimit, char[ ] dest, int destStart, int destLimit, int options ) :  int
Normalizer.Mode.normalize ( char[ ] src, int srcStart, int srcLimit, char[ ] dest, int destStart, int destLimit, UnicodeSet nx ) :  int
Normalizer.Mode.normalize ( String src, int options ) :  String
Normalizer.Mode.quickCheck ( char[ ] src, int start, int limit, boolean allowMaybe, UnicodeSet nx ) :  Normalizer.QuickCheckResult

cdk-1.4.0.jar, Model.class
package com.hp.hpl.jena.rdf.model
Model.abort ( ) [abstract] :  Model
Model.add ( List p1 ) [abstract] :  Model
Model.add ( Model p1 ) [abstract] :  Model
Model.add ( Model p1, boolean p2 ) [abstract] :  Model
Model.add ( Statement p1 ) [abstract] :  Model
Model.add ( Statement[ ] p1 ) [abstract] :  Model
Model.add ( StmtIterator p1 ) [abstract] :  Model
Model.begin ( ) [abstract] :  Model
Model.close ( ) [abstract] :  void
Model.commit ( ) [abstract] :  Model
Model.contains ( Resource p1, Property p2 ) [abstract] :  boolean
Model.contains ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  boolean
Model.contains ( Statement p1 ) [abstract] :  boolean
Model.containsAll ( Model p1 ) [abstract] :  boolean
Model.containsAll ( StmtIterator p1 ) [abstract] :  boolean
Model.containsAny ( Model p1 ) [abstract] :  boolean
Model.containsAny ( StmtIterator p1 ) [abstract] :  boolean
Model.containsResource ( RDFNode p1 ) [abstract] :  boolean
Model.createList ( ) [abstract] :  RDFList
Model.createList ( Iterator p1 ) [abstract] :  RDFList
Model.createList ( RDFNode[ ] p1 ) [abstract] :  RDFList
Model.createLiteral ( String p1, boolean p2 ) [abstract] :  Literal
Model.createLiteral ( String p1, String p2 ) [abstract] :  Literal
Model.createProperty ( String p1, String p2 ) [abstract] :  Property
Model.createReifiedStatement ( Statement p1 ) [abstract] :  ReifiedStatement
Model.createReifiedStatement ( String p1, Statement p2 ) [abstract] :  ReifiedStatement
Model.createResource ( ) [abstract] :  Resource
Model.createResource ( AnonId p1 ) [abstract] :  Resource
Model.createResource ( String p1 ) [abstract] :  Resource
Model.createStatement ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  Statement
Model.createTypedLiteral ( Object p1 ) [abstract] :  Literal
Model.createTypedLiteral ( Object p1, RDFDatatype p2 ) [abstract] :  Literal
Model.createTypedLiteral ( String p1, RDFDatatype p2 ) [abstract] :  Literal
Model.difference ( Model p1 ) [abstract] :  Model
Model.equals ( Object p1 ) [abstract] :  boolean
Model.executeInTransaction ( Command p1 ) [abstract] :  Object
Model.getAnyReifiedStatement ( Statement p1 ) [abstract] :  Resource
Model.getLock ( ) [abstract] :  Lock
Model.getProperty ( Resource p1, Property p2 ) [abstract] :  Statement
Model.getProperty ( String p1, String p2 ) [abstract] :  Property
Model.getReificationStyle ( ) [abstract] :  ReificationStyle
Model.getRequiredProperty ( Resource p1, Property p2 ) [abstract] :  Statement
Model.getResource ( String p1 ) [abstract] :  Resource
Model.independent ( ) [abstract] :  boolean
Model.intersection ( Model p1 ) [abstract] :  Model
Model.isClosed ( ) [abstract] :  boolean
Model.isEmpty ( ) [abstract] :  boolean
Model.isIsomorphicWith ( Model p1 ) [abstract] :  boolean
Model.isReified ( Statement p1 ) [abstract] :  boolean
Model.listNameSpaces ( ) [abstract] :  NsIterator
Model.listObjects ( ) [abstract] :  NodeIterator
Model.listObjectsOfProperty ( Property p1 ) [abstract] :  NodeIterator
Model.listObjectsOfProperty ( Resource p1, Property p2 ) [abstract] :  NodeIterator
Model.listReifiedStatements ( ) [abstract] :  RSIterator
Model.listReifiedStatements ( Statement p1 ) [abstract] :  RSIterator
Model.listResourcesWithProperty ( Property p1 ) [abstract] :  ResIterator
Model.listResourcesWithProperty ( Property p1, RDFNode p2 ) [abstract] :  ResIterator
Model.listStatements ( ) [abstract] :  StmtIterator
Model.listStatements ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  StmtIterator
Model.listStatements ( Selector p1 ) [abstract] :  StmtIterator
Model.listSubjects ( ) [abstract] :  ResIterator
Model.listSubjectsWithProperty ( Property p1 ) [abstract] :  ResIterator
Model.listSubjectsWithProperty ( Property p1, RDFNode p2 ) [abstract] :  ResIterator
Model.notifyEvent ( Object p1 ) [abstract] :  Model
Model.query ( Selector p1 ) [abstract] :  Model
Model.read ( InputStream p1, String p2 ) [abstract] :  Model
Model.read ( InputStream p1, String p2, String p3 ) [abstract] :  Model
Model.read ( Reader p1, String p2 ) [abstract] :  Model
Model.read ( Reader p1, String p2, String p3 ) [abstract] :  Model
Model.read ( String p1 ) [abstract] :  Model
Model.read ( String p1, String p2 ) [abstract] :  Model
Model.read ( String p1, String p2, String p3 ) [abstract] :  Model
Model.register ( ModelChangedListener p1 ) [abstract] :  Model
Model.remove ( List p1 ) [abstract] :  Model
Model.remove ( Statement p1 ) [abstract] :  Model
Model.remove ( Statement[ ] p1 ) [abstract] :  Model
Model.removeAll ( ) [abstract] :  Model
Model.removeAll ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  Model
Model.removeAllReifications ( Statement p1 ) [abstract] :  void
Model.removeReification ( ReifiedStatement p1 ) [abstract] :  void
Model.size ( ) [abstract] :  long
Model.supportsSetOperations ( ) [abstract] :  boolean
Model.supportsTransactions ( ) [abstract] :  boolean
Model.union ( Model p1 ) [abstract] :  Model
Model.unregister ( ModelChangedListener p1 ) [abstract] :  Model
Model.write ( OutputStream p1 ) [abstract] :  Model
Model.write ( OutputStream p1, String p2 ) [abstract] :  Model
Model.write ( OutputStream p1, String p2, String p3 ) [abstract] :  Model
Model.write ( Writer p1 ) [abstract] :  Model
Model.write ( Writer p1, String p2 ) [abstract] :  Model
Model.write ( Writer p1, String p2, String p3 ) [abstract] :  Model

cdk-1.4.0.jar, ModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
ModelAssembler.addContent ( Resource root, Model m, Content c ) :  void
ModelAssembler.getContent ( Assembler a, Resource root ) :  Content
ModelAssembler.getInitialContent ( Assembler a, Resource root ) :  Content
ModelAssembler.getReificationStyle ( Resource root ) [static] :  ReificationStyle
ModelAssembler.ModelAssembler ( )
ModelAssembler.open ( Assembler a, Resource root, Mode mode ) :  Object
ModelAssembler.openEmptyModel ( Assembler p1, Resource p2, Mode p3 ) [abstract] :  Model
ModelAssembler.openModel ( Assembler a, Resource root, Content initial, Mode mode ) :  Model
ModelAssembler.openModel ( Resource root, Mode mode ) :  Model
ModelAssembler.styleFor ( Resource root, Resource r ) [static] :  ReificationStyle

cdk-1.4.0.jar, ModelChangedListener.class
package com.hp.hpl.jena.rdf.model
ModelChangedListener.addedStatement ( Statement p1 ) [abstract] :  void
ModelChangedListener.addedStatements ( List p1 ) [abstract] :  void
ModelChangedListener.addedStatements ( Model p1 ) [abstract] :  void
ModelChangedListener.addedStatements ( Statement[ ] p1 ) [abstract] :  void
ModelChangedListener.addedStatements ( StmtIterator p1 ) [abstract] :  void
ModelChangedListener.notifyEvent ( Model p1, Object p2 ) [abstract] :  void
ModelChangedListener.removedStatement ( Statement p1 ) [abstract] :  void
ModelChangedListener.removedStatements ( List p1 ) [abstract] :  void
ModelChangedListener.removedStatements ( Model p1 ) [abstract] :  void
ModelChangedListener.removedStatements ( Statement[ ] p1 ) [abstract] :  void
ModelChangedListener.removedStatements ( StmtIterator p1 ) [abstract] :  void

cdk-1.4.0.jar, ModelCon.class
package com.hp.hpl.jena.rdf.model
ModelCon.add ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  Model
ModelCon.add ( Resource p1, Property p2, String p3 ) [abstract] :  Model
ModelCon.add ( Resource p1, Property p2, String p3, boolean p4 ) [abstract] :  Model
ModelCon.add ( Resource p1, Property p2, String p3, RDFDatatype p4 ) [abstract] :  Model
ModelCon.add ( Resource p1, Property p2, String p3, String p4 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, boolean p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, char p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, double p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, float p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, int p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, long p3 ) [abstract] :  Model
ModelCon.addLiteral ( Resource p1, Property p2, Object p3 ) [abstract] :  Model *DEPRECATED*
ModelCon.contains ( Resource p1, Property p2, String p3 ) [abstract] :  boolean
ModelCon.contains ( Resource p1, Property p2, String p3, String p4 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, boolean p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, char p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, double p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, float p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, int p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, long p3 ) [abstract] :  boolean
ModelCon.containsLiteral ( Resource p1, Property p2, Object p3 ) [abstract] :  boolean
ModelCon.createAlt ( ) [abstract] :  Alt
ModelCon.createAlt ( String p1 ) [abstract] :  Alt
ModelCon.createBag ( ) [abstract] :  Bag
ModelCon.createBag ( String p1 ) [abstract] :  Bag
ModelCon.createLiteral ( String p1 ) [abstract] :  Literal
ModelCon.createLiteralStatement ( Resource p1, Property p2, boolean p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, char p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, double p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, float p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, int p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, long p3 ) [abstract] :  Statement
ModelCon.createLiteralStatement ( Resource p1, Property p2, Object p3 ) [abstract] :  Statement
ModelCon.createProperty ( String p1 ) [abstract] :  Property
ModelCon.createResource ( Resource p1 ) [abstract] :  Resource
ModelCon.createResource ( ResourceF p1 ) [abstract] :  Resource
ModelCon.createResource ( String p1, Resource p2 ) [abstract] :  Resource
ModelCon.createResource ( String p1, ResourceF p2 ) [abstract] :  Resource
ModelCon.createSeq ( ) [abstract] :  Seq
ModelCon.createSeq ( String p1 ) [abstract] :  Seq
ModelCon.createStatement ( Resource p1, Property p2, String p3 ) [abstract] :  Statement
ModelCon.createStatement ( Resource p1, Property p2, String p3, boolean p4 ) [abstract] :  Statement
ModelCon.createStatement ( Resource p1, Property p2, String p3, String p4 ) [abstract] :  Statement
ModelCon.createStatement ( Resource p1, Property p2, String p3, String p4, boolean p5 ) [abstract] :  Statement
ModelCon.createTypedLiteral ( boolean p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( Calendar p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( char p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( double p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( float p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( int p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( long p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( Object p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( Object p1, String p2 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( String p1 ) [abstract] :  Literal
ModelCon.createTypedLiteral ( String p1, String p2 ) [abstract] :  Literal
ModelCon.getAlt ( Resource p1 ) [abstract] :  Alt
ModelCon.getAlt ( String p1 ) [abstract] :  Alt
ModelCon.getBag ( Resource p1 ) [abstract] :  Bag
ModelCon.getBag ( String p1 ) [abstract] :  Bag
ModelCon.getProperty ( String p1 ) [abstract] :  Property
ModelCon.getRDFNode ( Node p1 ) [abstract] :  RDFNode
ModelCon.getResource ( String p1, ResourceF p2 ) [abstract] :  Resource
ModelCon.getSeq ( Resource p1 ) [abstract] :  Seq
ModelCon.getSeq ( String p1 ) [abstract] :  Seq
ModelCon.listLiteralStatements ( Resource p1, Property p2, boolean p3 ) [abstract] :  StmtIterator
ModelCon.listLiteralStatements ( Resource p1, Property p2, char p3 ) [abstract] :  StmtIterator
ModelCon.listLiteralStatements ( Resource p1, Property p2, double p3 ) [abstract] :  StmtIterator
ModelCon.listLiteralStatements ( Resource p1, Property p2, float p3 ) [abstract] :  StmtIterator
ModelCon.listLiteralStatements ( Resource p1, Property p2, long p3 ) [abstract] :  StmtIterator
ModelCon.listResourcesWithProperty ( Property p1, boolean p2 ) [abstract] :  ResIterator
ModelCon.listResourcesWithProperty ( Property p1, char p2 ) [abstract] :  ResIterator
ModelCon.listResourcesWithProperty ( Property p1, double p2 ) [abstract] :  ResIterator
ModelCon.listResourcesWithProperty ( Property p1, float p2 ) [abstract] :  ResIterator
ModelCon.listResourcesWithProperty ( Property p1, long p2 ) [abstract] :  ResIterator
ModelCon.listResourcesWithProperty ( Property p1, Object p2 ) [abstract] :  ResIterator
ModelCon.listStatements ( Resource p1, Property p2, String p3 ) [abstract] :  StmtIterator
ModelCon.listStatements ( Resource p1, Property p2, String p3, String p4 ) [abstract] :  StmtIterator
ModelCon.listSubjectsWithProperty ( Property p1, String p2 ) [abstract] :  ResIterator
ModelCon.listSubjectsWithProperty ( Property p1, String p2, String p3 ) [abstract] :  ResIterator
ModelCon.remove ( Model p1 ) [abstract] :  Model
ModelCon.remove ( Model p1, boolean p2 ) [abstract] :  Model
ModelCon.remove ( Resource p1, Property p2, RDFNode p3 ) [abstract] :  Model
ModelCon.remove ( StmtIterator p1 ) [abstract] :  Model

cdk-1.4.0.jar, ModelExpansion.class
package com.hp.hpl.jena.assembler
ModelExpansion.addDomainTypes ( Model result, Model schema ) [static] :  void
ModelExpansion.addRangeTypes ( Model result, Model schema ) [static] :  void
ModelExpansion.addSubClassClosure ( Model m ) [static] :  void
ModelExpansion.addSubclassesFrom ( Model result, Model schema ) [static] :  void
ModelExpansion.addSupertypes ( Model result ) [static] :  void
ModelExpansion.ModelExpansion ( )
ModelExpansion.withSchema ( Model model, Model schema ) [static] :  Model

cdk-1.4.0.jar, ModelExtract.class
package com.hp.hpl.jena.rdf.model
ModelExtract.extract ( Resource r, Model s ) :  Model
ModelExtract.extractInto ( Model model, Resource r, Model s ) :  Model
ModelExtract.getGraphExtract ( TripleBoundary tb ) :  GraphExtract
ModelExtract.ModelExtract ( StatementBoundary b )

cdk-1.4.0.jar, ModelFactory.class
package com.hp.hpl.jena.rdf.model
ModelFactory.assembleModelFrom ( Model singleRoot ) [static] :  Model
ModelFactory.assembleModelFrom ( Resource root ) [static] :  Model
ModelFactory.createDefaultModel ( ) [static] :  Model
ModelFactory.createDefaultModel ( ReificationStyle style ) [static] :  Model
ModelFactory.createFileModelMaker ( String root ) [static] :  ModelMaker
ModelFactory.createFileModelMaker ( String root, ReificationStyle style ) [static] :  ModelMaker
ModelFactory.createInfModel ( InfGraph g ) [static] :  InfModel
ModelFactory.createInfModel ( Reasoner reasoner, Model model ) [static] :  InfModel
ModelFactory.createInfModel ( Reasoner reasoner, Model schema, Model model ) [static] :  InfModel
ModelFactory.createMemModelMaker ( ) [static] :  ModelMaker
ModelFactory.createMemModelMaker ( ReificationStyle style ) [static] :  ModelMaker
ModelFactory.createModelForGraph ( Graph g ) [static] :  Model
ModelFactory.createModelRDBMaker ( IDBConnection c ) [static] :  ModelMaker
ModelFactory.createModelRDBMaker ( IDBConnection c, ReificationStyle style ) [static] :  ModelMaker
ModelFactory.createNonreifyingModel ( ) [static] :  Model
ModelFactory.createOntologyModel ( ) [static] :  OntModel
ModelFactory.createOntologyModel ( OntModelSpec spec ) [static] :  OntModel
ModelFactory.createOntologyModel ( OntModelSpec spec, Model base ) [static] :  OntModel
ModelFactory.createOntologyModel ( OntModelSpec spec, ModelMaker maker, Model base ) [static] :  OntModel
ModelFactory.createOntologyModel ( String languageURI ) [static] :  OntModel
ModelFactory.createRDFSModel ( Model model ) [static] :  InfModel
ModelFactory.createRDFSModel ( Model schema, Model model ) [static] :  InfModel
ModelFactory.createSimpleRDBConnection ( ) [static] :  IDBConnection
ModelFactory.createSimpleRDBConnection ( String url, String user, String password, String dbType ) [static] :  IDBConnection
ModelFactory.createUnion ( Model m1, Model m2 ) [static] :  Model
ModelFactory.findAssemblerRoots ( Model m ) [static] :  Set
ModelFactory.getDefaultModelPrefixes ( ) [static] :  PrefixMapping
ModelFactory.setDefaultModelPrefixes ( PrefixMapping pm ) [static] :  PrefixMapping
ModelFactory.withHiddenStatements ( Model m ) [static] :  Model

cdk-1.4.0.jar, ModelFactoryBase.class
package com.hp.hpl.jena.rdf.model
ModelFactoryBase.extractType ( String dbURL ) [static] :  String
ModelFactoryBase.gp ( String name ) [static] :  String
ModelFactoryBase.gp ( String name, String ifAbsent ) [static] :  String
ModelFactoryBase.guessDBConcurrent ( ) [static] :  boolean
ModelFactoryBase.guessDBDriver ( ) [static] :  String
ModelFactoryBase.guessDBPassword ( ) [static] :  String
ModelFactoryBase.guessDBType ( ) [static] :  String
ModelFactoryBase.guessDBURL ( ) [static] :  String
ModelFactoryBase.guessDBUser ( ) [static] :  String
ModelFactoryBase.ModelFactoryBase ( )

cdk-1.4.0.jar, ModelGetter.class
package com.hp.hpl.jena.rdf.model
ModelGetter.getModel ( String p1 ) [abstract] :  Model
ModelGetter.getModel ( String p1, ModelReader p2 ) [abstract] :  Model

cdk-1.4.0.jar, ModelGraphInterface.class
package com.hp.hpl.jena.rdf.model
ModelGraphInterface.asRDFNode ( Node p1 ) [abstract] :  RDFNode
ModelGraphInterface.asStatement ( Triple p1 ) [abstract] :  Statement
ModelGraphInterface.getGraph ( ) [abstract] :  Graph
ModelGraphInterface.queryHandler ( ) [abstract] :  QueryHandler

cdk-1.4.0.jar, ModelLoader.class
package com.hp.hpl.jena.util
ModelLoader.connectToDB ( String urlStr, String dbUser, String dbPassword, String modelName, String dbType, String driverName ) [static] :  Model
ModelLoader.guessLang ( String urlStr ) [static] :  String *DEPRECATED*
ModelLoader.guessLang ( String urlStr, String defaultLang ) [static] :  String *DEPRECATED*
ModelLoader.loadModel ( Model model, String urlStr ) [static] :  Model *DEPRECATED*
ModelLoader.loadModel ( Model model, String urlStr, String lang ) [static] :  Model *DEPRECATED*
ModelLoader.loadModel ( String urlStr ) [static] :  Model *DEPRECATED*
ModelLoader.loadModel ( String urlStr, String lang ) [static] :  Model *DEPRECATED*
ModelLoader.loadModel ( String urlStr, String lang, String dbUser, String dbPassword, String modelName, String dbType, String driver ) [static] :  Model
ModelLoader.ModelLoader ( )

cdk-1.4.0.jar, ModelMaker.class
package com.hp.hpl.jena.rdf.model
ModelMaker.close ( ) [abstract] :  void
ModelMaker.createModel ( String p1 ) [abstract] :  Model
ModelMaker.createModel ( String p1, boolean p2 ) [abstract] :  Model
ModelMaker.getGraphMaker ( ) [abstract] :  GraphMaker
ModelMaker.hasModel ( String p1 ) [abstract] :  boolean
ModelMaker.listModels ( ) [abstract] :  ExtendedIterator
ModelMaker.openModel ( String p1, boolean p2 ) [abstract] :  Model
ModelMaker.removeModel ( String p1 ) [abstract] :  void

cdk-1.4.0.jar, ModelQueryUtil.class
package com.hp.hpl.jena.util
ModelQueryUtil.asRDF ( Model m, Node n ) [static] :  RDFNode
ModelQueryUtil.mappy ( Model m, Domain L ) [static] :  List
ModelQueryUtil.queryBindingsWith ( Model model, Model query, Resource[ ] variables ) [static] :  ExtendedIterator

cdk-1.4.0.jar, ModelRDB.class
package com.hp.hpl.jena.db
ModelRDB.close ( ) :  void
ModelRDB.createModel ( IDBConnection dbcon ) [static] :  ModelRDB
ModelRDB.createModel ( IDBConnection dbcon, Model modelProperties ) [static] :  ModelRDB
ModelRDB.createModel ( IDBConnection dbcon, String name ) [static] :  ModelRDB
ModelRDB.createModel ( IDBConnection dbcon, String name, Model modelProperties ) [static] :  ModelRDB
ModelRDB.getConnection ( ) :  IDBConnection
ModelRDB.getDefaultModelProperties ( IDBConnection dbcon ) [static] :  Model
ModelRDB.getDoDuplicateCheck ( ) :  boolean
ModelRDB.getDoFastpath ( ) :  boolean
ModelRDB.getModelProperties ( ) :  Model
ModelRDB.getQueryFullReified ( ) :  boolean
ModelRDB.getQueryOnlyAsserted ( ) :  boolean
ModelRDB.getQueryOnlyReified ( ) :  boolean
ModelRDB.listModels ( IDBConnection dbcon ) [static] :  ExtendedIterator
ModelRDB.ModelRDB ( GraphRDB graph )
ModelRDB.ModelRDB ( Personality p, GraphRDB graph )
ModelRDB.open ( IDBConnection dbcon ) [static] :  ModelRDB
ModelRDB.open ( IDBConnection dbcon, String name ) [static] :  ModelRDB
ModelRDB.remove ( ) :  void
ModelRDB.setDoDuplicateCheck ( boolean bool ) :  void
ModelRDB.setDoFastpath ( boolean val ) :  void
ModelRDB.setDoImplicitJoin ( boolean val ) :  void
ModelRDB.setQueryFullReified ( boolean opt ) :  void
ModelRDB.setQueryOnlyAsserted ( boolean opt ) :  void
ModelRDB.setQueryOnlyReified ( boolean opt ) :  void

cdk-1.4.0.jar, ModelReader.class
package com.hp.hpl.jena.rdf.model
ModelReader.readModel ( Model p1, String p2 ) [abstract] :  Model

cdk-1.4.0.jar, ModelSource.class
package com.hp.hpl.jena.rdf.model
ModelSource.createDefaultModel ( ) [abstract] :  Model
ModelSource.createFreshModel ( ) [abstract] :  Model
ModelSource.openModel ( String p1 ) [abstract] :  Model
ModelSource.openModelIfPresent ( String p1 ) [abstract] :  Model

cdk-1.4.0.jar, ModelSourceAssembler.class
package com.hp.hpl.jena.assembler.assemblers
ModelSourceAssembler.createRDBGetter ( ConnectionDescription c ) :  ModelGetter
ModelSourceAssembler.ModelSourceAssembler ( )
ModelSourceAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, Molecule.class
package signature.chemistry
Molecule.addAtom ( int i, String symbol ) :  void
Molecule.addAtom ( String symbol ) :  void
Molecule.addBond ( int atomNumberA, int atomNumberB, int order ) :  void
Molecule.addMultipleAtoms ( int count, String symbol ) :  void
Molecule.addMultipleSingleBonds ( int i, int[ ] js ) :  void
Molecule.addSingleBond ( int atomNumberA, int atomNumberB ) :  void
Molecule.bonds ( ) :  List
Molecule.bondsOrdered ( ) :  boolean
Molecule.getAtomCount ( ) :  int
Molecule.getBondCount ( ) :  int
Molecule.getBondOrder ( int atomIndex, int otherAtomIndex ) :  int
Molecule.getBondOrder ( int bondIndex ) :  int
Molecule.getConnected ( int atomIndex ) :  int[ ]
Molecule.getFirstInBond ( int bondIndex ) :  int
Molecule.getSecondInBond ( int bondIndex ) :  int
Molecule.getSymbolFor ( int atomIndex ) :  String
Molecule.getTotalOrder ( int atomIndex ) :  int
Molecule.identical ( Molecule other ) :  boolean
Molecule.isConnected ( int i, int j ) :  boolean
Molecule.Molecule ( )
Molecule.Molecule ( Molecule other )
Molecule.Molecule ( Molecule other, int[ ] permutation )
Molecule.Molecule ( String atomSymbol, int count )
Molecule.toEdgeString ( ) :  String
Molecule.toString ( ) :  String

cdk-1.4.0.jar, MoleculeBuilder.class
package signature.chemistry
MoleculeBuilder.fromTree ( ColoredTree tree ) :  Molecule
MoleculeBuilder.getMolecule ( ) :  Molecule
MoleculeBuilder.makeEdge ( int vertexIndex1, int vertexIndex2, String symbolA, String symbolB, String edgeLabel ) :  void
MoleculeBuilder.makeGraph ( ) :  void
MoleculeBuilder.makeVertex ( String label ) :  void
MoleculeBuilder.MoleculeBuilder ( )

cdk-1.4.0.jar, MoleculeFactory.class
package org.openscience.cdk.templates
MoleculeFactory.makeCyclopentane ( ) [static] :  Molecule
package signature.chemistry
MoleculeFactory.fiveCycle ( ) [static] :  Molecule
MoleculeFactory.fiveStar ( ) [static] :  Molecule
MoleculeFactory.fourCycle ( ) [static] :  Molecule
MoleculeFactory.fourStar ( ) [static] :  Molecule
MoleculeFactory.methane ( ) [static] :  Molecule
MoleculeFactory.methylatedCyclobutane ( ) [static] :  Molecule
MoleculeFactory.MoleculeFactory ( )
MoleculeFactory.propellane ( ) [static] :  Molecule
MoleculeFactory.pseudopropellane ( ) [static] :  Molecule
MoleculeFactory.sixCage ( ) [static] :  Molecule
MoleculeFactory.sixCycle ( ) [static] :  Molecule
MoleculeFactory.threeCycle ( ) [static] :  Molecule
MoleculeFactory.threeStar ( ) [static] :  Molecule

cdk-1.4.0.jar, MoleculeFromSignatureBuilder.class
package org.openscience.cdk.signature
MoleculeFromSignatureBuilder.getAtomContainer ( ) :  IAtomContainer
MoleculeFromSignatureBuilder.makeEdge ( int vertexIndex1, int vertexIndex2, String vertexSymbol1, String vertexSymbol2, String edgeLabel ) :  void
MoleculeFromSignatureBuilder.makeGraph ( ) :  void
MoleculeFromSignatureBuilder.makeVertex ( String label ) :  void
MoleculeFromSignatureBuilder.MoleculeFromSignatureBuilder ( IChemObjectBuilder builder )

cdk-1.4.0.jar, MoleculeQuotientGraph.class
package signature.chemistry
MoleculeQuotientGraph.isConnected ( int i, int j ) :  boolean
MoleculeQuotientGraph.MoleculeQuotientGraph ( Molecule molecule )
MoleculeQuotientGraph.MoleculeQuotientGraph ( Molecule molecule, List sigStrings )

cdk-1.4.0.jar, MoleculeReader.class
package signature.chemistry
MoleculeReader.MoleculeReader ( )
MoleculeReader.readMolfile ( String filename ) [static] :  Molecule
MoleculeReader.readSDFFile ( String filename ) [static] :  List
MoleculeReader.readSDFfromStream ( InputStream stream ) [static] :  List

cdk-1.4.0.jar, MoleculeSanityCheck.class
package org.openscience.cdk.smsd.tools
MoleculeSanityCheck.checkAndCleanMolecule ( IAtomContainer molecule ) [static] :  IAtomContainer
MoleculeSanityCheck.configure ( IAtomContainer mol ) [static] :  void
MoleculeSanityCheck.MoleculeSanityCheck ( )

cdk-1.4.0.jar, MoleculeSignature.class
package org.openscience.cdk.signature
MoleculeSignature.calculateOrbits ( ) :  List
MoleculeSignature.fromSignatureString ( String signatureString, IChemObjectBuilder coBuilder ) [static] :  IAtomContainer
MoleculeSignature.getVertexCount ( ) :  int
MoleculeSignature.MoleculeSignature ( IAtomContainer molecule )
MoleculeSignature.MoleculeSignature ( IMolecule molecule, int height )
MoleculeSignature.signatureForVertex ( int vertexIndex ) :  AbstractVertexSignature
MoleculeSignature.signatureStringForVertex ( int vertexIndex ) :  String
MoleculeSignature.signatureStringForVertex ( int vertexIndex, int height ) :  String
MoleculeSignature.toCanonicalSignatureString ( int height ) :  String
package signature.chemistry
MoleculeSignature.getMolecularSignature ( ) :  String
MoleculeSignature.getVertexCount ( ) :  int
MoleculeSignature.isCanonicallyLabelled ( Molecule molecule ) [static] :  boolean
MoleculeSignature.MoleculeSignature ( Molecule molecule )
MoleculeSignature.MoleculeSignature ( Molecule molecule, AbstractVertexSignature.InvariantType invariantType )
MoleculeSignature.signatureForVertex ( int vertexIndex ) :  AbstractVertexSignature
MoleculeSignature.signatureStringForVertex ( int vertexIndex ) :  String
MoleculeSignature.signatureStringForVertex ( int vertexIndex, int height ) :  String

cdk-1.4.0.jar, MoleculeSignatureLabellingAdaptor.class
package org.openscience.cdk.smsd.labelling
MoleculeSignatureLabellingAdaptor.getCanonicalMolecule ( IAtomContainer container ) :  IAtomContainer
MoleculeSignatureLabellingAdaptor.getCanonicalPermutation ( IAtomContainer container ) :  int[ ]
MoleculeSignatureLabellingAdaptor.MoleculeSignatureLabellingAdaptor ( )

cdk-1.4.0.jar, MoleculeSignatureTest.class
package signature.chemistry
MoleculeSignatureTest.minimalTest ( ) :  void
MoleculeSignatureTest.MoleculeSignatureTest ( )
MoleculeSignatureTest.testCage ( ) :  void
MoleculeSignatureTest.testCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testCanonicalIsUnique ( Molecule molecule ) :  void
MoleculeSignatureTest.testCanonicalLabelling ( ) :  void
MoleculeSignatureTest.testCarbonChainUnique ( ) :  void
MoleculeSignatureTest.testCarbonHydrogenCanonicalChain ( ) :  void
MoleculeSignatureTest.testColoredTreeCreation ( ) :  void
MoleculeSignatureTest.testFiveCycle ( ) :  void
MoleculeSignatureTest.testFiveStarCanonicalUnique ( ) :  void
MoleculeSignatureTest.testFourStarCanonicalUnique ( ) :  void
MoleculeSignatureTest.testHexagonCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testLargeExample ( ) :  void
MoleculeSignatureTest.testMethaneIsCanonicallyUnique ( ) :  void
MoleculeSignatureTest.testMethaneSignatures ( ) :  void
MoleculeSignatureTest.testMetheneFragmentIsCanonicallyUnique ( ) :  void
MoleculeSignatureTest.testMetheneFragmentSignatures ( ) :  void
MoleculeSignatureTest.testMethylCyclobutaneCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testMethyneFragmentSignatures ( ) :  void
MoleculeSignatureTest.testOddCycleReadin ( ) :  void
MoleculeSignatureTest.testPentagonCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testPropellaneCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testPseudopropellaneCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testRoundtrip ( ) :  void
MoleculeSignatureTest.testSDF ( ) :  void
MoleculeSignatureTest.testSixcageCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testSquareCanonicalIsUnique ( ) :  void
MoleculeSignatureTest.testThreeStarCanonicalUnique ( ) :  void
MoleculeSignatureTest.testTriangleCanonicalIsUnique ( ) :  void

cdk-1.4.0.jar, MoleculeWriter.class
package signature.chemistry
MoleculeWriter.MoleculeWriter ( )
MoleculeWriter.writeMolfile ( String filename, Molecule molecule ) [static] :  void
MoleculeWriter.writeToStream ( OutputStream stream, Molecule molecule ) [static] :  void

cdk-1.4.0.jar, MolHandler.class
package org.openscience.cdk.smsd.tools
MolHandler.getMolecule ( ) :  IAtomContainer
MolHandler.getRemoveHydrogenFlag ( ) :  boolean
MolHandler.MolHandler ( IAtomContainer container, boolean removeHydrogen, boolean cleanMolecule )
MolHandler.MolHandler ( String MolFile, boolean removeHydrogen, boolean cleanMolecule )

cdk-1.4.0.jar, MonitorGraph.class
package com.hp.hpl.jena.util
MonitorGraph.MonitorGraph ( Graph g )
MonitorGraph.snapshot ( List additions, List deletions ) :  void

cdk-1.4.0.jar, MonitorModel.class
package com.hp.hpl.jena.util
MonitorModel.MonitorModel ( Model base )
MonitorModel.snapshot ( ) :  void
MonitorModel.snapshot ( List additions, List deletions ) :  void

cdk-1.4.0.jar, MoSSOutputFormat.class
package org.openscience.cdk.io.formats
MoSSOutputFormat.getFormatName ( ) :  String
MoSSOutputFormat.getInstance ( ) [static] :  IResourceFormat
MoSSOutputFormat.getMIMEType ( ) :  String
MoSSOutputFormat.getNameExtensions ( ) :  String[ ]
MoSSOutputFormat.getPreferredNameExtension ( ) :  String
MoSSOutputFormat.getReaderClassName ( ) :  String
MoSSOutputFormat.getRequiredDataFeatures ( ) :  int
MoSSOutputFormat.getSupportedDataFeatures ( ) :  int
MoSSOutputFormat.getWriterClassName ( ) :  String
MoSSOutputFormat.isXMLBased ( ) :  boolean
MoSSOutputFormat.matches ( int lineNumber, String line ) :  boolean

cdk-1.4.0.jar, MoSSOutputReader.class
package org.openscience.cdk.io
MoSSOutputReader.accepts ( Class testClass ) :  boolean
MoSSOutputReader.close ( ) :  void
MoSSOutputReader.getFormat ( ) :  IResourceFormat
MoSSOutputReader.MoSSOutputReader ( )
MoSSOutputReader.MoSSOutputReader ( InputStream input )
MoSSOutputReader.MoSSOutputReader ( Reader input )
MoSSOutputReader.read ( IChemObject object ) :  IChemObject
MoSSOutputReader.setReader ( InputStream input ) :  void
MoSSOutputReader.setReader ( Reader reader ) :  void

cdk-1.4.0.jar, MovedKeysIterator.class
package com.hp.hpl.jena.mem
HashCommon.MovedKeysIterator.HashCommon.MovedKeysIterator ( HashCommon initialChanges, int container, HashCommon.NotifyEmpty keys, List p4 )
HashCommon.MovedKeysIterator.hasNext ( ) :  boolean
HashCommon.MovedKeysIterator.next ( ) :  Object
HashCommon.MovedKeysIterator.remove ( ) :  void

cdk-1.4.0.jar, MoveTo.class
package org.openscience.cdk.renderer.elements.path
MoveTo.MoveTo ( Point2d point )
MoveTo.points ( ) :  float[ ]

cdk-1.4.0.jar, MultiOperandTree.class
package com.hp.hpl.jena.graph.query.regexptrees
MultiOperandTree.equals ( Object other ) :  boolean
MultiOperandTree.hashCode ( ) :  int
MultiOperandTree.hashCode ( int base ) :  int
MultiOperandTree.MultiOperandTree ( RegexpTree[ ] operands )
MultiOperandTree.sameOperands ( MultiOperandTree other ) :  boolean
MultiOperandTree.toString ( String kind ) :  String

cdk-1.4.0.jar, MultipleBondTest.class
package signature.chemistry
MultipleBondTest.benzeneTest ( ) :  void
MultipleBondTest.cocoTest ( ) :  void
MultipleBondTest.cyclobut_1_ene ( ) :  void
MultipleBondTest.cyclobut_2_ene ( ) :  void
MultipleBondTest.multipleBondedFragmentTest ( ) :  void
MultipleBondTest.MultipleBondTest ( )

cdk-1.4.0.jar, MultiUnion.class
package com.hp.hpl.jena.graph.compose
MultiUnion.addGraph ( Graph graph ) :  void
MultiUnion.createStatisticsHandler ( ) :  GraphStatisticsHandler
MultiUnion.getReifier ( ) :  Reifier
MultiUnion.graphBaseContains ( Triple t ) :  boolean
MultiUnion.graphBaseFind ( TripleMatch t ) :  ExtendedIterator
MultiUnion.MultiUnion ( )
MultiUnion.MultiUnion ( Graph[ ] graphs )
MultiUnion.MultiUnion ( Iterator graphs )
MultiUnion.performAdd ( Triple t ) :  void
MultiUnion.performDelete ( Triple t ) :  void
MultiUnion.queryHandler ( ) :  QueryHandler

cdk-1.4.0.jar, MultiUnionStatisticsHandler.class
package com.hp.hpl.jena.graph.compose
MultiUnion.MultiUnionStatisticsHandler.getStatistic ( Node S, Node P, Node O ) :  long
MultiUnion.MultiUnionStatisticsHandler.getUnion ( ) :  MultiUnion
MultiUnion.MultiUnionStatisticsHandler.MultiUnion.MultiUnionStatisticsHandler ( MultiUnion mu )

cdk-1.4.0.jar, MurckoFragmenter.class
package org.openscience.cdk.fragment
MurckoFragmenter.generateFragments ( IAtomContainer atomContainer ) :  void
MurckoFragmenter.getFragments ( ) :  String[ ]
MurckoFragmenter.getFragmentsAsContainers ( ) :  IAtomContainer[ ]
MurckoFragmenter.getFrameworks ( ) :  String[ ]
MurckoFragmenter.getFrameworksAsContainers ( ) :  IAtomContainer[ ]
MurckoFragmenter.getRingSystems ( ) :  String[ ]
MurckoFragmenter.getRingSystemsAsContainers ( ) :  IAtomContainer[ ]
MurckoFragmenter.MurckoFragmenter ( )
MurckoFragmenter.MurckoFragmenter ( boolean singleFrameworkOnly, int minimumFragmentSize )

cdk-1.4.0.jar, MustNotMatchException.class
package com.hp.hpl.jena.graph.query
QueryNode.MustNotMatchException.QueryNode.MustNotMatchException ( QueryNode message, String p2 )

cdk-1.4.0.jar, N3IndentedWriter.class
package com.hp.hpl.jena.n3
N3IndentedWriter.close ( ) :  void
N3IndentedWriter.decIndent ( int x ) :  void
N3IndentedWriter.flush ( ) :  void
N3IndentedWriter.getCol ( ) :  int
N3IndentedWriter.getIndent ( ) :  int
N3IndentedWriter.getRow ( ) :  int
N3IndentedWriter.getWriter ( ) :  Writer
N3IndentedWriter.incIndent ( int x ) :  void
N3IndentedWriter.N3IndentedWriter ( Writer w )
N3IndentedWriter.padTo ( ) :  void
N3IndentedWriter.print ( String s ) :  void
N3IndentedWriter.println ( ) :  void
N3IndentedWriter.println ( String s ) :  void
N3IndentedWriter.setIndent ( int x ) :  void

cdk-1.4.0.jar, N3JenaWriter.class
package com.hp.hpl.jena.n3
N3JenaWriter.N3JenaWriter ( )
N3JenaWriter.N3JenaWriter ( N3JenaWriterCommon w )
N3JenaWriter.setErrorHandler ( RDFErrorHandler errHandler ) :  RDFErrorHandler
N3JenaWriter.setProperty ( String propName, Object propValue ) :  Object
N3JenaWriter.write ( Model model, OutputStream out, String base ) :  void
N3JenaWriter.write ( Model model, Writer out, String base ) :  void

cdk-1.4.0.jar, N3JenaWriterCommon.class
package com.hp.hpl.jena.n3
N3JenaWriterCommon.absolutePropName ( String propName ) :  String
N3JenaWriterCommon.calcPropertyPadding ( String propStr ) :  int
N3JenaWriterCommon.checkLocalPart ( String s ) [static] :  boolean
N3JenaWriterCommon.checkNamePart ( String s ) [static] :  boolean
N3JenaWriterCommon.checkPrefixedName ( String ns, String local ) [static] :  boolean
N3JenaWriterCommon.checkPrefixPart ( String s ) [static] :  boolean
N3JenaWriterCommon.countArcsTo ( Property prop, Resource resource ) :  int
N3JenaWriterCommon.countArcsTo ( Resource resource ) :  int
N3JenaWriterCommon.countProperties ( Resource r ) :  int
N3JenaWriterCommon.countProperties ( Resource r, Property p ) :  int
N3JenaWriterCommon.finishWriting ( ) :  void
N3JenaWriterCommon.formatLiteral ( Literal literal ) :  String
N3JenaWriterCommon.formatNode ( RDFNode node ) :  String
N3JenaWriterCommon.formatProperty ( Property p ) :  String
N3JenaWriterCommon.formatResource ( Resource r ) :  String
N3JenaWriterCommon.formatURI ( String uriStr ) :  String
N3JenaWriterCommon.getBooleanValue ( String prop, boolean defaultValue ) :  boolean
N3JenaWriterCommon.getIntValue ( String prop, int defaultValue ) :  int
N3JenaWriterCommon.getOutput ( ) :  N3IndentedWriter
N3JenaWriterCommon.getPrefixes ( ) :  Map
N3JenaWriterCommon.getPropValue ( String prop ) :  String
N3JenaWriterCommon.getStringValue ( String prop, String defaultValue ) :  String
N3JenaWriterCommon.listSubjects ( Model model ) :  ResIterator
N3JenaWriterCommon.localPropName ( String propName ) :  String
N3JenaWriterCommon.N3JenaWriterCommon ( )
N3JenaWriterCommon.pad ( int cols ) [static] :  String
N3JenaWriterCommon.prepare ( Model model ) :  void
N3JenaWriterCommon.preparePropertiesForSubject ( Resource r ) :  ClosableIterator
N3JenaWriterCommon.processModel ( Model baseModel ) :  void
N3JenaWriterCommon.rdfListIterator ( Resource r ) :  Iterator
N3JenaWriterCommon.setErrorHandler ( RDFErrorHandler errHandler ) :  RDFErrorHandler
N3JenaWriterCommon.setProperty ( String propName, Object propValue ) :  Object
N3JenaWriterCommon.skipThisSubject ( Resource r ) :  boolean
N3JenaWriterCommon.splitIdx ( String uriStr ) [static] :  int
N3JenaWriterCommon.startWriting ( ) :  void
N3JenaWriterCommon.string ( StringBuffer sbuff, String s, boolean singleQuoteLiteral ) [static] :  void
N3JenaWriterCommon.write ( Model baseModel, Writer _out, String base ) :  void
N3JenaWriterCommon.write ( Model model, OutputStream output, String base ) :  void
N3JenaWriterCommon.writeHeader ( Model model ) :  void
N3JenaWriterCommon.writeLiteral ( Literal literal ) :  void
N3JenaWriterCommon.writeModel ( Model model ) :  void
N3JenaWriterCommon.writeObject ( RDFNode node ) :  void
N3JenaWriterCommon.writeObjectList ( Resource subject, Property property ) :  void
N3JenaWriterCommon.writeOneGraphNode ( Resource subject ) :  void
N3JenaWriterCommon.writePrefixes ( Model model ) :  void
N3JenaWriterCommon.writePropertiesForSubject ( Resource subj, ClosableIterator iter ) :  void
N3JenaWriterCommon.writeSubject ( Resource subject ) :  void

cdk-1.4.0.jar, N3JenaWriterPlain.class
package com.hp.hpl.jena.n3
N3JenaWriterPlain.N3JenaWriterPlain ( )

cdk-1.4.0.jar, N3JenaWriterPP.class
package com.hp.hpl.jena.n3
N3JenaWriterPP.allocateDatastructures ( ) :  void
N3JenaWriterPP.checkListElement ( Resource listElement ) :  boolean
N3JenaWriterPP.clearDatastructures ( ) :  void
N3JenaWriterPP.finishWriting ( ) :  void
N3JenaWriterPP.isSimpleObject ( RDFNode node ) :  boolean
N3JenaWriterPP.N3JenaWriterPP ( )
N3JenaWriterPP.prepare ( Model model ) :  void
N3JenaWriterPP.prepareLists ( Model model ) :  void
N3JenaWriterPP.prepareOneRefBNodes ( Model model ) :  void
N3JenaWriterPP.preparePropertiesForSubject ( Resource r ) :  ClosableIterator
N3JenaWriterPP.skipThisSubject ( Resource subj ) :  boolean
N3JenaWriterPP.startWriting ( ) :  void
N3JenaWriterPP.testOneRefBNode ( RDFNode n ) :  boolean
N3JenaWriterPP.writeList ( Resource resource ) :  void
N3JenaWriterPP.writeObject ( RDFNode node ) :  void
N3JenaWriterPP.writeObjectList ( Resource subject, Property property ) :  void

cdk-1.4.0.jar, N3JenaWriterTriples.class
package com.hp.hpl.jena.n3
N3JenaWriterTriples.N3JenaWriterTriples ( )
N3JenaWriterTriples.writeModel ( Model model ) :  void

cdk-1.4.0.jar, N3TurtleJenaWriter.class
package com.hp.hpl.jena.n3
N3TurtleJenaWriter.N3TurtleJenaWriter ( )

cdk-1.4.0.jar, NamedGraphMap.class
package com.hp.hpl.jena.graph.query
NamedGraphMap.get ( String name ) :  Graph
NamedGraphMap.put ( String name, Graph g ) :  NamedGraphMap

cdk-1.4.0.jar, NamedModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
NamedModelAssembler.getModelName ( Resource root ) :  String
NamedModelAssembler.NamedModelAssembler ( )

cdk-1.4.0.jar, NamedTripleBunches.class
package com.hp.hpl.jena.graph.query
NamedTripleBunches.add ( String name, Triple pattern ) :  void
NamedTripleBunches.entrySetIterator ( ) :  Iterator
NamedTripleBunches.NamedTripleBunches ( )

cdk-1.4.0.jar, NamespaceEndsWithNameCharException.class
package com.hp.hpl.jena.shared
NamespaceEndsWithNameCharException.NamespaceEndsWithNameCharException ( String ns )

cdk-1.4.0.jar, NamespaceHandler.class
package com.hp.hpl.jena.rdf.arp
NamespaceHandler.endPrefixMapping ( String p1 ) [abstract] :  void
NamespaceHandler.startPrefixMapping ( String p1, String p2 ) [abstract] :  void

cdk-1.4.0.jar, NativeArtefactLocator.class
package net.sf.jnati.deploy
NativeArtefactLocator.findArtefact ( String id, String version ) [static] :  ArtefactDescriptor

cdk-1.4.0.jar, NewRegression.class
package com.hp.hpl.jena.regression
NewRegression.NewRegression ( String name )
NewRegression.suite ( ) [static] :  TestSuite
NewRegression.testNothing ( ) :  void

cdk-1.4.0.jar, NewRegressionAddAndContains.class
package com.hp.hpl.jena.regression
NewRegressionAddAndContains.getModel ( ) :  Model
NewRegressionAddAndContains.NewRegressionAddAndContains ( String name )
NewRegressionAddAndContains.setUp ( ) :  void
NewRegressionAddAndContains.suite ( ) [static] :  TestSuite
NewRegressionAddAndContains.tearDown ( ) :  void
NewRegressionAddAndContains.testAddContainLiteralByStatement ( ) :  void
NewRegressionAddAndContains.testAddContainsBoolean ( ) :  void
NewRegressionAddAndContains.testAddContainsByte ( ) :  void
NewRegressionAddAndContains.testAddContainsChar ( ) :  void
NewRegressionAddAndContains.testAddContainsDouble ( ) :  void
NewRegressionAddAndContains.testAddContainsFloat ( ) :  void
NewRegressionAddAndContains.testAddContainsInt ( ) :  void
NewRegressionAddAndContains.testAddContainsLanguagedString ( ) :  void
NewRegressionAddAndContains.testAddContainsLong ( ) :  void
NewRegressionAddAndContains.testAddContainsPlainString ( ) :  void
NewRegressionAddAndContains.testAddContainsResource ( ) :  void
NewRegressionAddAndContains.testAddContainsShort ( ) :  void
NewRegressionAddAndContains.testAddDuplicateLeavesSizeSame ( ) :  void
NewRegressionAddAndContains.testEmpty ( ) :  void

cdk-1.4.0.jar, NewRegressionAddModel.class
package com.hp.hpl.jena.regression
NewRegressionAddModel.assertContainsAll ( Model m1, Model m2 ) :  void
NewRegressionAddModel.assertSameStatements ( Model m1, Model m2 ) :  void
NewRegressionAddModel.getModel ( ) :  Model
NewRegressionAddModel.NewRegressionAddModel ( String name )
NewRegressionAddModel.setUp ( ) :  void
NewRegressionAddModel.suite ( ) [static] :  Test
NewRegressionAddModel.tearDown ( ) :  void
NewRegressionAddModel.testAddByIterator ( ) :  void
NewRegressionAddModel.testAddByModel ( ) :  void
NewRegressionAddModel.testRemoveByModel ( ) :  void

cdk-1.4.0.jar, NewRegressionAltMethods.class
package com.hp.hpl.jena.regression
NewRegressionAltMethods.createContainer ( ) :  Container
NewRegressionAltMethods.getContainerType ( ) :  Resource
NewRegressionAltMethods.NewRegressionAltMethods ( String name )
NewRegressionAltMethods.suite ( ) [static] :  Test
NewRegressionAltMethods.testDefaults ( ) :  void

cdk-1.4.0.jar, NewRegressionBagMethods.class
package com.hp.hpl.jena.regression
NewRegressionBagMethods.createContainer ( ) :  Container
NewRegressionBagMethods.getContainerType ( ) :  Resource
NewRegressionBagMethods.NewRegressionBagMethods ( String name )
NewRegressionBagMethods.suite ( ) [static] :  TestSuite

cdk-1.4.0.jar, NewRegressionBase.class
package com.hp.hpl.jena.regression
NewRegressionBase.NewRegressionBase ( String name )

cdk-1.4.0.jar, NewRegressionContainerMethods.class
package com.hp.hpl.jena.regression
NewRegressionContainerMethods.createContainer ( ) [abstract] :  Container
NewRegressionContainerMethods.getContainerType ( ) [abstract] :  Resource
NewRegressionContainerMethods.getModel ( ) :  Model
NewRegressionContainerMethods.NewRegressionContainerMethods ( String name )
NewRegressionContainerMethods.setUp ( ) :  void
NewRegressionContainerMethods.testContainerOfIntegers ( ) :  void
NewRegressionContainerMethods.testContainerOfIntegersRemovingA ( ) :  void
NewRegressionContainerMethods.testContainerOfIntegersRemovingB ( ) :  void
NewRegressionContainerMethods.testContainerOfIntegersRemovingC ( ) :  void
NewRegressionContainerMethods.testContainerOfIntegersWithRemoving ( boolean[ ] retain ) :  void
NewRegressionContainerMethods.testEmptyContainer ( ) :  void
NewRegressionContainerMethods.testFillingContainer ( ) :  void

cdk-1.4.0.jar, NewRegressionContainers.class
package com.hp.hpl.jena.regression
NewRegressionContainers.getModel ( ) :  Model
NewRegressionContainers.NewRegressionContainers ( String name )
NewRegressionContainers.setUp ( ) :  void
NewRegressionContainers.suite ( ) [static] :  TestSuite
NewRegressionContainers.tearDown ( ) :  void
NewRegressionContainers.testCreateAnonAlt ( ) :  void
NewRegressionContainers.testCreateAnonBag ( ) :  void
NewRegressionContainers.testCreateAnonSeq ( ) :  void
NewRegressionContainers.testCreateNamedAlt ( ) :  void
NewRegressionContainers.testCreateNamedBag ( ) :  void
NewRegressionContainers.testCreateNamedSeq ( ) :  void

cdk-1.4.0.jar, NewRegressionGet.class
package com.hp.hpl.jena.regression
NewRegressionGet.getModel ( ) :  Model
NewRegressionGet.NewRegressionGet ( String name )
NewRegressionGet.setUp ( ) :  void
NewRegressionGet.suite ( ) [static] :  TestSuite
NewRegressionGet.tearDown ( ) :  void
NewRegressionGet.testGetAlt ( ) :  void
NewRegressionGet.testGetBag ( ) :  void
NewRegressionGet.testGetPropertyOneArg ( ) :  void
NewRegressionGet.testGetPropertyTwoArgs ( ) :  void
NewRegressionGet.testGetResource ( ) :  void
NewRegressionGet.testGetResourceFactory ( ) :  void
NewRegressionGet.testGetSeq ( ) :  void

cdk-1.4.0.jar, NewRegressionListSubjects.class
package com.hp.hpl.jena.regression
NewRegressionListSubjects.assertEquiv ( Set set, Iterator iterator ) :  void
NewRegressionListSubjects.fillModel ( ) :  void
NewRegressionListSubjects.getModel ( ) :  Model
NewRegressionListSubjects.NewRegressionListSubjects ( String name )
NewRegressionListSubjects.setUp ( ) :  void
NewRegressionListSubjects.subjectsTo ( String prefix, int limit ) :  Set
NewRegressionListSubjects.suite ( ) [static] :  Test
NewRegressionListSubjects.tearDown ( ) :  void
NewRegressionListSubjects.test8 ( ) :  void
NewRegressionListSubjects.testGetRequiredProperty ( ) :  void

cdk-1.4.0.jar, NewRegressionLiterals.class
package com.hp.hpl.jena.regression
NewRegressionLiterals.assertInRange ( long min, long x, long max ) :  void
NewRegressionLiterals.assertOutsideRange ( long min, long x, long max ) :  void
NewRegressionLiterals.getModel ( ) :  Model
NewRegressionLiterals.NewRegressionLiterals ( String name )
NewRegressionLiterals.suite ( ) [static] :  TestSuite
NewRegressionLiterals.testBooleans ( ) :  void
NewRegressionLiterals.testByte ( Model m, byte tv ) :  void
NewRegressionLiterals.testByteLiterals ( ) :  void
NewRegressionLiterals.testCharacter ( Model m, char tv ) :  void
NewRegressionLiterals.testCharacterLiterals ( ) :  void
NewRegressionLiterals.testDouble ( Model m, double tv ) :  void
NewRegressionLiterals.testDoubleLiterals ( ) :  void
NewRegressionLiterals.testFloat ( Model m, float tv ) :  void
NewRegressionLiterals.testFloatLiterals ( ) :  void
NewRegressionLiterals.testInt ( Model m, int tv ) :  void
NewRegressionLiterals.testIntLiterals ( ) :  void
NewRegressionLiterals.testLanguagedString ( Model m, String tv, String lang ) :  void
NewRegressionLiterals.testLanguagedStringLiterals ( ) :  void
NewRegressionLiterals.testLiteralObject ( Model m, int x ) :  void
NewRegressionLiterals.testLiteralObjects ( ) :  void
NewRegressionLiterals.testLong ( Model m, long tv ) :  void
NewRegressionLiterals.testLongLiterals ( ) :  void
NewRegressionLiterals.testPlainString ( Model m, String tv ) :  void
NewRegressionLiterals.testPlainStringLiterals ( ) :  void
NewRegressionLiterals.testShort ( Model m, short tv ) :  void
NewRegressionLiterals.testShortLiterals ( ) :  void
NewRegressionLiterals.testStringLiteralEquality ( ) :  void

cdk-1.4.0.jar, NewRegressionObjects.class
package com.hp.hpl.jena.regression
NewRegressionObjects.fill ( Model m ) :  Set
NewRegressionObjects.getModel ( ) :  Model
NewRegressionObjects.literalsFor ( int predicate ) :  Set
NewRegressionObjects.literalsUpto ( int limit ) :  Set
NewRegressionObjects.NewRegressionObjects ( String name )
NewRegressionObjects.predicateSet ( int limit ) :  Set
NewRegressionObjects.setUp ( ) :  void
NewRegressionObjects.subjectSet ( int limit ) :  Set
NewRegressionObjects.suite ( ) [static] :  TestSuite
NewRegressionObjects.tearDown ( ) :  void
NewRegressionObjects.testListNamespaces ( ) :  void
NewRegressionObjects.testListObjects ( ) :  void
NewRegressionObjects.testListObjectsOfPropertyByProperty ( ) :  void
NewRegressionObjects.testListObjectsOfPropertyBySubject ( ) :  void
NewRegressionObjects.testListStatements ( ) :  void
NewRegressionObjects.testListSubjects ( ) :  void

cdk-1.4.0.jar, NewRegressionResourceMethods.class
package com.hp.hpl.jena.regression
NewRegressionResourceMethods.getModel ( ) :  Model
NewRegressionResourceMethods.NewRegressionResourceMethods ( String name )
NewRegressionResourceMethods.setUp ( ) :  void
NewRegressionResourceMethods.suite ( ) [static] :  Test
NewRegressionResourceMethods.testAllSubjectsCorrect ( ) :  void
NewRegressionResourceMethods.testBoolean ( ) :  void
NewRegressionResourceMethods.testByte ( ) :  void
NewRegressionResourceMethods.testChar ( ) :  void
NewRegressionResourceMethods.testCorrectSubject ( ) :  void
NewRegressionResourceMethods.testCountsCorrect ( ) :  void
NewRegressionResourceMethods.testDouble ( ) :  void
NewRegressionResourceMethods.testFloat ( ) :  void
NewRegressionResourceMethods.testHasSubjectR ( StmtIterator it ) :  void
NewRegressionResourceMethods.testInt ( ) :  void
NewRegressionResourceMethods.testLiteral ( ) :  void
NewRegressionResourceMethods.testLong ( ) :  void
NewRegressionResourceMethods.testNoSuchPropertyException ( ) :  void
NewRegressionResourceMethods.testNoSuchPropertyNull ( ) :  void
NewRegressionResourceMethods.testObject ( ) :  void
NewRegressionResourceMethods.testRemoveProperties ( ) :  void
NewRegressionResourceMethods.testResource ( ) :  void
NewRegressionResourceMethods.testShort ( ) :  void
NewRegressionResourceMethods.testString ( ) :  void
NewRegressionResourceMethods.testStringWithLanguage ( ) :  void

cdk-1.4.0.jar, NewRegressionResources.class
package com.hp.hpl.jena.regression
NewRegressionResources.checkNumericContent ( Container cont2, int num ) :  void
NewRegressionResources.getModel ( ) :  Model
NewRegressionResources.NewRegressionResources ( String name )
NewRegressionResources.retainOnlySpecified ( Container cont2, int num, boolean[ ] retain ) :  void
NewRegressionResources.seeWhatsThere ( Container cont2, boolean[ ] found ) :  void
NewRegressionResources.setOf ( Object x ) :  Set
NewRegressionResources.suite ( ) [static] :  TestSuite
NewRegressionResources.testContainer ( Model m, Container cont1, Container cont2 ) :  void
NewRegressionResources.testCreateAnonByFactory ( ) :  void
NewRegressionResources.testCreateAnonResource ( ) :  void
NewRegressionResources.testCreateAnonResourceWithNull ( ) :  void
NewRegressionResources.testCreateNamedResource ( ) :  void
NewRegressionResources.testCreateNullPropertyFails ( ) :  void
NewRegressionResources.testCreatePropertyOneArg ( ) :  void
NewRegressionResources.testCreatePropertyStrangeURI ( ) :  void
NewRegressionResources.testCreatePropertyStrangeURITwoArgs ( ) :  void
NewRegressionResources.testCreatePropertyTwoArgs ( ) :  void
NewRegressionResources.testCreateResourceByFactory ( ) :  void
NewRegressionResources.testCreateTypedAnonResource ( ) :  void
NewRegressionResources.testCreateTypedNamedresource ( ) :  void
NewRegressionResources.testEnhancedResources ( ) :  void
NewRegressionResources.testResource ( Model m, Resource r, int numProps ) :  void

cdk-1.4.0.jar, NewRegressionSelector.class
package com.hp.hpl.jena.regression
NewRegressionSelector.getModel ( ) :  Model
NewRegressionSelector.NewRegressionSelector ( String name )
NewRegressionSelector.setUp ( ) :  void
NewRegressionSelector.suite ( ) [static] :  Test
NewRegressionSelector.tearDown ( ) :  void
NewRegressionSelector.test9 ( ) :  void

cdk-1.4.0.jar, NewRegressionSeq.class
package com.hp.hpl.jena.regression
NewRegressionSeq.bools ( String s ) :  boolean[ ]
NewRegressionSeq.getModel ( ) :  Model
NewRegressionSeq.NewRegressionSeq ( String name )
NewRegressionSeq.setUp ( ) :  void
NewRegressionSeq.suite ( ) [static] :  Test
NewRegressionSeq.tearDown ( ) :  void
NewRegressionSeq.testMoreIndexing ( ) :  void
NewRegressionSeq.testRemove ( boolean[ ] retain ) :  void
NewRegressionSeq.testRemoveA ( ) :  void
NewRegressionSeq.testRemoveB ( ) :  void
NewRegressionSeq.testRemoveC ( ) :  void
NewRegressionSeq.testSeqAccessByIndexing ( ) :  void
NewRegressionSeq.testSeqAdd ( ) :  void
NewRegressionSeq.testSeqAddInts ( ) :  void
NewRegressionSeq.testSeqInsertByIndexing ( ) :  void
NewRegressionSeq.testSet ( ) :  void

cdk-1.4.0.jar, NewRegressionSeqMethods.class
package com.hp.hpl.jena.regression
NewRegressionSeqMethods.createContainer ( ) :  Container
NewRegressionSeqMethods.error ( String test, int n ) :  void
NewRegressionSeqMethods.getContainerType ( ) :  Resource
NewRegressionSeqMethods.NewRegressionSeqMethods ( String name )
NewRegressionSeqMethods.setUp ( ) :  void
NewRegressionSeqMethods.suite ( ) [static] :  TestSuite
NewRegressionSeqMethods.testSeq4 ( ) :  void
NewRegressionSeqMethods.testSeq5 ( ) :  void
NewRegressionSeqMethods.testSeq6 ( ) :  void
NewRegressionSeqMethods.testSeq7 ( ) :  void

cdk-1.4.0.jar, NewRegressionSet.class
package com.hp.hpl.jena.regression
NewRegressionSet.getModel ( ) :  Model
NewRegressionSet.NewRegressionSet ( String name )
NewRegressionSet.setUp ( ) :  void
NewRegressionSet.suite ( ) [static] :  Test
NewRegressionSet.testDifference ( ) :  void
NewRegressionSet.testIntersection ( ) :  void
NewRegressionSet.testUnion ( ) :  void

cdk-1.4.0.jar, NewRegressionStatementMethods.class
package com.hp.hpl.jena.regression
NewRegressionStatementMethods.checkChangedStatementSP ( Statement changed ) :  void
NewRegressionStatementMethods.checkCorrectStatements ( Statement sTrue, Statement changed ) :  void
NewRegressionStatementMethods.getModel ( ) :  Model
NewRegressionStatementMethods.loadInitialStatement ( ) :  Statement
NewRegressionStatementMethods.NewRegressionStatementMethods ( String name )
NewRegressionStatementMethods.setUp ( ) :  void
NewRegressionStatementMethods.suite ( ) [static] :  Test
NewRegressionStatementMethods.testAlt ( ) :  void
NewRegressionStatementMethods.testBag ( ) :  void
NewRegressionStatementMethods.testBoolean ( ) :  void
NewRegressionStatementMethods.testByte ( ) :  void
NewRegressionStatementMethods.testChangeObjectBoolean ( ) :  void
NewRegressionStatementMethods.testChangeObjectByte ( ) :  void
NewRegressionStatementMethods.testChangeObjectChar ( ) :  void
NewRegressionStatementMethods.testChangeObjectDouble ( ) :  void
NewRegressionStatementMethods.testChangeObjectFloat ( ) :  void
NewRegressionStatementMethods.testChangeObjectInt ( ) :  void
NewRegressionStatementMethods.testChangeObjectLiteral ( ) :  void
NewRegressionStatementMethods.testChangeObjectLong ( ) :  void
NewRegressionStatementMethods.testChangeObjectResObject ( ) :  void
NewRegressionStatementMethods.testChangeObjectShort ( ) :  void
NewRegressionStatementMethods.testChangeObjectString ( ) :  void
NewRegressionStatementMethods.testChangeObjectStringWithLanguage ( ) :  void
NewRegressionStatementMethods.testChangeObjectYByte ( ) :  void
NewRegressionStatementMethods.testChar ( ) :  void
NewRegressionStatementMethods.testDouble ( ) :  void
NewRegressionStatementMethods.testFloat ( ) :  void
NewRegressionStatementMethods.testGetLiteralFailure ( ) :  void
NewRegressionStatementMethods.testGetResource ( ) :  void
NewRegressionStatementMethods.testGetResourceFailure ( ) :  void
NewRegressionStatementMethods.testGetTrueBoolean ( ) :  void
NewRegressionStatementMethods.testInt ( ) :  void
NewRegressionStatementMethods.testLitObj ( ) :  void
NewRegressionStatementMethods.testLong ( ) :  void
NewRegressionStatementMethods.testResObj ( ) :  void
NewRegressionStatementMethods.testSeq ( ) :  void
NewRegressionStatementMethods.testShort ( ) :  void
NewRegressionStatementMethods.testString ( ) :  void
NewRegressionStatementMethods.testStringWithLanguage ( ) :  void

cdk-1.4.0.jar, NewRegressionStatements.class
package com.hp.hpl.jena.regression
NewRegressionStatements.getModel ( ) :  Model
NewRegressionStatements.NewRegressionStatements ( String name )
NewRegressionStatements.setUp ( ) :  void
NewRegressionStatements.suite ( ) [static] :  TestSuite
NewRegressionStatements.tearDown ( ) :  void
NewRegressionStatements.testCreateStatementByteMax ( ) :  void
NewRegressionStatements.testCreateStatementChar ( ) :  void
NewRegressionStatements.testCreateStatementDouble ( ) :  void
NewRegressionStatements.testCreateStatementFactory ( ) :  void
NewRegressionStatements.testCreateStatementFloat ( ) :  void
NewRegressionStatements.testCreateStatementIntMax ( ) :  void
NewRegressionStatements.testCreateStatementLongMax ( ) :  void
NewRegressionStatements.testCreateStatementResource ( ) :  void
NewRegressionStatements.testCreateStatementShortMax ( ) :  void
NewRegressionStatements.testCreateStatementString ( ) :  void
NewRegressionStatements.testCreateStatementTrue ( ) :  void
NewRegressionStatements.testCreateStatementTypeLiteral ( ) :  void

cdk-1.4.0.jar, NiceIterator.class
package com.hp.hpl.jena.util.iterator
NiceIterator.andThen ( Iterator a, Iterator b ) [static] :  ExtendedIterator
NiceIterator.andThen ( Iterator other ) :  ExtendedIterator
NiceIterator.asList ( ExtendedIterator it ) [static] :  List
NiceIterator.asSet ( ExtendedIterator it ) [static] :  Set
NiceIterator.close ( ) :  void
NiceIterator.close ( Iterator it ) [static] :  void
NiceIterator.emptyIterator ( ) [static] :  ExtendedIterator
NiceIterator.ensureHasNext ( ) :  void
NiceIterator.filterDrop ( Filter f ) :  ExtendedIterator
NiceIterator.filterKeep ( Filter f ) :  ExtendedIterator
NiceIterator.hasNext ( ) :  boolean
NiceIterator.mapWith ( Map1 map1 ) :  ExtendedIterator
NiceIterator.next ( ) :  Object
NiceIterator.NiceIterator ( )
NiceIterator.noElements ( String message ) :  Object
NiceIterator.remove ( ) :  void
NiceIterator.removeNext ( ) :  Object
NiceIterator.toList ( ) :  List
NiceIterator.toSet ( ) :  Set

cdk-1.4.0.jar, NNBond.class
package org.openscience.cdk.nonotify
NNBond.NNBond ( IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo )

cdk-1.4.0.jar, Node.class
package com.hp.hpl.jena.graph
Node.cache ( boolean wantCache ) [static] :  void
Node.create ( Node.NodeMaker maker, Object label ) [static] :  Node
Node.createAnon ( ) [static] :  Node
Node.createAnon ( AnonId id ) [static] :  Node
Node.createLiteral ( LiteralLabel lit ) [static] :  Node
Node.createLiteral ( String lex, String lang, RDFDatatype dtype ) [static] :  Node
Node.createLiteral ( String lit, String lang, boolean isXml ) [static] :  Node
Node.createLiteral ( String value ) [static] :  Node
Node.createUncachedLiteral ( Object value, String lang, RDFDatatype dtype ) [static] :  Node
Node.createURI ( String uri ) [static] :  Node
Node.createVariable ( String name ) [static] :  Node
Node.equals ( Object p1 ) [abstract] :  boolean
Node.getBlankNodeId ( ) :  AnonId
Node.getBlankNodeLabel ( ) :  String
Node.getIndexingValue ( ) :  Object
Node.getLiteral ( ) :  LiteralLabel
Node.getLiteralDatatype ( ) :  RDFDatatype
Node.getLiteralDatatypeURI ( ) :  String
Node.getLiteralIsXML ( ) :  boolean
Node.getLiteralLanguage ( ) :  String
Node.getLiteralLexicalForm ( ) :  String
Node.getLiteralValue ( ) :  Object
Node.getLocalName ( ) :  String
Node.getName ( ) :  String
Node.getNameSpace ( ) :  String
Node.getType ( String s ) [static] :  RDFDatatype
Node.getURI ( ) :  String
Node.hashCode ( ) :  int
Node.hasURI ( String uri ) :  boolean
Node.isBlank ( ) :  boolean
Node.isConcrete ( ) [abstract] :  boolean
Node.isLiteral ( ) :  boolean
Node.isURI ( ) :  boolean
Node.isVariable ( ) :  boolean
Node.matches ( Node other ) :  boolean
Node.sameValueAs ( Object o ) :  boolean
Node.toString ( ) :  String
Node.toString ( boolean quoting ) :  String
Node.toString ( PrefixMapping pm ) :  String
Node.toString ( PrefixMapping pm, boolean quoting ) :  String
Node.visitWith ( NodeVisitor p1 ) [abstract] :  Object
package signature
ColoredTree.Node.accept ( ColoredTreeVisitor visitor ) :  void
ColoredTree.Node.buildString ( StringBuilder builder ) :  void
ColoredTree.Node.ColoredTree.Node ( ColoredTree label, String parent, ColoredTree.Node height, int color, int edgeLabel, String p6 )
ColoredTree.Node.ColoredTree.Node ( ColoredTree label, String parent, ColoredTree.Node height, int color, int p5 )
ColoredTree.Node.ColoredTree.Node ( ColoredTree label, String parent, ColoredTree.Node height, int p4 )
ColoredTree.Node.isColored ( ) :  boolean
ColoredTree.Node.toString ( ) :  String
DAG.Node.accept ( DAGVisitor visitor ) :  void
DAG.Node.addChild ( DAG.Node node ) :  void
DAG.Node.addEdgeColor ( int partnerIndex, int edgeColor ) :  void
DAG.Node.addParent ( DAG.Node node ) :  void
DAG.Node.DAG.Node ( DAG vertexIndex, int layer, int p3 )
DAG.Node.toString ( ) :  String

cdk-1.4.0.jar, Node_ANY.class
package com.hp.hpl.jena.graph
Node_ANY.equals ( Object other ) :  boolean
Node_ANY.matches ( Node other ) :  boolean
Node_ANY.toString ( ) :  String
Node_ANY.toString ( PrefixMapping pm, boolean quoting ) :  String
Node_ANY.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, Node_Blank.class
package com.hp.hpl.jena.graph
Node_Blank.equals ( Object other ) :  boolean
Node_Blank.getBlankNodeId ( ) :  AnonId
Node_Blank.isBlank ( ) :  boolean
Node_Blank.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, Node_Concrete.class
package com.hp.hpl.jena.graph
Node_Concrete.isConcrete ( ) :  boolean
Node_Concrete.Node_Concrete ( Object label )

cdk-1.4.0.jar, Node_Fluid.class
package com.hp.hpl.jena.graph
Node_Fluid.isConcrete ( ) :  boolean
Node_Fluid.Node_Fluid ( Object label )

cdk-1.4.0.jar, Node_Literal.class
package com.hp.hpl.jena.graph
Node_Literal.equals ( Object other ) :  boolean
Node_Literal.getIndexingValue ( ) :  Object
Node_Literal.getLiteral ( ) :  LiteralLabel
Node_Literal.getLiteralDatatype ( ) :  RDFDatatype
Node_Literal.getLiteralDatatypeURI ( ) :  String
Node_Literal.getLiteralIsXML ( ) :  boolean
Node_Literal.getLiteralLanguage ( ) :  String
Node_Literal.getLiteralLexicalForm ( ) :  String
Node_Literal.getLiteralValue ( ) :  Object
Node_Literal.isLiteral ( ) :  boolean
Node_Literal.matches ( Node x ) :  boolean
Node_Literal.sameValueAs ( Object o ) :  boolean
Node_Literal.toString ( PrefixMapping pm, boolean quoting ) :  String
Node_Literal.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, Node_NULL.class
package com.hp.hpl.jena.graph
Node_NULL.equals ( Object other ) :  boolean
Node_NULL.toString ( ) :  String
Node_NULL.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, Node_RuleVariable.class
package com.hp.hpl.jena.reasoner.rulesys
Node_RuleVariable.cloneNode ( ) :  Node_RuleVariable
Node_RuleVariable.deref ( ) :  Node
Node_RuleVariable.getIndex ( ) :  int
Node_RuleVariable.getRawBoundValue ( ) :  Node
Node_RuleVariable.isUnbound ( ) :  boolean
Node_RuleVariable.Node_RuleVariable ( String label, int index )
Node_RuleVariable.sameNodeAs ( Node n, Node m ) [static] :  boolean
Node_RuleVariable.sameValueAs ( Object o ) :  boolean
Node_RuleVariable.setIndex ( int index ) :  void
Node_RuleVariable.simpleBind ( Node node ) :  void
Node_RuleVariable.toString ( ) :  String
Node_RuleVariable.unbind ( ) :  void

cdk-1.4.0.jar, Node_URI.class
package com.hp.hpl.jena.graph
Node_URI.equals ( Object other ) :  boolean
Node_URI.getLocalName ( ) :  String
Node_URI.getNameSpace ( ) :  String
Node_URI.getURI ( ) :  String
Node_URI.hasURI ( String uri ) :  boolean
Node_URI.isURI ( ) :  boolean
Node_URI.Node_URI ( Object uri )
Node_URI.toString ( PrefixMapping pm, boolean quoting ) :  String
Node_URI.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, Node_Variable.class
package com.hp.hpl.jena.graph
Node_Variable.equals ( Object other ) :  boolean
Node_Variable.getName ( ) :  String
Node_Variable.isVariable ( ) :  boolean
Node_Variable.Node_Variable ( Object name )
Node_Variable.Node_Variable ( String name )
Node_Variable.toString ( ) :  String
Node_Variable.variable ( String name ) [static] :  Object
Node_Variable.visitWith ( NodeVisitor v ) :  Object

cdk-1.4.0.jar, NodeBuilder.class
package org.openscience.cdk.smsd.algorithm.vflib.builder
NodeBuilder.addEdge ( EdgeBuilder edge ) :  void
NodeBuilder.addNeighbor ( NodeBuilder node ) :  void
NodeBuilder.countNeighbors ( ) :  int
NodeBuilder.getAtomMatcher ( ) :  VFAtomMatcher
NodeBuilder.getEdges ( ) :  List
NodeBuilder.neighbors ( ) :  Iterable
NodeBuilder.NodeBuilder ( VFAtomMatcher matcher )

cdk-1.4.0.jar, NodeCache.class
package com.hp.hpl.jena.graph
NodeCache.clear ( ) :  void
NodeCache.get ( Object label ) :  Node
NodeCache.NodeCache ( )
NodeCache.put ( Object label, Node cached ) :  void
NodeCache.size ( ) :  int

cdk-1.4.0.jar, NodeIntegerLabelComparator.class
package signature
DAG.NodeIntegerLabelComparator.compare ( DAG.Node o1, DAG.Node o2 ) :  int
DAG.NodeIntegerLabelComparator.compare ( Object x0, Object x1 ) :  int
DAG.NodeIntegerLabelComparator.DAG.NodeIntegerLabelComparator ( DAG vertexLabels, int[ ] p2 )

cdk-1.4.0.jar, NodeIterator.class
package com.hp.hpl.jena.rdf.model
NodeIterator.close ( ) [abstract] :  void
NodeIterator.hasNext ( ) [abstract] :  boolean
NodeIterator.next ( ) [abstract] :  RDFNode
NodeIterator.nextNode ( ) [abstract] :  RDFNode
NodeIterator.remove ( ) [abstract] :  void

cdk-1.4.0.jar, NodePersonality.class
package com.hp.hpl.jena.enhanced
NodePersonality.NodePersonality ( )

cdk-1.4.0.jar, Nodes.class
package com.hp.hpl.jena.vocabulary
RDF.Nodes.RDF.Nodes ( )
RDFS.Nodes.RDFS.Nodes ( )

cdk-1.4.0.jar, NodeStringLabelComparator.class
package signature
DAG.NodeStringLabelComparator.compare ( DAG.Node o1, DAG.Node o2 ) :  int
DAG.NodeStringLabelComparator.compare ( Object x0, Object x1 ) :  int
DAG.NodeStringLabelComparator.DAG.NodeStringLabelComparator ( DAG vertexLabels, String[ ] p2 )

cdk-1.4.0.jar, NodeToTriplesMap.class
package com.hp.hpl.jena.mem
NodeToTriplesMap.add ( Triple t ) :  boolean
NodeToTriplesMap.contains ( Triple t ) :  boolean
NodeToTriplesMap.containsBySameValueAs ( Triple t ) :  boolean
NodeToTriplesMap.equalsObjectOK ( Triple t ) [static] :  boolean
NodeToTriplesMap.iterateAll ( Triple pattern ) :  ExtendedIterator
NodeToTriplesMap.iterator ( Node index, Node n2, Node n3 ) :  ExtendedIterator
NodeToTriplesMap.iterator ( Object o, HashCommon.NotifyEmpty container ) :  ExtendedIterator
NodeToTriplesMap.iterator ( Object x0, HashCommon.NotifyEmpty x1 ) :  Iterator
NodeToTriplesMap.iteratorForIndexed ( Object y ) :  Iterator
NodeToTriplesMap.NodeToTriplesMap ( Triple.Field indexField, Triple.Field f2, Triple.Field f3 )
NodeToTriplesMap.remove ( Triple t ) :  boolean
NodeToTriplesMap.slowContains ( Triple t ) :  boolean

cdk-1.4.0.jar, NodeToTriplesMapBase.class
package com.hp.hpl.jena.mem
NodeToTriplesMapBase.add ( Triple p1 ) [abstract] :  boolean
NodeToTriplesMapBase.clear ( ) :  void
NodeToTriplesMapBase.contains ( Triple p1 ) [abstract] :  boolean
NodeToTriplesMapBase.containsBySameValueAs ( Triple p1 ) [abstract] :  boolean
NodeToTriplesMapBase.domain ( ) :  Iterator
NodeToTriplesMapBase.getIndexField ( Triple t ) :  Object
NodeToTriplesMapBase.isEmpty ( ) :  boolean
NodeToTriplesMapBase.iterateAll ( ) :  ExtendedIterator
NodeToTriplesMapBase.iterator ( Node p1, Node p2, Node p3 ) [abstract] :  ExtendedIterator
NodeToTriplesMapBase.iterator ( Object p1, HashCommon.NotifyEmpty p2 ) [abstract] :  Iterator
NodeToTriplesMapBase.iteratorForIndexed ( Object p1 ) [abstract] :  Iterator
NodeToTriplesMapBase.NodeToTriplesMapBase ( Triple.Field indexField, Triple.Field f2, Triple.Field f3 )
NodeToTriplesMapBase.remove ( Triple p1 ) [abstract] :  boolean
NodeToTriplesMapBase.removedOneViaIterator ( ) :  void
NodeToTriplesMapBase.size ( ) :  int

cdk-1.4.0.jar, NodeToTriplesMapFaster.class
package com.hp.hpl.jena.mem.faster
NodeToTriplesMapFaster.add ( Triple t ) :  boolean
NodeToTriplesMapFaster.contains ( Triple t ) :  boolean
NodeToTriplesMapFaster.containsBySameValueAs ( Triple t ) :  boolean
NodeToTriplesMapFaster.createBoundOApplyer ( ProcessedTriple pt ) :  Applyer
NodeToTriplesMapFaster.createBoundSApplyer ( ProcessedTriple pt ) :  Applyer
NodeToTriplesMapFaster.createFixedOApplyer ( ProcessedTriple Q ) :  Applyer
NodeToTriplesMapFaster.createFixedSApplyer ( ProcessedTriple Q ) :  Applyer
NodeToTriplesMapFaster.get ( Object index ) :  TripleBunch
NodeToTriplesMapFaster.iterator ( Node index, Node n2, Node n3 ) :  ExtendedIterator
NodeToTriplesMapFaster.iterator ( Object o, HashCommon.NotifyEmpty container ) :  Iterator
NodeToTriplesMapFaster.iteratorForIndexed ( Object y ) :  Iterator
NodeToTriplesMapFaster.NodeToTriplesMapFaster ( Triple.Field indexField, Triple.Field f2, Triple.Field f3 )
NodeToTriplesMapFaster.remove ( Triple t ) :  boolean

cdk-1.4.0.jar, NodeVisitor.class
package com.hp.hpl.jena.graph
NodeVisitor.visitAny ( Node_ANY p1 ) [abstract] :  Object
NodeVisitor.visitBlank ( Node_Blank p1, AnonId p2 ) [abstract] :  Object
NodeVisitor.visitLiteral ( Node_Literal p1, LiteralLabel p2 ) [abstract] :  Object
NodeVisitor.visitURI ( Node_URI p1, String p2 ) [abstract] :  Object
NodeVisitor.visitVariable ( Node_Variable p1, String p2 ) [abstract] :  Object

cdk-1.4.0.jar, NoImplementationException.class
package com.hp.hpl.jena.assembler.exceptions
NoImplementationException.getAssembler ( ) :  Assembler
NoImplementationException.getType ( ) :  Resource
NoImplementationException.NoImplementationException ( Assembler assembler, Resource root, Resource type )

cdk-1.4.0.jar, NoneOf.class
package com.hp.hpl.jena.graph.query.regexptrees
NoneOf.equals ( Object other ) :  boolean
NoneOf.hashCode ( ) :  int
NoneOf.NoneOf ( String impossibles )
NoneOf.toString ( ) :  String

cdk-1.4.0.jar, NoNotificationChemObjectBuilder.class
package org.openscience.cdk.nonotify
NoNotificationChemObjectBuilder.getInstance ( ) [static] :  IChemObjectBuilder
NoNotificationChemObjectBuilder.newInstance ( Class clazz, Object[ ] params ) :  ICDKObject

cdk-1.4.0.jar, NOPLogger.class
package org.slf4j.helpers
NOPLogger.debug ( String format, Object arg ) :  void
NOPLogger.debug ( String format, Object arg1, Object arg2 ) :  void
NOPLogger.debug ( String format, Object[ ] argArray ) :  void
NOPLogger.debug ( String msg ) :  void
NOPLogger.debug ( String msg, Throwable t ) :  void
NOPLogger.error ( String format, Object arg1 ) :  void
NOPLogger.error ( String format, Object arg1, Object arg2 ) :  void
NOPLogger.error ( String format, Object[ ] argArray ) :  void
NOPLogger.error ( String msg ) :  void
NOPLogger.error ( String msg, Throwable t ) :  void
NOPLogger.getName ( ) :  String
NOPLogger.info ( String format, Object arg1 ) :  void
NOPLogger.info ( String format, Object arg1, Object arg2 ) :  void
NOPLogger.info ( String format, Object[ ] argArray ) :  void
NOPLogger.info ( String msg ) :  void
NOPLogger.info ( String msg, Throwable t ) :  void
NOPLogger.isDebugEnabled ( ) :  boolean
NOPLogger.isErrorEnabled ( ) :  boolean
NOPLogger.isInfoEnabled ( ) :  boolean
NOPLogger.isTraceEnabled ( ) :  boolean
NOPLogger.isWarnEnabled ( ) :  boolean
NOPLogger.NOPLogger ( )
NOPLogger.trace ( String format, Object arg ) :  void
NOPLogger.trace ( String format, Object arg1, Object arg2 ) :  void
NOPLogger.trace ( String format, Object[ ] argArray ) :  void
NOPLogger.trace ( String msg ) :  void
NOPLogger.trace ( String msg, Throwable t ) :  void
NOPLogger.warn ( String format, Object arg1 ) :  void
NOPLogger.warn ( String format, Object arg1, Object arg2 ) :  void
NOPLogger.warn ( String format, Object[ ] argArray ) :  void
NOPLogger.warn ( String msg ) :  void
NOPLogger.warn ( String msg, Throwable t ) :  void

cdk-1.4.0.jar, NOPMakerAdapter.class
package org.slf4j.helpers
NOPMakerAdapter.clear ( ) :  void
NOPMakerAdapter.get ( String key ) :  String
NOPMakerAdapter.getCopyOfContextMap ( ) :  Map
NOPMakerAdapter.NOPMakerAdapter ( )
NOPMakerAdapter.put ( String key, String val ) :  void
NOPMakerAdapter.remove ( String key ) :  void
NOPMakerAdapter.setContextMap ( Map contextMap ) :  void

cdk-1.4.0.jar, NoReaderForLangException.class
package com.hp.hpl.jena.shared
NoReaderForLangException.NoReaderForLangException ( String lang )

cdk-1.4.0.jar, NoReasonerSuppliedException.class
package com.hp.hpl.jena.shared
NoReasonerSuppliedException.NoReasonerSuppliedException ( )

cdk-1.4.0.jar, Normalizer.class
package com.ibm.icu.text
Normalizer.clone ( ) :  Object
Normalizer.compare ( char[ ] s1, char[ ] s2, int options ) [static] :  int
Normalizer.compare ( char[ ] s1, int s1Start, int s1Limit, char[ ] s2, int s2Start, int s2Limit, int options ) [static] :  int
Normalizer.compare ( int char32a, int char32b, int options ) [static] :  int
Normalizer.compare ( int char32a, String str2, int options ) [static] :  int
Normalizer.compare ( String s1, String s2, int options ) [static] :  int
Normalizer.compose ( char[ ] source, char[ ] target, boolean compat, int options ) [static] :  int
Normalizer.compose ( char[ ] src, int srcStart, int srcLimit, char[ ] dest, int destStart, int destLimit, boolean compat, int options ) [static] :  int
Normalizer.compose ( String str, boolean compat ) [static] :  String
Normalizer.compose ( String str, boolean compat, int options ) [static] :  String
Normalizer.concatenate ( char[ ] left, char[ ] right, Normalizer.Mode mode, int options ) [static] :  String
Normalizer.concatenate ( char[ ] left, int leftStart, int leftLimit, char[ ] right, int rightStart, int rightLimit, char[ ] dest, int destStart, int destLimit, Normalizer.Mode mode, int options ) [static] :  int
Normalizer.concatenate ( String left, String right, Normalizer.Mode mode, int options ) [static] :  String
Normalizer.current ( ) :  int
Normalizer.decompose ( char[ ] source, char[ ] target, boolean compat, int options ) [static] :  int
Normalizer.decompose ( char[ ] src, int srcStart, int srcLimit, char[ ] dest, int destStart, int destLimit, boolean compat, int options ) [static] :  int
Normalizer.decompose ( String str, boolean compat ) [static] :  String
Normalizer.decompose ( String str, boolean compat, int options ) [static] :  String
Normalizer.endIndex ( ) :  int
Normalizer.first ( ) :  int
Normalizer.getBeginIndex ( ) :  int *DEPRECATED*
Normalizer.getEndIndex ( ) :  int *DEPRECATED*
Normalizer.getFC_NFKC_Closure ( int c ) [static] :  String
Normalizer.getFC_NFKC_Closure ( int c, char[ ] dest ) [static] :  int
Normalizer.getIndex ( ) :  int
Normalizer.getLength ( ) :  int
Normalizer.getMode ( ) :  Normalizer.Mode
Normalizer.getOption ( int option ) :  int
Normalizer.getText ( ) :  String
Normalizer.getText ( char[ ] fillIn ) :  int
Normalizer.isNFSkippable ( int c, Normalizer.Mode mode ) [static] :  boolean
Normalizer.isNormalized ( char[ ] src, int start, int limit, Normalizer.Mode mode, int options ) [static] :  boolean
Normalizer.isNormalized ( int char32, Normalizer.Mode mode, int options ) [static] :  boolean
Normalizer.isNormalized ( String str, Normalizer.Mode mode, int options ) [static] :  boolean
Normalizer.last ( ) :  int
Normalizer.next ( ) :  int
Normalizer.normalize ( char[ ] source, char[ ] target, Normalizer.Mode mode, int options ) [static] :  int
Normalizer.normalize ( char[ ] src, int srcStart, int srcLimit, char[ ] dest, int destStart, int destLimit, Normalizer.Mode mode, int options ) [static] :  int
Normalizer.normalize ( int char32, Normalizer.Mode mode ) [static] :  String
Normalizer.normalize ( int char32, Normalizer.Mode mode, int options ) [static] :  String
Normalizer.normalize ( String src, Normalizer.Mode mode ) [static] :  String
Normalizer.normalize ( String str, Normalizer.Mode mode, int options ) [static] :  String
Normalizer.Normalizer ( CharacterIterator iter, Normalizer.Mode mode, int opt )
Normalizer.Normalizer ( String str, Normalizer.Mode mode, int opt )
Normalizer.Normalizer ( UCharacterIterator iter, Normalizer.Mode mode, int options )
Normalizer.previous ( ) :  int
Normalizer.quickCheck ( char[ ] source, int start, int limit, Normalizer.Mode mode, int options ) [static] :  Normalizer.QuickCheckResult
Normalizer.quickCheck ( char[ ] source, Normalizer.Mode mode, int options ) [static] :  Normalizer.QuickCheckResult
Normalizer.quickCheck ( String source, Normalizer.Mode mode ) [static] :  Normalizer.QuickCheckResult
Normalizer.quickCheck ( String source, Normalizer.Mode mode, int options ) [static] :  Normalizer.QuickCheckResult
Normalizer.reset ( ) :  void
Normalizer.setIndex ( int index ) :  int *DEPRECATED*
Normalizer.setIndexOnly ( int index ) :  void
Normalizer.setMode ( Normalizer.Mode newMode ) :  void
Normalizer.setOption ( int option, boolean value ) :  void
Normalizer.setText ( char[ ] newText ) :  void
Normalizer.setText ( CharacterIterator newText ) :  void
Normalizer.setText ( String newText ) :  void
Normalizer.setText ( StringBuffer newText ) :  void
Normalizer.setText ( UCharacterIterator newText ) :  void
Normalizer.startIndex ( ) :  int
package org.openscience.cdk.normalize
Normalizer.normalize ( IAtomContainer ac, Document doc ) [static] :  boolean
Normalizer.Normalizer ( )

cdk-1.4.0.jar, NoSpecificTypeException.class
package com.hp.hpl.jena.assembler.exceptions
NoSpecificTypeException.NoSpecificTypeException ( Resource root )

cdk-1.4.0.jar, NoSuchReasonerException.class
package com.hp.hpl.jena.shared
NoSuchReasonerException.getURI ( ) :  String
NoSuchReasonerException.NoSuchReasonerException ( String uri )

cdk-1.4.0.jar, NotBNode.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
NotBNode.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NotBNode.getArgLength ( ) :  int
NotBNode.getName ( ) :  String
NotBNode.NotBNode ( )

cdk-1.4.0.jar, NotDType.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
NotDType.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NotDType.getArgLength ( ) :  int
NotDType.getName ( ) :  String
NotDType.NotDType ( )

cdk-1.4.0.jar, NotEqual.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
NotEqual.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NotEqual.getArgLength ( ) :  int
NotEqual.getName ( ) :  String
NotEqual.NotEqual ( )

cdk-1.4.0.jar, NotExpectedTypeException.class
package com.hp.hpl.jena.assembler.exceptions
NotExpectedTypeException.getActualType ( ) :  Class
NotExpectedTypeException.getExpectedType ( ) :  Class
NotExpectedTypeException.NotExpectedTypeException ( Resource root, Class expectedType, Class actualType )

cdk-1.4.0.jar, NotFoundException.class
package com.hp.hpl.jena.shared
NotFoundException.NotFoundException ( String name )

cdk-1.4.0.jar, NotFunctor.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
NotFunctor.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NotFunctor.getArgLength ( ) :  int
NotFunctor.getName ( ) :  String
NotFunctor.NotFunctor ( )

cdk-1.4.0.jar, Nothing.class
package com.hp.hpl.jena.graph.query.regexptrees
Nothing.equals ( Object other ) :  boolean
Nothing.hashCode ( ) :  int
Nothing.Nothing ( )
Nothing.toString ( ) :  String

cdk-1.4.0.jar, NotifyEmpty.class
package com.hp.hpl.jena.mem
HashCommon.NotifyEmpty.emptied ( ) [abstract] :  void

cdk-1.4.0.jar, NotifyMe.class
package com.hp.hpl.jena.mem.faster
NodeToTriplesMapFaster.NotifyMe.emptied ( ) :  void
NodeToTriplesMapFaster.NotifyMe.NodeToTriplesMapFaster.NotifyMe ( NodeToTriplesMapFaster key, Object p2 )

cdk-1.4.0.jar, NotLiteral.class
package com.hp.hpl.jena.graph
Node.NotLiteral.Node.NotLiteral ( Node it )
package com.hp.hpl.jena.reasoner.rulesys.builtins
NotLiteral.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NotLiteral.getArgLength ( ) :  int
NotLiteral.getName ( ) :  String
NotLiteral.NotLiteral ( )

cdk-1.4.0.jar, NotUniqueException.class
package com.hp.hpl.jena.assembler.exceptions
NotUniqueException.getProperty ( ) :  Property
NotUniqueException.NotUniqueException ( Resource root, Property property )

cdk-1.4.0.jar, NoValue.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
NoValue.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
NoValue.getName ( ) :  String
NoValue.isMonotonic ( ) :  boolean
NoValue.NoValue ( )

cdk-1.4.0.jar, Now.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Now.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Now.getArgLength ( ) :  int
Now.getName ( ) :  String
Now.Now ( )

cdk-1.4.0.jar, NoWriterForLangException.class
package com.hp.hpl.jena.shared
NoWriterForLangException.NoWriterForLangException ( String lang )

cdk-1.4.0.jar, NsIterator.class
package com.hp.hpl.jena.rdf.model
NsIterator.nextNs ( ) [abstract] :  String

cdk-1.4.0.jar, NTriple.class
package com.hp.hpl.jena.rdf.arp
NTriple.main ( String[ ] args ) [static] :  void
NTriple.mainEh ( String[ ] args, ErrorHandler eh, ARPEventHandler ap ) [static] :  void
NTriple.NTriple ( )

cdk-1.4.0.jar, NullIterator.class
package com.hp.hpl.jena.util.iterator
NullIterator.andThen ( Iterator it ) :  ExtendedIterator
NullIterator.instance ( ) [static] :  NullIterator
NullIterator.NullIterator ( )

cdk-1.4.0.jar, NullListener.class
package com.hp.hpl.jena.rdf.listeners
NullListener.addedStatement ( Statement s ) :  void
NullListener.addedStatements ( List statements ) :  void
NullListener.addedStatements ( Model m ) :  void
NullListener.addedStatements ( Statement[ ] statements ) :  void
NullListener.addedStatements ( StmtIterator statements ) :  void
NullListener.notifyEvent ( Model m, Object event ) :  void
NullListener.NullListener ( )
NullListener.removedStatement ( Statement s ) :  void
NullListener.removedStatements ( List statements ) :  void
NullListener.removedStatements ( Model m ) :  void
NullListener.removedStatements ( Statement[ ] statements ) :  void
NullListener.removedStatements ( StmtIterator statements ) :  void

cdk-1.4.0.jar, NumberFormat.class
package com.ibm.icu.text
NumberFormat.clone ( ) :  Object
NumberFormat.equals ( Object obj ) :  boolean
NumberFormat.format ( BigDecimal number ) :  String
NumberFormat.format ( BigDecimal number ) :  String
NumberFormat.format ( BigDecimal p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
NumberFormat.format ( BigDecimal p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
NumberFormat.format ( BigInteger number ) :  String
NumberFormat.format ( BigInteger p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
NumberFormat.format ( CurrencyAmount currAmt ) :  String *DEPRECATED*
NumberFormat.format ( CurrencyAmount currAmt, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer *DEPRECATED*
NumberFormat.format ( double number ) :  String
NumberFormat.format ( double p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
NumberFormat.format ( long number ) :  String
NumberFormat.format ( long p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
NumberFormat.format ( Object number, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
NumberFormat.getAvailableLocales ( ) [static] :  Locale[ ]
NumberFormat.getAvailableULocales ( ) [static] :  ULocale[ ] *DEPRECATED*
NumberFormat.getCurrency ( ) :  Currency
NumberFormat.getCurrencyInstance ( ) [static] :  NumberFormat
NumberFormat.getCurrencyInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getCurrencyInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.getEffectiveCurrency ( ) :  Currency
NumberFormat.getInstance ( ) [static] :  NumberFormat
NumberFormat.getInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.getIntegerInstance ( ) [static] :  NumberFormat
NumberFormat.getIntegerInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getIntegerInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.getMaximumFractionDigits ( ) :  int
NumberFormat.getMaximumIntegerDigits ( ) :  int
NumberFormat.getMinimumFractionDigits ( ) :  int
NumberFormat.getMinimumIntegerDigits ( ) :  int
NumberFormat.getNumberInstance ( ) [static] :  NumberFormat
NumberFormat.getNumberInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getNumberInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.getPattern ( Locale forLocale, int choice ) [static] :  String *DEPRECATED*
NumberFormat.getPattern ( ULocale forLocale, int choice ) [static] :  String *DEPRECATED*
NumberFormat.getPercentInstance ( ) [static] :  NumberFormat
NumberFormat.getPercentInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getPercentInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.getScientificInstance ( ) [static] :  NumberFormat
NumberFormat.getScientificInstance ( Locale inLocale ) [static] :  NumberFormat
NumberFormat.getScientificInstance ( ULocale inLocale ) [static] :  NumberFormat *DEPRECATED*
NumberFormat.hashCode ( ) :  int
NumberFormat.isGroupingUsed ( ) :  boolean
NumberFormat.isParseIntegerOnly ( ) :  boolean
NumberFormat.NumberFormat ( )
NumberFormat.parse ( String p1, ParsePosition p2 ) [abstract] :  Number
NumberFormat.parse ( String text ) :  Number
NumberFormat.parseObject ( String source, ParsePosition parsePosition ) :  Object
NumberFormat.registerFactory ( NumberFormat.NumberFormatFactory factory ) [static] :  Object
NumberFormat.setCurrency ( Currency theCurrency ) :  void
NumberFormat.setGroupingUsed ( boolean newValue ) :  void
NumberFormat.setMaximumFractionDigits ( int newValue ) :  void
NumberFormat.setMaximumIntegerDigits ( int newValue ) :  void
NumberFormat.setMinimumFractionDigits ( int newValue ) :  void
NumberFormat.setMinimumIntegerDigits ( int newValue ) :  void
NumberFormat.setParseIntegerOnly ( boolean value ) :  void
NumberFormat.unregister ( Object registryKey ) [static] :  boolean

cdk-1.4.0.jar, NumberFormatFactory.class
package com.ibm.icu.text
NumberFormat.NumberFormatFactory.createFormat ( Locale loc, int formatType ) :  NumberFormat
NumberFormat.NumberFormatFactory.createFormat ( ULocale loc, int formatType ) :  NumberFormat *DEPRECATED*
NumberFormat.NumberFormatFactory.getSupportedLocaleNames ( ) [abstract] :  Set
NumberFormat.NumberFormatFactory.NumberFormat.NumberFormatFactory ( )
NumberFormat.NumberFormatFactory.visible ( ) :  boolean

cdk-1.4.0.jar, NumberLabelsTest.class
package signature.chemistry
NumberLabelsTest.choTest ( ) :  void
NumberLabelsTest.NumberLabelsTest ( )

cdk-1.4.0.jar, ObjectF.class
package com.hp.hpl.jena.rdf.model
ObjectF.createObject ( String p1 ) [abstract] :  Object

cdk-1.4.0.jar, ObjectIterator.class
package com.hp.hpl.jena.mem
ObjectIterator.hasNext ( ) :  boolean
ObjectIterator.iteratorFor ( Object p1 ) [abstract] :  Iterator
ObjectIterator.next ( ) :  Node
ObjectIterator.next ( ) :  Object
ObjectIterator.ObjectIterator ( Iterator domain )
ObjectIterator.refillPending ( ) :  void
ObjectIterator.remove ( ) :  void

cdk-1.4.0.jar, ObjectListener.class
package com.hp.hpl.jena.rdf.listeners
ObjectListener.added ( Object x ) :  void
ObjectListener.addedStatement ( Statement s ) :  void
ObjectListener.addedStatements ( List statements ) :  void
ObjectListener.addedStatements ( Model m ) :  void
ObjectListener.addedStatements ( Statement[ ] statements ) :  void
ObjectListener.addedStatements ( StmtIterator statements ) :  void
ObjectListener.notifyEvent ( Model m, Object event ) :  void
ObjectListener.ObjectListener ( )
ObjectListener.removed ( Object x ) :  void
ObjectListener.removedStatement ( Statement s ) :  void
ObjectListener.removedStatements ( List statements ) :  void
ObjectListener.removedStatements ( Model m ) :  void
ObjectListener.removedStatements ( Statement[ ] statements ) :  void
ObjectListener.removedStatements ( StmtIterator statements ) :  void

cdk-1.4.0.jar, OneElectronJob.class
package org.openscience.cdk.math.qm
OneElectronJob.calculate ( ) :  Orbitals
OneElectronJob.getEnergies ( ) :  Vector
OneElectronJob.OneElectronJob ( Orbitals orbitals )

cdk-1.4.0.jar, OneOrMore.class
package com.hp.hpl.jena.graph.query.regexptrees
OneOrMore.equals ( Object x ) :  boolean
OneOrMore.hashCode ( ) :  int
OneOrMore.OneOrMore ( RegexpTree operand )
OneOrMore.toString ( ) :  String

cdk-1.4.0.jar, OneToManyMap.class
package com.hp.hpl.jena.util
OneToManyMap.clear ( ) :  void
OneToManyMap.contains ( Object key, Object value ) :  boolean
OneToManyMap.containsKey ( Object key ) :  boolean
OneToManyMap.containsValue ( Object value ) :  boolean
OneToManyMap.entrySet ( ) :  Set
OneToManyMap.equals ( Object o ) :  boolean
OneToManyMap.get ( Object key ) :  Object
OneToManyMap.getAll ( Object key ) :  Iterator
OneToManyMap.hashCode ( ) :  int
OneToManyMap.isEmpty ( ) :  boolean
OneToManyMap.keySet ( ) :  Set
OneToManyMap.OneToManyMap ( )
OneToManyMap.OneToManyMap ( OneToManyMap map )
OneToManyMap.put ( Object key, Object value ) :  Object
OneToManyMap.putAll ( Map m ) :  void
OneToManyMap.remove ( Object key ) :  Object
OneToManyMap.remove ( Object key, Object value ) :  void
OneToManyMap.size ( ) :  int
OneToManyMap.toString ( ) :  String
OneToManyMap.values ( ) :  Collection

cdk-1.4.0.jar, OntClass.class
package com.hp.hpl.jena.ontology
OntClass.addDisjointWith ( Resource p1 ) [abstract] :  void
OntClass.addEquivalentClass ( Resource p1 ) [abstract] :  void
OntClass.addSubClass ( Resource p1 ) [abstract] :  void
OntClass.addSuperClass ( Resource p1 ) [abstract] :  void
OntClass.asComplementClass ( ) [abstract] :  ComplementClass
OntClass.asEnumeratedClass ( ) [abstract] :  EnumeratedClass
OntClass.asIntersectionClass ( ) [abstract] :  IntersectionClass
OntClass.asRestriction ( ) [abstract] :  Restriction
OntClass.asUnionClass ( ) [abstract] :  UnionClass
OntClass.convertToComplementClass ( Resource p1 ) [abstract] :  ComplementClass
OntClass.convertToEnumeratedClass ( RDFList p1 ) [abstract] :  EnumeratedClass
OntClass.convertToIntersectionClass ( RDFList p1 ) [abstract] :  IntersectionClass
OntClass.convertToRestriction ( Property p1 ) [abstract] :  Restriction
OntClass.convertToUnionClass ( RDFList p1 ) [abstract] :  UnionClass
OntClass.createIndividual ( ) [abstract] :  Individual
OntClass.createIndividual ( String p1 ) [abstract] :  Individual
OntClass.dropIndividual ( Resource p1 ) [abstract] :  void
OntClass.getDisjointWith ( ) [abstract] :  OntClass
OntClass.getEquivalentClass ( ) [abstract] :  OntClass
OntClass.getSubClass ( ) [abstract] :  OntClass
OntClass.getSuperClass ( ) [abstract] :  OntClass
OntClass.hasDeclaredProperty ( Property p1, boolean p2 ) [abstract] :  boolean
OntClass.hasEquivalentClass ( Resource p1 ) [abstract] :  boolean
OntClass.hasSubClass ( ) [abstract] :  boolean
OntClass.hasSubClass ( Resource p1 ) [abstract] :  boolean
OntClass.hasSubClass ( Resource p1, boolean p2 ) [abstract] :  boolean
OntClass.hasSuperClass ( ) [abstract] :  boolean
OntClass.hasSuperClass ( Resource p1 ) [abstract] :  boolean
OntClass.hasSuperClass ( Resource p1, boolean p2 ) [abstract] :  boolean
OntClass.isComplementClass ( ) [abstract] :  boolean
OntClass.isDisjointWith ( Resource p1 ) [abstract] :  boolean
OntClass.isEnumeratedClass ( ) [abstract] :  boolean
OntClass.isHierarchyRoot ( ) [abstract] :  boolean
OntClass.isIntersectionClass ( ) [abstract] :  boolean
OntClass.isRestriction ( ) [abstract] :  boolean
OntClass.isUnionClass ( ) [abstract] :  boolean
OntClass.listDeclaredProperties ( ) [abstract] :  ExtendedIterator
OntClass.listDeclaredProperties ( boolean p1 ) [abstract] :  ExtendedIterator
OntClass.listDisjointWith ( ) [abstract] :  ExtendedIterator
OntClass.listEquivalentClasses ( ) [abstract] :  ExtendedIterator
OntClass.listInstances ( ) [abstract] :  ExtendedIterator
OntClass.listInstances ( boolean p1 ) [abstract] :  ExtendedIterator
OntClass.listSubClasses ( ) [abstract] :  ExtendedIterator
OntClass.listSubClasses ( boolean p1 ) [abstract] :  ExtendedIterator
OntClass.listSuperClasses ( ) [abstract] :  ExtendedIterator
OntClass.listSuperClasses ( boolean p1 ) [abstract] :  ExtendedIterator
OntClass.removeDisjointWith ( Resource p1 ) [abstract] :  void
OntClass.removeEquivalentClass ( Resource p1 ) [abstract] :  void
OntClass.removeSubClass ( Resource p1 ) [abstract] :  void
OntClass.removeSuperClass ( Resource p1 ) [abstract] :  void
OntClass.setDisjointWith ( Resource p1 ) [abstract] :  void
OntClass.setEquivalentClass ( Resource p1 ) [abstract] :  void
OntClass.setSubClass ( Resource p1 ) [abstract] :  void
OntClass.setSuperClass ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, OntDocManagerVocab.class
package com.hp.hpl.jena.vocabulary
OntDocManagerVocab.getURI ( ) [static] :  String
OntDocManagerVocab.OntDocManagerVocab ( )

cdk-1.4.0.jar, OntDocumentManager.class
package com.hp.hpl.jena.ontology
OntDocumentManager.addAltEntry ( String docURI, String locationURL ) :  void
OntDocumentManager.addIgnoreImport ( String uri ) :  void
OntDocumentManager.addModel ( String docURI, Model model ) :  void
OntDocumentManager.addModel ( String docURI, Model model, boolean replace ) :  void
OntDocumentManager.clearCache ( ) :  void
OntDocumentManager.configure ( Model config ) :  void
OntDocumentManager.configure ( Model config, boolean reset ) :  void
OntDocumentManager.doAltURLMapping ( String uri ) :  String
OntDocumentManager.findMetadata ( String configPath ) :  Model
OntDocumentManager.forget ( String docURI ) :  void
OntDocumentManager.getCacheModels ( ) :  boolean
OntDocumentManager.getFileManager ( ) :  FileManager
OntDocumentManager.getInstance ( ) [static] :  OntDocumentManager
OntDocumentManager.getLoadedPolicyURL ( ) :  String
OntDocumentManager.getMetadataSearchPath ( ) :  String
OntDocumentManager.getModel ( String uri ) :  Model
OntDocumentManager.getOntology ( String uri, OntModelSpec spec ) :  OntModel
OntDocumentManager.getProcessImports ( ) :  boolean
OntDocumentManager.getReadFailureHandler ( ) :  OntDocumentManager.ReadFailureHandler
OntDocumentManager.getReadHook ( ) :  OntDocumentManager.ReadHook
OntDocumentManager.ignoringImport ( String uri ) :  boolean
OntDocumentManager.initialiseMetadata ( String path ) :  void
OntDocumentManager.listDocuments ( ) :  Iterator
OntDocumentManager.listIgnoredImports ( ) :  Iterator
OntDocumentManager.loadImport ( OntModel model, String importURI, List readQueue ) :  void
OntDocumentManager.loadImport ( OntModel model, String uri ) :  void
OntDocumentManager.loadImports ( OntModel model ) :  void
OntDocumentManager.loadImports ( OntModel model, List readQueue ) :  void
OntDocumentManager.OntDocumentManager ( )
OntDocumentManager.OntDocumentManager ( FileManager fileMgr, Model config )
OntDocumentManager.OntDocumentManager ( FileManager fileMgr, String path )
OntDocumentManager.OntDocumentManager ( Model config )
OntDocumentManager.OntDocumentManager ( String path )
OntDocumentManager.processMetadata ( Model metadata ) :  void
OntDocumentManager.queueImports ( Model model, List readQueue, Profile profile ) :  void
OntDocumentManager.read ( Model model, String uri, boolean warn ) :  boolean
OntDocumentManager.removeIgnoreImport ( String uri ) :  void
OntDocumentManager.reset ( ) :  void
OntDocumentManager.reset ( boolean reload ) :  void
OntDocumentManager.setCacheModels ( boolean cacheModels ) :  void
OntDocumentManager.setDefaultPrefixMappings ( ) :  void
OntDocumentManager.setDefaults ( ) :  void
OntDocumentManager.setFileManager ( ) :  void
OntDocumentManager.setFileManager ( FileManager fileMgr ) :  void
OntDocumentManager.setMetadataSearchPath ( String path, boolean replace ) :  void
OntDocumentManager.setProcessImports ( boolean processImports ) :  void
OntDocumentManager.setReadFailureHandler ( OntDocumentManager.ReadFailureHandler rfHandler ) :  void
OntDocumentManager.setReadHook ( OntDocumentManager.ReadHook hook ) :  OntDocumentManager.ReadHook
OntDocumentManager.unloadImport ( OntModel model, String uri ) :  void
OntDocumentManager.unloadImports ( OntModel model, List unloadQueue ) :  void

cdk-1.4.0.jar, OntEventsVocab.class
package com.hp.hpl.jena.vocabulary
OntEventsVocab.getURI ( ) [static] :  String
OntEventsVocab.OntEventsVocab ( )

cdk-1.4.0.jar, OntModel.class
package com.hp.hpl.jena.ontology
OntModel.addLoadedImport ( String p1 ) [abstract] :  void
OntModel.addSubModel ( Model p1 ) [abstract] :  void
OntModel.addSubModel ( Model p1, boolean p2 ) [abstract] :  void
OntModel.countSubModels ( ) [abstract] :  int
OntModel.createAllDifferent ( ) [abstract] :  AllDifferent
OntModel.createAllDifferent ( RDFList p1 ) [abstract] :  AllDifferent
OntModel.createAllValuesFromRestriction ( String p1, Property p2, Resource p3 ) [abstract] :  AllValuesFromRestriction
OntModel.createAnnotationProperty ( String p1 ) [abstract] :  AnnotationProperty
OntModel.createCardinalityQRestriction ( String p1, Property p2, int p3, OntClass p4 ) [abstract] :  CardinalityQRestriction
OntModel.createCardinalityRestriction ( String p1, Property p2, int p3 ) [abstract] :  CardinalityRestriction
OntModel.createClass ( ) [abstract] :  OntClass
OntModel.createClass ( String p1 ) [abstract] :  OntClass
OntModel.createComplementClass ( String p1, Resource p2 ) [abstract] :  ComplementClass
OntModel.createDataRange ( RDFList p1 ) [abstract] :  DataRange
OntModel.createDatatypeProperty ( String p1 ) [abstract] :  DatatypeProperty
OntModel.createDatatypeProperty ( String p1, boolean p2 ) [abstract] :  DatatypeProperty
OntModel.createEnumeratedClass ( String p1, RDFList p2 ) [abstract] :  EnumeratedClass
OntModel.createHasValueRestriction ( String p1, Property p2, RDFNode p3 ) [abstract] :  HasValueRestriction
OntModel.createIndividual ( Resource p1 ) [abstract] :  Individual
OntModel.createIndividual ( String p1, Resource p2 ) [abstract] :  Individual
OntModel.createIntersectionClass ( String p1, RDFList p2 ) [abstract] :  IntersectionClass
OntModel.createInverseFunctionalProperty ( String p1 ) [abstract] :  InverseFunctionalProperty
OntModel.createInverseFunctionalProperty ( String p1, boolean p2 ) [abstract] :  InverseFunctionalProperty
OntModel.createMaxCardinalityQRestriction ( String p1, Property p2, int p3, OntClass p4 ) [abstract] :  MaxCardinalityQRestriction
OntModel.createMaxCardinalityRestriction ( String p1, Property p2, int p3 ) [abstract] :  MaxCardinalityRestriction
OntModel.createMinCardinalityQRestriction ( String p1, Property p2, int p3, OntClass p4 ) [abstract] :  MinCardinalityQRestriction
OntModel.createMinCardinalityRestriction ( String p1, Property p2, int p3 ) [abstract] :  MinCardinalityRestriction
OntModel.createObjectProperty ( String p1 ) [abstract] :  ObjectProperty
OntModel.createObjectProperty ( String p1, boolean p2 ) [abstract] :  ObjectProperty
OntModel.createOntology ( String p1 ) [abstract] :  Ontology
OntModel.createOntProperty ( String p1 ) [abstract] :  OntProperty
OntModel.createOntResource ( Class p1, Resource p2, String p3 ) [abstract] :  OntResource
OntModel.createOntResource ( String p1 ) [abstract] :  OntResource
OntModel.createRestriction ( Property p1 ) [abstract] :  Restriction
OntModel.createRestriction ( String p1, Property p2 ) [abstract] :  Restriction
OntModel.createSomeValuesFromRestriction ( String p1, Property p2, Resource p3 ) [abstract] :  SomeValuesFromRestriction
OntModel.createSymmetricProperty ( String p1 ) [abstract] :  SymmetricProperty
OntModel.createSymmetricProperty ( String p1, boolean p2 ) [abstract] :  SymmetricProperty
OntModel.createTransitiveProperty ( String p1 ) [abstract] :  TransitiveProperty
OntModel.createTransitiveProperty ( String p1, boolean p2 ) [abstract] :  TransitiveProperty
OntModel.createUnionClass ( String p1, RDFList p2 ) [abstract] :  UnionClass
OntModel.getAllValuesFromRestriction ( String p1 ) [abstract] :  AllValuesFromRestriction
OntModel.getAnnotationProperty ( String p1 ) [abstract] :  AnnotationProperty
OntModel.getBaseModel ( ) [abstract] :  Model
OntModel.getCardinalityQRestriction ( String p1 ) [abstract] :  CardinalityQRestriction
OntModel.getCardinalityRestriction ( String p1 ) [abstract] :  CardinalityRestriction
OntModel.getComplementClass ( String p1 ) [abstract] :  ComplementClass
OntModel.getDatatypeProperty ( String p1 ) [abstract] :  DatatypeProperty
OntModel.getDocumentManager ( ) [abstract] :  OntDocumentManager
OntModel.getDynamicImports ( ) [abstract] :  boolean
OntModel.getEnumeratedClass ( String p1 ) [abstract] :  EnumeratedClass
OntModel.getHasValueRestriction ( String p1 ) [abstract] :  HasValueRestriction
OntModel.getImportedModel ( String p1 ) [abstract] :  OntModel
OntModel.getImportModelMaker ( ) [abstract] :  ModelMaker
OntModel.getIndividual ( String p1 ) [abstract] :  Individual
OntModel.getIntersectionClass ( String p1 ) [abstract] :  IntersectionClass
OntModel.getInverseFunctionalProperty ( String p1 ) [abstract] :  InverseFunctionalProperty
OntModel.getMaxCardinalityQRestriction ( String p1 ) [abstract] :  MaxCardinalityQRestriction
OntModel.getMaxCardinalityRestriction ( String p1 ) [abstract] :  MaxCardinalityRestriction
OntModel.getMinCardinalityQRestriction ( String p1 ) [abstract] :  MinCardinalityQRestriction
OntModel.getMinCardinalityRestriction ( String p1 ) [abstract] :  MinCardinalityRestriction
OntModel.getModelMaker ( ) [abstract] :  ModelMaker *DEPRECATED*
OntModel.getObjectProperty ( String p1 ) [abstract] :  ObjectProperty
OntModel.getOntClass ( String p1 ) [abstract] :  OntClass
OntModel.getOntology ( String p1 ) [abstract] :  Ontology
OntModel.getOntProperty ( String p1 ) [abstract] :  OntProperty
OntModel.getOntResource ( Resource p1 ) [abstract] :  OntResource
OntModel.getOntResource ( String p1 ) [abstract] :  OntResource
OntModel.getProfile ( ) [abstract] :  Profile
OntModel.getQualifiedRestriction ( String p1 ) [abstract] :  QualifiedRestriction
OntModel.getRestriction ( String p1 ) [abstract] :  Restriction
OntModel.getSomeValuesFromRestriction ( String p1 ) [abstract] :  SomeValuesFromRestriction
OntModel.getSpecification ( ) [abstract] :  OntModelSpec
OntModel.getSubGraphs ( ) [abstract] :  List
OntModel.getSymmetricProperty ( String p1 ) [abstract] :  SymmetricProperty
OntModel.getTransitiveProperty ( String p1 ) [abstract] :  TransitiveProperty
OntModel.getUnionClass ( String p1 ) [abstract] :  UnionClass
OntModel.hasLoadedImport ( String p1 ) [abstract] :  boolean
OntModel.isInBaseModel ( RDFNode p1 ) [abstract] :  boolean
OntModel.isInBaseModel ( Statement p1 ) [abstract] :  boolean
OntModel.listAllDifferent ( ) [abstract] :  ExtendedIterator
OntModel.listAllOntProperties ( ) [abstract] :  ExtendedIterator
OntModel.listAnnotationProperties ( ) [abstract] :  ExtendedIterator
OntModel.listClasses ( ) [abstract] :  ExtendedIterator
OntModel.listComplementClasses ( ) [abstract] :  ExtendedIterator
OntModel.listDataRanges ( ) [abstract] :  ExtendedIterator
OntModel.listDatatypeProperties ( ) [abstract] :  ExtendedIterator
OntModel.listEnumeratedClasses ( ) [abstract] :  ExtendedIterator
OntModel.listFunctionalProperties ( ) [abstract] :  ExtendedIterator
OntModel.listHierarchyRootClasses ( ) [abstract] :  ExtendedIterator
OntModel.listImportedModels ( ) [abstract] :  ExtendedIterator *DEPRECATED*
OntModel.listImportedOntologyURIs ( ) [abstract] :  Set
OntModel.listImportedOntologyURIs ( boolean p1 ) [abstract] :  Set
OntModel.listIndividuals ( ) [abstract] :  ExtendedIterator
OntModel.listIndividuals ( Resource p1 ) [abstract] :  ExtendedIterator
OntModel.listIntersectionClasses ( ) [abstract] :  ExtendedIterator
OntModel.listInverseFunctionalProperties ( ) [abstract] :  ExtendedIterator
OntModel.listNamedClasses ( ) [abstract] :  ExtendedIterator
OntModel.listObjectProperties ( ) [abstract] :  ExtendedIterator
OntModel.listOntologies ( ) [abstract] :  ExtendedIterator
OntModel.listOntProperties ( ) [abstract] :  ExtendedIterator
OntModel.listRestrictions ( ) [abstract] :  ExtendedIterator
OntModel.listSubModels ( ) [abstract] :  ExtendedIterator
OntModel.listSubModels ( boolean p1 ) [abstract] :  ExtendedIterator
OntModel.listSymmetricProperties ( ) [abstract] :  ExtendedIterator
OntModel.listTransitiveProperties ( ) [abstract] :  ExtendedIterator
OntModel.listUnionClasses ( ) [abstract] :  ExtendedIterator
OntModel.loadImports ( ) [abstract] :  void
OntModel.queryFor ( BindingQueryPlan p1, List p2, Class p3 ) [abstract] :  ExtendedIterator
OntModel.removeLoadedImport ( String p1 ) [abstract] :  void
OntModel.removeSubModel ( Model p1 ) [abstract] :  void
OntModel.removeSubModel ( Model p1, boolean p2 ) [abstract] :  void
OntModel.setDynamicImports ( boolean p1 ) [abstract] :  void
OntModel.setStrictMode ( boolean p1 ) [abstract] :  void
OntModel.strictMode ( ) [abstract] :  boolean
OntModel.write ( OutputStream p1 ) [abstract] :  Model
OntModel.write ( OutputStream p1, String p2 ) [abstract] :  Model
OntModel.write ( OutputStream p1, String p2, String p3 ) [abstract] :  Model
OntModel.write ( Writer p1 ) [abstract] :  Model
OntModel.write ( Writer p1, String p2 ) [abstract] :  Model
OntModel.write ( Writer p1, String p2, String p3 ) [abstract] :  Model
OntModel.writeAll ( OutputStream p1, String p2, String p3 ) [abstract] :  Model
OntModel.writeAll ( Writer p1, String p2, String p3 ) [abstract] :  Model

cdk-1.4.0.jar, OntModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
OntModelAssembler.getOntModelSpec ( Assembler a, Resource root ) :  OntModelSpec
OntModelAssembler.OntModelAssembler ( )
OntModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode mode ) :  Model

cdk-1.4.0.jar, OntModelSpec.class
package com.hp.hpl.jena.ontology
OntModelSpec.assemble ( Model model ) [static] :  OntModelSpec
OntModelSpec.assemble ( Resource root ) [static] :  OntModelSpec
OntModelSpec.createBaseModel ( ) :  Model
OntModelSpec.doCreateModel ( ) :  Model
OntModelSpec.equals ( Object other ) :  boolean
OntModelSpec.getBaseModelMaker ( ) :  ModelMaker
OntModelSpec.getDefaultSpec ( String languageURI ) [static] :  OntModelSpec
OntModelSpec.getDocumentManager ( ) :  OntDocumentManager
OntModelSpec.getImportModelGetter ( ) :  ModelGetter
OntModelSpec.getImportModelMaker ( ) :  ModelMaker
OntModelSpec.getKnownPrefixes ( ) :  String[ ][ ]
OntModelSpec.getLanguage ( ) :  String
OntModelSpec.getProfile ( ) :  Profile
OntModelSpec.getReasoner ( ) :  Reasoner
OntModelSpec.getReasonerFactory ( ) :  ReasonerFactory
OntModelSpec.implementCreateModelOver ( String name ) :  Model
OntModelSpec.OntModelSpec ( ModelMaker baseMaker, ModelMaker importsMaker, OntDocumentManager docMgr, ReasonerFactory rFactory, String languageURI )
OntModelSpec.OntModelSpec ( ModelMaker importsMaker, OntDocumentManager docMgr, ReasonerFactory rFactory, String languageURI )
OntModelSpec.OntModelSpec ( OntModelSpec spec )
OntModelSpec.OntModelSpec ( String baseModelName, ModelMaker baseMaker, ModelMaker importsMaker, OntDocumentManager docMgr, ReasonerFactory rFactory, String languageURI )
OntModelSpec.setBaseModelMaker ( ModelMaker m ) :  void
OntModelSpec.setDocumentManager ( OntDocumentManager docMgr ) :  void
OntModelSpec.setImportModelGetter ( ModelGetter mg ) :  void
OntModelSpec.setImportModelMaker ( ModelMaker maker ) :  void
OntModelSpec.setLanguage ( String languageURI ) :  void
OntModelSpec.setReasoner ( Reasoner reasoner ) :  void
OntModelSpec.setReasonerFactory ( ReasonerFactory rFactory ) :  void

cdk-1.4.0.jar, OntModelSpecAssembler.class
package com.hp.hpl.jena.assembler.assemblers
OntModelSpecAssembler.getOntModelSpecField ( String name ) [static] :  OntModelSpec
OntModelSpecAssembler.isConstant ( int mods ) [static] :  boolean
OntModelSpecAssembler.OntModelSpecAssembler ( )
OntModelSpecAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object

cdk-1.4.0.jar, Ontology.class
package com.hp.hpl.jena.ontology
Ontology.addBackwardCompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.addImport ( Resource p1 ) [abstract] :  void
Ontology.addIncompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.addPriorVersion ( Resource p1 ) [abstract] :  void
Ontology.getBackwardCompatibleWith ( ) [abstract] :  OntResource
Ontology.getImport ( ) [abstract] :  OntResource
Ontology.getIncompatibleWith ( ) [abstract] :  OntResource
Ontology.getPriorVersion ( ) [abstract] :  OntResource
Ontology.hasPriorVersion ( Resource p1 ) [abstract] :  boolean
Ontology.imports ( Resource p1 ) [abstract] :  boolean
Ontology.isBackwardCompatibleWith ( Resource p1 ) [abstract] :  boolean
Ontology.isIncompatibleWith ( Resource p1 ) [abstract] :  boolean
Ontology.listBackwardCompatibleWith ( ) [abstract] :  ExtendedIterator
Ontology.listImports ( ) [abstract] :  ExtendedIterator
Ontology.listIncompatibleWith ( ) [abstract] :  ExtendedIterator
Ontology.listPriorVersion ( ) [abstract] :  ExtendedIterator
Ontology.removeBackwardCompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.removeImport ( Resource p1 ) [abstract] :  void
Ontology.removeIncompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.removePriorVersion ( Resource p1 ) [abstract] :  void
Ontology.setBackwardCompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.setImport ( Resource p1 ) [abstract] :  void
Ontology.setIncompatibleWith ( Resource p1 ) [abstract] :  void
Ontology.setPriorVersion ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, OntologyException.class
package com.hp.hpl.jena.ontology
OntologyException.OntologyException ( String msg )

cdk-1.4.0.jar, OntProperty.class
package com.hp.hpl.jena.ontology
OntProperty.addDomain ( Resource p1 ) [abstract] :  void
OntProperty.addEquivalentProperty ( Property p1 ) [abstract] :  void
OntProperty.addInverseOf ( Property p1 ) [abstract] :  void
OntProperty.addRange ( Resource p1 ) [abstract] :  void
OntProperty.addSubProperty ( Property p1 ) [abstract] :  void
OntProperty.addSuperProperty ( Property p1 ) [abstract] :  void
OntProperty.asDatatypeProperty ( ) [abstract] :  DatatypeProperty
OntProperty.asFunctionalProperty ( ) [abstract] :  FunctionalProperty
OntProperty.asInverseFunctionalProperty ( ) [abstract] :  InverseFunctionalProperty
OntProperty.asObjectProperty ( ) [abstract] :  ObjectProperty
OntProperty.asSymmetricProperty ( ) [abstract] :  SymmetricProperty
OntProperty.asTransitiveProperty ( ) [abstract] :  TransitiveProperty
OntProperty.convertToDatatypeProperty ( ) [abstract] :  DatatypeProperty
OntProperty.convertToFunctionalProperty ( ) [abstract] :  FunctionalProperty
OntProperty.convertToInverseFunctionalProperty ( ) [abstract] :  InverseFunctionalProperty
OntProperty.convertToObjectProperty ( ) [abstract] :  ObjectProperty
OntProperty.convertToSymmetricProperty ( ) [abstract] :  SymmetricProperty
OntProperty.convertToTransitiveProperty ( ) [abstract] :  TransitiveProperty
OntProperty.getDomain ( ) [abstract] :  OntResource
OntProperty.getEquivalentProperty ( ) [abstract] :  OntProperty
OntProperty.getInverse ( ) [abstract] :  OntProperty
OntProperty.getInverseOf ( ) [abstract] :  OntProperty
OntProperty.getRange ( ) [abstract] :  OntResource
OntProperty.getSubProperty ( ) [abstract] :  OntProperty
OntProperty.getSuperProperty ( ) [abstract] :  OntProperty
OntProperty.hasDomain ( Resource p1 ) [abstract] :  boolean
OntProperty.hasEquivalentProperty ( Property p1 ) [abstract] :  boolean
OntProperty.hasInverse ( ) [abstract] :  boolean
OntProperty.hasRange ( Resource p1 ) [abstract] :  boolean
OntProperty.hasSubProperty ( Property p1, boolean p2 ) [abstract] :  boolean
OntProperty.hasSuperProperty ( Property p1, boolean p2 ) [abstract] :  boolean
OntProperty.isDatatypeProperty ( ) [abstract] :  boolean
OntProperty.isFunctionalProperty ( ) [abstract] :  boolean
OntProperty.isInverseFunctionalProperty ( ) [abstract] :  boolean
OntProperty.isInverseOf ( Property p1 ) [abstract] :  boolean
OntProperty.isObjectProperty ( ) [abstract] :  boolean
OntProperty.isSymmetricProperty ( ) [abstract] :  boolean
OntProperty.isTransitiveProperty ( ) [abstract] :  boolean
OntProperty.listDeclaringClasses ( ) [abstract] :  ExtendedIterator
OntProperty.listDeclaringClasses ( boolean p1 ) [abstract] :  ExtendedIterator
OntProperty.listDomain ( ) [abstract] :  ExtendedIterator
OntProperty.listEquivalentProperties ( ) [abstract] :  ExtendedIterator
OntProperty.listInverse ( ) [abstract] :  ExtendedIterator
OntProperty.listInverseOf ( ) [abstract] :  ExtendedIterator
OntProperty.listRange ( ) [abstract] :  ExtendedIterator
OntProperty.listReferringRestrictions ( ) [abstract] :  ExtendedIterator
OntProperty.listSubProperties ( ) [abstract] :  ExtendedIterator
OntProperty.listSubProperties ( boolean p1 ) [abstract] :  ExtendedIterator
OntProperty.listSuperProperties ( ) [abstract] :  ExtendedIterator
OntProperty.listSuperProperties ( boolean p1 ) [abstract] :  ExtendedIterator
OntProperty.removeDomain ( Resource p1 ) [abstract] :  void
OntProperty.removeEquivalentProperty ( Property p1 ) [abstract] :  void
OntProperty.removeInverseProperty ( Property p1 ) [abstract] :  void
OntProperty.removeRange ( Resource p1 ) [abstract] :  void
OntProperty.removeSubProperty ( Property p1 ) [abstract] :  void
OntProperty.removeSuperProperty ( Property p1 ) [abstract] :  void
OntProperty.setDomain ( Resource p1 ) [abstract] :  void
OntProperty.setEquivalentProperty ( Property p1 ) [abstract] :  void
OntProperty.setInverseOf ( Property p1 ) [abstract] :  void
OntProperty.setRange ( Resource p1 ) [abstract] :  void
OntProperty.setSubProperty ( Property p1 ) [abstract] :  void
OntProperty.setSuperProperty ( Property p1 ) [abstract] :  void

cdk-1.4.0.jar, OntResource.class
package com.hp.hpl.jena.ontology
OntResource.addComment ( Literal p1 ) [abstract] :  void
OntResource.addComment ( String p1, String p2 ) [abstract] :  void
OntResource.addDifferentFrom ( Resource p1 ) [abstract] :  void
OntResource.addIsDefinedBy ( Resource p1 ) [abstract] :  void
OntResource.addLabel ( Literal p1 ) [abstract] :  void
OntResource.addLabel ( String p1, String p2 ) [abstract] :  void
OntResource.addRDFType ( Resource p1 ) [abstract] :  void
OntResource.addSameAs ( Resource p1 ) [abstract] :  void
OntResource.addSeeAlso ( Resource p1 ) [abstract] :  void
OntResource.addVersionInfo ( String p1 ) [abstract] :  void
OntResource.asAllDifferent ( ) [abstract] :  AllDifferent
OntResource.asAnnotationProperty ( ) [abstract] :  AnnotationProperty
OntResource.asClass ( ) [abstract] :  OntClass
OntResource.asDataRange ( ) [abstract] :  DataRange
OntResource.asDatatypeProperty ( ) [abstract] :  DatatypeProperty
OntResource.asIndividual ( ) [abstract] :  Individual
OntResource.asObjectProperty ( ) [abstract] :  ObjectProperty
OntResource.asOntology ( ) [abstract] :  Ontology
OntResource.asProperty ( ) [abstract] :  OntProperty
OntResource.getCardinality ( Property p1 ) [abstract] :  int
OntResource.getComment ( String p1 ) [abstract] :  String
OntResource.getDifferentFrom ( ) [abstract] :  OntResource
OntResource.getIsDefinedBy ( ) [abstract] :  Resource
OntResource.getLabel ( String p1 ) [abstract] :  String
OntResource.getOntModel ( ) [abstract] :  OntModel
OntResource.getProfile ( ) [abstract] :  Profile
OntResource.getPropertyValue ( Property p1 ) [abstract] :  RDFNode
OntResource.getRDFType ( ) [abstract] :  Resource
OntResource.getRDFType ( boolean p1 ) [abstract] :  Resource
OntResource.getSameAs ( ) [abstract] :  OntResource
OntResource.getSeeAlso ( ) [abstract] :  Resource
OntResource.getVersionInfo ( ) [abstract] :  String
OntResource.hasComment ( Literal p1 ) [abstract] :  boolean
OntResource.hasComment ( String p1, String p2 ) [abstract] :  boolean
OntResource.hasLabel ( Literal p1 ) [abstract] :  boolean
OntResource.hasLabel ( String p1, String p2 ) [abstract] :  boolean
OntResource.hasRDFType ( Resource p1 ) [abstract] :  boolean
OntResource.hasRDFType ( Resource p1, boolean p2 ) [abstract] :  boolean
OntResource.hasRDFType ( String p1 ) [abstract] :  boolean
OntResource.hasSeeAlso ( Resource p1 ) [abstract] :  boolean
OntResource.hasVersionInfo ( String p1 ) [abstract] :  boolean
OntResource.isAllDifferent ( ) [abstract] :  boolean
OntResource.isAnnotationProperty ( ) [abstract] :  boolean
OntResource.isClass ( ) [abstract] :  boolean
OntResource.isDataRange ( ) [abstract] :  boolean
OntResource.isDatatypeProperty ( ) [abstract] :  boolean
OntResource.isDefinedBy ( Resource p1 ) [abstract] :  boolean
OntResource.isDifferentFrom ( Resource p1 ) [abstract] :  boolean
OntResource.isIndividual ( ) [abstract] :  boolean
OntResource.isObjectProperty ( ) [abstract] :  boolean
OntResource.isOntLanguageTerm ( ) [abstract] :  boolean
OntResource.isOntology ( ) [abstract] :  boolean
OntResource.isProperty ( ) [abstract] :  boolean
OntResource.isSameAs ( Resource p1 ) [abstract] :  boolean
OntResource.listComments ( String p1 ) [abstract] :  ExtendedIterator
OntResource.listDifferentFrom ( ) [abstract] :  ExtendedIterator
OntResource.listIsDefinedBy ( ) [abstract] :  ExtendedIterator
OntResource.listLabels ( String p1 ) [abstract] :  ExtendedIterator
OntResource.listPropertyValues ( Property p1 ) [abstract] :  NodeIterator
OntResource.listRDFTypes ( boolean p1 ) [abstract] :  ExtendedIterator
OntResource.listSameAs ( ) [abstract] :  ExtendedIterator
OntResource.listSeeAlso ( ) [abstract] :  ExtendedIterator
OntResource.listVersionInfo ( ) [abstract] :  ExtendedIterator
OntResource.remove ( ) [abstract] :  void
OntResource.removeComment ( Literal p1 ) [abstract] :  void
OntResource.removeComment ( String p1, String p2 ) [abstract] :  void
OntResource.removeDefinedBy ( Resource p1 ) [abstract] :  void
OntResource.removeDifferentFrom ( Resource p1 ) [abstract] :  void
OntResource.removeLabel ( Literal p1 ) [abstract] :  void
OntResource.removeLabel ( String p1, String p2 ) [abstract] :  void
OntResource.removeProperty ( Property p1, RDFNode p2 ) [abstract] :  void
OntResource.removeRDFType ( Resource p1 ) [abstract] :  void
OntResource.removeSameAs ( Resource p1 ) [abstract] :  void
OntResource.removeSeeAlso ( Resource p1 ) [abstract] :  void
OntResource.removeVersionInfo ( String p1 ) [abstract] :  void
OntResource.setComment ( String p1, String p2 ) [abstract] :  void
OntResource.setDifferentFrom ( Resource p1 ) [abstract] :  void
OntResource.setIsDefinedBy ( Resource p1 ) [abstract] :  void
OntResource.setLabel ( String p1, String p2 ) [abstract] :  void
OntResource.setPropertyValue ( Property p1, RDFNode p2 ) [abstract] :  void
OntResource.setRDFType ( Resource p1 ) [abstract] :  void
OntResource.setSameAs ( Resource p1 ) [abstract] :  void
OntResource.setSeeAlso ( Resource p1 ) [abstract] :  void
OntResource.setVersionInfo ( String p1 ) [abstract] :  void

cdk-1.4.0.jar, OntTools.class
package com.hp.hpl.jena.ontology
OntTools.checkSolution ( OntClass uCls, OntClass vCls, OntTools.LCAIndex index ) [static] :  void
OntTools.findShortestPath ( Model m, Resource start, RDFNode end, Filter onPath ) [static] :  OntTools.Path
OntTools.getLCA ( OntModel m, OntClass root, OntClass u, OntClass v ) [static] :  OntClass
OntTools.getLCA ( OntModel m, OntClass u, OntClass v ) [static] :  OntClass
OntTools.lca ( OntClass cls, OntClass uCls, OntClass vCls, OntTools.LCAIndex index ) [static] :  OntTools.DisjointSet
OntTools.namedHierarchyRoots ( OntModel m ) [static] :  List
OntTools.OntTools ( )
OntTools.partitionByNamed ( Iterator i, List named, List anon ) [static] :  void

cdk-1.4.0.jar, Option.class
package org.apache.commons.cli
Option.addValue ( String value ) :  boolean
Option.clone ( ) :  Object
Option.getArgName ( ) :  String
Option.getArgs ( ) :  int
Option.getDescription ( ) :  String
Option.getId ( ) :  int
Option.getLongOpt ( ) :  String
Option.getOpt ( ) :  String
Option.getType ( ) :  Object
Option.getValue ( ) :  String
Option.getValue ( int index ) :  String
Option.getValue ( String defaultValue ) :  String
Option.getValues ( ) :  String[ ]
Option.getValueSeparator ( ) :  char
Option.getValuesList ( ) :  List
Option.hasArg ( ) :  boolean
Option.hasArgName ( ) :  boolean
Option.hasArgs ( ) :  boolean
Option.hasLongOpt ( ) :  boolean
Option.hasOptionalArg ( ) :  boolean
Option.isRequired ( ) :  boolean
Option.Option ( String opt, boolean hasArg, String description )
Option.Option ( String opt, String description )
Option.Option ( String opt, String longOpt, boolean hasArg, String description )
Option.setArgName ( String argName ) :  void
Option.setArgs ( int num ) :  void
Option.setLongOpt ( String longOpt ) :  void
Option.setOptionalArg ( boolean optionalArg ) :  void
Option.setRequired ( boolean required ) :  void
Option.setType ( Object type ) :  void
Option.setValueSeparator ( char sep ) :  void
Option.toString ( ) :  String

cdk-1.4.0.jar, Optional.class
package com.hp.hpl.jena.graph.query.regexptrees
Optional.equals ( Object x ) :  boolean
Optional.hashCode ( ) :  int
Optional.Optional ( RegexpTree operand )
Optional.toString ( ) :  String

cdk-1.4.0.jar, OptionBuilder.class
package org.apache.commons.cli
OptionBuilder.create ( ) [static] :  Option
OptionBuilder.create ( char opt ) [static] :  Option
OptionBuilder.create ( String opt ) [static] :  Option
OptionBuilder.hasArg ( ) [static] :  OptionBuilder
OptionBuilder.hasArg ( boolean hasArg ) [static] :  OptionBuilder
OptionBuilder.hasArgs ( ) [static] :  OptionBuilder
OptionBuilder.hasArgs ( int num ) [static] :  OptionBuilder
OptionBuilder.hasOptionalArg ( ) [static] :  OptionBuilder
OptionBuilder.hasOptionalArgs ( ) [static] :  OptionBuilder
OptionBuilder.hasOptionalArgs ( int numArgs ) [static] :  OptionBuilder
OptionBuilder.isRequired ( ) [static] :  OptionBuilder
OptionBuilder.isRequired ( boolean required ) [static] :  OptionBuilder
OptionBuilder.withArgName ( String name ) [static] :  OptionBuilder
OptionBuilder.withDescription ( String description ) [static] :  OptionBuilder
OptionBuilder.withLongOpt ( String longopt ) [static] :  OptionBuilder
OptionBuilder.withType ( Object type ) [static] :  OptionBuilder
OptionBuilder.withValueSeparator ( ) [static] :  OptionBuilder
OptionBuilder.withValueSeparator ( char sep ) [static] :  OptionBuilder

cdk-1.4.0.jar, OptionDefinition.class
package jena
schemagen.OptionDefinition.getResource ( ) :  Resource
schemagen.OptionDefinition.getValue ( ) :  String
schemagen.OptionDefinition.hasResourceValue ( ) :  boolean
schemagen.OptionDefinition.hasValue ( ) :  boolean
schemagen.OptionDefinition.isTrue ( ) :  boolean
schemagen.OptionDefinition.schemagen.OptionDefinition ( schemagen cmdLineForm, String name, String p3 )

cdk-1.4.0.jar, OptionGroup.class
package org.apache.commons.cli
OptionGroup.addOption ( Option opt ) :  OptionGroup
OptionGroup.getNames ( ) :  Collection
OptionGroup.getOptions ( ) :  Collection
OptionGroup.getSelected ( ) :  String
OptionGroup.isRequired ( ) :  boolean
OptionGroup.OptionGroup ( )
OptionGroup.setRequired ( boolean required ) :  void
OptionGroup.setSelected ( Option opt ) :  void
OptionGroup.toString ( ) :  String

cdk-1.4.0.jar, Options.class
package org.apache.commons.cli
Options.addOption ( Option opt ) :  Options
Options.addOption ( String opt, boolean hasArg, String description ) :  Options
Options.addOption ( String opt, String longOpt, boolean hasArg, String description ) :  Options
Options.addOptionGroup ( OptionGroup group ) :  Options
Options.getOption ( String opt ) :  Option
Options.getOptionGroup ( Option opt ) :  OptionGroup
Options.getOptions ( ) :  Collection
Options.getRequiredOptions ( ) :  List
Options.hasOption ( String opt ) :  boolean
Options.Options ( )
Options.toString ( ) :  String

cdk-1.4.0.jar, Orbit.class
package org.openscience.cdk.signature
Orbit.addAtom ( int atomIndex ) :  void
Orbit.clone ( ) :  Object
Orbit.contains ( int atomIndex ) :  boolean
Orbit.getAtomIndices ( ) :  List
Orbit.getFirstAtom ( ) :  int
Orbit.getHeight ( ) :  int
Orbit.getLabel ( ) :  String
Orbit.hasLabel ( String otherLabel ) :  boolean
Orbit.isEmpty ( ) :  boolean
Orbit.iterator ( ) :  Iterator
Orbit.Orbit ( String label, int height )
Orbit.remove ( int atomIndex ) :  void
Orbit.sort ( ) :  void
Orbit.toString ( ) :  String

cdk-1.4.0.jar, Orbitals.class
package org.openscience.cdk.math.qm
Orbitals.getBasis ( ) :  IBasis
Orbitals.getCoefficients ( ) :  Matrix
Orbitals.getCountBasis ( ) :  int
Orbitals.getCountElectrons ( ) :  int
Orbitals.getCountOrbitals ( ) :  int
Orbitals.getValue ( int index, double x, double y, double z ) :  double
Orbitals.getValues ( int index, Matrix m ) :  Vector
Orbitals.Orbitals ( IBasis basis )
Orbitals.Orbitals ( IBasis basis, Matrix C )
Orbitals.setCoefficients ( Matrix C ) :  void
Orbitals.setCountElectrons ( int count ) :  void

cdk-1.4.0.jar, OuterXMLLiteral.class
package com.hp.hpl.jena.rdf.arp.states
OuterXMLLiteral.endElement ( ) :  void
OuterXMLLiteral.OuterXMLLiteral ( WantsObjectFrameI s, AbsXMLContext x, String pt )

cdk-1.4.0.jar, OvalElement.class
package org.openscience.cdk.renderer.elements
OvalElement.accept ( IRenderingVisitor visitor ) :  void
OvalElement.OvalElement ( double xCoord, double yCoord, Color color )
OvalElement.OvalElement ( double xCoord, double yCoord, double radius, boolean fill, Color color )
OvalElement.OvalElement ( double xCoord, double yCoord, double radius, Color color )

cdk-1.4.0.jar, OverlayBundle.class
package com.ibm.icu.util
OverlayBundle.getKeys ( ) :  Enumeration *DEPRECATED*
OverlayBundle.handleGetObject ( String key ) :  Object *DEPRECATED*
OverlayBundle.OverlayBundle ( String[ ] baseNames, Locale locale ) *DEPRECATED*

cdk-1.4.0.jar, OWL.class
package com.hp.hpl.jena.vocabulary
OWL.getURI ( ) [static] :  String
OWL.OWL ( )

cdk-1.4.0.jar, OWLFBRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
OWLFBRuleReasoner.bind ( Graph data ) :  InfGraph
OWLFBRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
OWLFBRuleReasoner.getPreload ( ) :  InfGraph
OWLFBRuleReasoner.loadRules ( ) [static] :  List
OWLFBRuleReasoner.OWLFBRuleReasoner ( ReasonerFactory factory )

cdk-1.4.0.jar, OWLFBRuleReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
OWLFBRuleReasonerFactory.create ( Resource configuration ) :  Reasoner
OWLFBRuleReasonerFactory.getCapabilities ( ) :  Model
OWLFBRuleReasonerFactory.getURI ( ) :  String
OWLFBRuleReasonerFactory.OWLFBRuleReasonerFactory ( )
OWLFBRuleReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, OWLMicroReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
OWLMicroReasoner.bind ( Graph data ) :  InfGraph
OWLMicroReasoner.getGraphCapabilities ( ) :  Capabilities
OWLMicroReasoner.loadRules ( ) [static] :  List
OWLMicroReasoner.OWLMicroReasoner ( ReasonerFactory factory )

cdk-1.4.0.jar, OWLMicroReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
OWLMicroReasonerFactory.create ( Resource configuration ) :  Reasoner
OWLMicroReasonerFactory.getCapabilities ( ) :  Model
OWLMicroReasonerFactory.getURI ( ) :  String
OWLMicroReasonerFactory.OWLMicroReasonerFactory ( )
OWLMicroReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, OWLMiniReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
OWLMiniReasoner.bind ( Graph data ) :  InfGraph
OWLMiniReasoner.getGraphCapabilities ( ) :  Capabilities
OWLMiniReasoner.loadRules ( ) [static] :  List
OWLMiniReasoner.OWLMiniReasoner ( ReasonerFactory factory )

cdk-1.4.0.jar, OWLMiniReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
OWLMiniReasonerFactory.create ( Resource configuration ) :  Reasoner
OWLMiniReasonerFactory.getCapabilities ( ) :  Model
OWLMiniReasonerFactory.getURI ( ) :  String
OWLMiniReasonerFactory.OWLMiniReasonerFactory ( )
OWLMiniReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, OWLResults.class
package com.hp.hpl.jena.vocabulary
OWLResults.getURI ( ) [static] :  String
OWLResults.OWLResults ( )

cdk-1.4.0.jar, OWLTest.class
package com.hp.hpl.jena.vocabulary
OWLTest.getURI ( ) [static] :  String
OWLTest.OWLTest ( )

cdk-1.4.0.jar, PaperSize.class
package com.ibm.icu.util
LocaleData.PaperSize.getHeight ( ) :  int
LocaleData.PaperSize.getWidth ( ) :  int

cdk-1.4.0.jar, Paren.class
package com.hp.hpl.jena.graph.query.regexptrees
Paren.equals ( Object other ) :  boolean
Paren.getIndex ( ) :  int
Paren.getOperand ( ) :  RegexpTree
Paren.hashCode ( ) :  int
Paren.Paren ( RegexpTree tree )
Paren.Paren ( RegexpTree tree, int index )
Paren.toString ( ) :  String

cdk-1.4.0.jar, ParseException.class
package com.hp.hpl.jena.n3.turtle.parser
ParseException.add_escapes ( String str ) :  String
ParseException.getMessage ( ) :  String
ParseException.ParseException ( )
ParseException.ParseException ( String message )
ParseException.ParseException ( Token currentTokenVal, int[ ][ ] expectedTokenSequencesVal, String[ ] tokenImageVal )
package com.hp.hpl.jena.rdf.arp
ParseException.errorCode ( String upper ) [static] :  int
ParseException.errorCodeName ( int errNo ) [static] :  String
ParseException.formatMessage ( Exception e ) [static] :  String
ParseException.getErrorNumber ( ) :  int
ParseException.getMessage ( ) :  String
ParseException.isPromoted ( ) :  boolean
ParseException.isSyntaxError ( ) :  boolean
ParseException.ParseException ( int id, Location where, Exception e )
ParseException.ParseException ( int id, Location where, String msg )
ParseException.promote ( ) :  void
package org.apache.commons.cli
ParseException.ParseException ( String message )

cdk-1.4.0.jar, Parser.class
package com.hp.hpl.jena.reasoner.rulesys
Rule.Parser.getPrefixMap ( ) :  Map
Rule.Parser.getRulesPreload ( ) :  List
Rule.Parser.parseRule ( ) :  Rule
Rule.Parser.recentTokens ( ) :  String
Rule.Parser.registerPrefix ( String prefix, String namespace ) :  void
Rule.Parser.registerPrefixMap ( Map map ) :  void
package org.apache.commons.cli
Parser.flatten ( Options p1, String[ ] p2, boolean p3 ) [abstract] :  String[ ]
Parser.parse ( Options options, String[ ] arguments ) :  CommandLine
Parser.parse ( Options opts, String[ ] arguments, boolean stopAtNonOption ) :  CommandLine
Parser.Parser ( )
Parser.processArgs ( Option opt, ListIterator iter ) :  void

cdk-1.4.0.jar, ParserBase.class
package com.hp.hpl.jena.n3.turtle
ParserBase.createBNode ( ) :  Node
ParserBase.createBNode ( String label, int line, int column ) :  Node
ParserBase.createListNode ( ) :  Node
ParserBase.createLiteral ( String lexicalForm, String langTag, Node datatype ) :  Node
ParserBase.createLiteral ( String lexicalForm, String langTag, String datatypeURI ) :  Node
ParserBase.createLiteralDecimal ( String lexicalForm ) :  Node
ParserBase.createLiteralDouble ( String lexicalForm ) :  Node
ParserBase.createLiteralInteger ( String lexicalForm ) :  Node
ParserBase.createNode ( String iri ) :  Node
ParserBase.createVariable ( String s, int line, int column ) :  Node
ParserBase.doubleValue ( String s ) :  double
ParserBase.emitTriple ( int line, int col, Triple triple ) :  void
ParserBase.endFormula ( int line, int col ) :  void
ParserBase.exMsg ( String msg, int line, int column ) [static] :  String
ParserBase.fixupPrefix ( String prefix, int line, int column ) :  String
ParserBase.getBaseURI ( ) :  String
ParserBase.getPrefixMapping ( ) :  PrefixMapping
ParserBase.integerValue ( String s ) :  long
ParserBase.isBNodeIRI ( String iri ) :  boolean
ParserBase.makePositiveInteger ( String lexicalForm ) :  int
ParserBase.ParserBase ( )
ParserBase.resolveIRI ( String iriStr, int line, int column ) :  String
ParserBase.resolvePName ( String qname, int line, int column ) :  String
ParserBase.resolveQuotedIRI ( String iriStr, int line, int column ) :  String
ParserBase.setBase ( String iriStr, int line, int column ) :  void
ParserBase.setBaseURI ( String u ) :  void
ParserBase.setEventHandler ( TurtleEventHandler h ) :  void
ParserBase.setPrefix ( int line, int col, String prefix, String uri ) :  void
ParserBase.startFormula ( int line, int col ) :  void
ParserBase.stripChars ( String s, int n ) :  String
ParserBase.stripQuotes ( String s ) :  String
ParserBase.stripQuotes3 ( String s ) :  String
ParserBase.throwParseException ( String s, int line, int column ) :  void
ParserBase.unescapeStr ( String s ) [static] :  String
ParserBase.unescapeStr ( String s, int line, int column ) :  String

cdk-1.4.0.jar, ParserException.class
package com.hp.hpl.jena.reasoner.rulesys
Rule.ParserException.Rule.ParserException ( String message, Rule.Parser parser )

cdk-1.4.0.jar, ParserTurtle.class
package com.hp.hpl.jena.n3.turtle
ParserTurtle.parse ( Graph graph, String baseURI, InputStream in ) :  void
ParserTurtle.parse ( Graph graph, String baseURI, Reader reader ) :  void
ParserTurtle.ParserTurtle ( )

cdk-1.4.0.jar, ParsingTest.class
package signature
ParsingTest.basicParseTest ( ) :  void
ParsingTest.edgeLabelMultipleChildrenParseTest ( ) :  void
ParsingTest.edgeLabelMultipleLevelsParseTest ( ) :  void
ParsingTest.edgeLabelParseTest ( ) :  void
ParsingTest.multipleChildrenParseTest ( ) :  void
ParsingTest.multipleLevelsParseTest ( ) :  void
ParsingTest.ParsingTest ( )

cdk-1.4.0.jar, PartialFilledStructureMerger.class
package org.openscience.cdk.structgen.stochastic
PartialFilledStructureMerger.generate ( IAtomContainerSet atomContainers ) :  IAtomContainer

cdk-1.4.0.jar, Path.class
package com.hp.hpl.jena.ontology
OntTools.Path.append ( Statement s ) :  OntTools.Path
OntTools.Path.getStatement ( int i ) :  Statement
OntTools.Path.getTerminal ( ) :  RDFNode
OntTools.Path.getTerminalResource ( ) :  Resource
OntTools.Path.hasTerminus ( RDFNode n ) :  boolean
OntTools.Path.OntTools.Path ( )
OntTools.Path.OntTools.Path ( OntTools.Path basePath )

cdk-1.4.0.jar, PathBuilder.class
package org.openscience.cdk.renderer.elements.path
PathBuilder.close ( ) :  void
PathBuilder.color ( Color color ) :  PathBuilder
PathBuilder.createPath ( ) :  GeneralPath
PathBuilder.cubicTo ( Point2d cp1, Point2d cp2, Point2d ep ) :  PathBuilder
PathBuilder.lineTo ( Point2d point ) :  PathBuilder
PathBuilder.moveTo ( Point2d point ) :  PathBuilder
PathBuilder.PathBuilder ( )
PathBuilder.PathBuilder ( Color color )
PathBuilder.quadTo ( Point2d cp, Point2d ep ) :  PathBuilder

cdk-1.4.0.jar, PathEdge.class
package org.openscience.cdk.smsd.ring
PathEdge.getAtoms ( ) :  List
PathEdge.getSource ( ) :  IAtom
PathEdge.getTarget ( ) :  IAtom
PathEdge.isCycle ( ) :  boolean
PathEdge.PathEdge ( List atoms )
PathEdge.splice ( PathEdge other ) :  PathEdge

cdk-1.4.0.jar, PathElement.class
package org.openscience.cdk.renderer.elements
PathElement.accept ( IRenderingVisitor v ) :  void
PathElement.PathElement ( List points, Color color )
package org.openscience.cdk.renderer.elements.path
PathElement.PathElement ( Type type )
PathElement.points ( ) [abstract] :  float[ ]
PathElement.type ( ) :  Type

cdk-1.4.0.jar, PathGraph.class
package org.openscience.cdk.smsd.ring
PathGraph.PathGraph ( IAtomContainer molecule )
PathGraph.printPaths ( ) :  void
PathGraph.remove ( IAtom atom ) :  List

cdk-1.4.0.jar, Pattern.class
package com.hp.hpl.jena.graph.query
Pattern.asTripleMatch ( Domain d ) :  TripleMatch
Pattern.match ( Domain d, Triple t ) :  boolean
Pattern.Pattern ( Element S, Element P, Element O )
Pattern.toString ( ) :  String

cdk-1.4.0.jar, PatternCompiler.class
package com.hp.hpl.jena.graph.query
PatternCompiler.any ( ) [abstract] :  Element
PatternCompiler.bind ( Node p1, int p2 ) [abstract] :  Element
PatternCompiler.bound ( Node p1, int p2 ) [abstract] :  Element
PatternCompiler.fixed ( Node p1 ) [abstract] :  Element

cdk-1.4.0.jar, PatternLiteral.class
package com.hp.hpl.jena.graph.query
PatternLiteral.getPatternLanguage ( ) [abstract] :  String
PatternLiteral.getPatternModifiers ( ) [abstract] :  String
PatternLiteral.getPatternString ( ) [abstract] :  String

cdk-1.4.0.jar, PatternOptionBuilder.class
package org.apache.commons.cli
PatternOptionBuilder.getValueClass ( char ch ) [static] :  Object
PatternOptionBuilder.isValueCode ( char ch ) [static] :  boolean
PatternOptionBuilder.parsePattern ( String pattern ) [static] :  Options
PatternOptionBuilder.PatternOptionBuilder ( )

cdk-1.4.0.jar, PatternStage.class
package com.hp.hpl.jena.graph.query
PatternStage.PatternStage ( Graph graph, Mapping map, ExpressionSet constraints, Triple[ ] triples )

cdk-1.4.0.jar, PatternStageBase.class
package com.hp.hpl.jena.graph.query
PatternStageBase.deliver ( Pipe sink ) :  Pipe
PatternStageBase.makeFinalStageElement ( Pipe sink ) :  StageElement.PutBindings
PatternStageBase.makeFindStageElement ( int index, StageElement next ) :  StageElement
PatternStageBase.makeIntermediateStageElement ( Pipe sink, int index ) :  StageElement
PatternStageBase.makeNextStageElement ( Pipe sink, int index ) :  StageElement
PatternStageBase.makeStageElementChain ( Pipe sink, int index ) :  StageElement
PatternStageBase.PatternStageBase ( QueryNodeFactory factory, Graph graph, Mapping map, ExpressionSet constraints, Triple[ ] triples )
PatternStageBase.run ( Pipe source, Pipe sink, StageElement se ) :  void

cdk-1.4.0.jar, PatternStageCompiler.class
package com.hp.hpl.jena.graph.query
PatternStageCompiler.any ( ) :  Element
PatternStageCompiler.bind ( Node n, int index ) :  Element
PatternStageCompiler.bound ( Node n, int index ) :  Element
PatternStageCompiler.compile ( PatternCompiler compiler, Mapping map, Triple[ ] source ) [static] :  Pattern[ ]
PatternStageCompiler.fixed ( Node value ) :  Element
PatternStageCompiler.PatternStageCompiler ( )

cdk-1.4.0.jar, PDBWriter.class
package org.openscience.cdk.io
PDBWriter.getIOSettings ( ) :  IOSetting[ ]

cdk-1.4.0.jar, PeriodicTable.class
package org.openscience.cdk.tools.periodictable
PeriodicTable.getAtomicNumber ( String symbol ) [static] :  Integer
PeriodicTable.getCASId ( String symbol ) [static] :  String
PeriodicTable.getChemicalSeries ( String symbol ) [static] :  String
PeriodicTable.getCovalentRadius ( String symbol ) [static] :  Double
PeriodicTable.getElementCount ( ) [static] :  int
PeriodicTable.getGroup ( String symbol ) [static] :  Integer
PeriodicTable.getName ( String symbol ) [static] :  String
PeriodicTable.getPaulingElectronegativity ( String symbol ) [static] :  Double
PeriodicTable.getPeriod ( String symbol ) [static] :  Integer
PeriodicTable.getPhase ( String symbol ) [static] :  String
PeriodicTable.getSymbol ( int atomicNumber ) [static] :  String
PeriodicTable.getVdwRadius ( String symbol ) [static] :  Double
PeriodicTable.PeriodicTable ( )

cdk-1.4.0.jar, PerlPatternParser.class
package com.hp.hpl.jena.graph.query.regexptrees
PerlPatternParser.backReferenceOrOctalChar ( char ch ) :  RegexpTree
PerlPatternParser.control ( char ch ) :  RegexpTree
PerlPatternParser.getPointer ( ) :  int
PerlPatternParser.getString ( ) :  String
PerlPatternParser.hexEscape ( ) :  RegexpTree
PerlPatternParser.nextChar ( ) :  char
PerlPatternParser.numeric ( char[ ] chars, int base, int limit ) :  char
PerlPatternParser.parse ( String string ) [static] :  RegexpTree
PerlPatternParser.parse ( String string, RegexpTreeGenerator gen ) [static] :  RegexpTree
PerlPatternParser.parseAlts ( ) :  RegexpTree
PerlPatternParser.parseAtom ( ) :  RegexpTree
PerlPatternParser.parseClass ( ) :  RegexpTree
PerlPatternParser.parseClassNegation ( ) :  boolean
PerlPatternParser.parseElement ( ) :  RegexpTree
PerlPatternParser.parseParens ( ) :  RegexpTree
PerlPatternParser.parseQuantifier ( RegexpTree d ) :  RegexpTree
PerlPatternParser.parseSeq ( ) :  RegexpTree
PerlPatternParser.PerlPatternParser ( String toParse )
PerlPatternParser.PerlPatternParser ( String toParse, RegexpTreeGenerator gen )

cdk-1.4.0.jar, PermutationTest.class
package signature
PermutationTest.doubleBondChainTest ( ) :  void
PermutationTest.PermutationTest ( )
PermutationTest.permuteCNOMolecule ( ) :  void
PermutationTest.permuteCompletely ( Molecule molecule ) :  void
PermutationTest.permuteOCCCSC ( ) :  void
PermutationTest.permuteOCCOCO ( ) :  void
PermutationTest.printIdentity ( Molecule molecule, String signature ) :  void
PermutationTest.testSpecificPermutation ( Molecule molecule, int[ ] permutation ) :  void
PermutationTest.toSignatureString ( Molecule molecule ) :  String

cdk-1.4.0.jar, Permutor.class
package org.openscience.cdk.smsd.labelling
Permutor.calculateMaxRank ( ) :  int
Permutor.getCurrentPermutation ( ) :  int[ ]
Permutor.getNextPermutation ( ) :  int[ ]
Permutor.getRandomNextPermutation ( ) :  int[ ]
Permutor.getRank ( ) :  int
Permutor.hasNext ( ) :  boolean
Permutor.Permutor ( int size )
Permutor.setPermutation ( int[ ] permutation ) :  void
Permutor.setRank ( int rank ) :  void
package signature
Permutor.calculateMaxRank ( ) :  int
Permutor.getCurrentPermutation ( ) :  int[ ]
Permutor.getNextPermutation ( ) :  int[ ]
Permutor.getRandomNextPermutation ( ) :  int[ ]
Permutor.getRank ( ) :  int
Permutor.hasNext ( ) :  boolean
Permutor.Permutor ( int size )
Permutor.setPermutation ( int[ ] permutation ) :  void
Permutor.setRank ( int rank ) :  void

cdk-1.4.0.jar, Personality.class
package com.hp.hpl.jena.enhanced
Personality.add ( Class interf, Implementation impl ) :  Personality
Personality.add ( Personality p ) :  Personality
Personality.copy ( ) :  Personality
Personality.getImplementation ( Class t ) :  Implementation
Personality.getMap ( ) :  Map
Personality.newInstance ( Class interf, Node n, EnhGraph that ) :  Object
Personality.Personality ( )
Personality.Personality ( Personality other )

cdk-1.4.0.jar, PersonalityConfigException.class
package com.hp.hpl.jena.enhanced
PersonalityConfigException.PersonalityConfigException ( )
PersonalityConfigException.PersonalityConfigException ( String msg )

cdk-1.4.0.jar, PharmacophoreMatcher.class
package org.openscience.cdk.pharmacophore
PharmacophoreMatcher.getPharmacophoreQuery ( ) :  PharmacophoreQuery
PharmacophoreMatcher.PharmacophoreMatcher ( PharmacophoreQuery pharmacophoreQuery )
PharmacophoreMatcher.setPharmacophoreQuery ( PharmacophoreQuery query ) :  void

cdk-1.4.0.jar, PharmacophoreQuery.class
package org.openscience.cdk.pharmacophore
PharmacophoreQuery.PharmacophoreQuery ( )
PharmacophoreQuery.toString ( ) :  String

cdk-1.4.0.jar, PharmacophoreQueryAngleBond.class
package org.openscience.cdk.pharmacophore
PharmacophoreQueryAngleBond.toString ( ) :  String

cdk-1.4.0.jar, PharmacophoreQueryAtom.class
package org.openscience.cdk.pharmacophore
PharmacophoreQueryAtom.toString ( ) :  String

cdk-1.4.0.jar, PharmacophoreQueryBond.class
package org.openscience.cdk.pharmacophore
PharmacophoreQueryBond.toString ( ) :  String

cdk-1.4.0.jar, PharmacophoreUtils.class
package org.openscience.cdk.pharmacophore
PharmacophoreUtils.writePharmacophoreDefinition ( PharmacophoreQuery query, OutputStream out ) [static] :  void
PharmacophoreUtils.writePharmacophoreDefinition ( PharmacophoreQuery[ ] queries, OutputStream out ) [static] :  void

cdk-1.4.0.jar, Pipe.class
package com.hp.hpl.jena.graph.query
Pipe.close ( ) [abstract] :  void
Pipe.close ( Exception p1 ) [abstract] :  void
Pipe.get ( ) [abstract] :  Domain
Pipe.hasNext ( ) [abstract] :  boolean
Pipe.put ( Domain p1 ) [abstract] :  void

cdk-1.4.0.jar, Polyadic.class
package com.hp.hpl.jena.graph.compose
Polyadic.addGraph ( Graph graph ) :  void
Polyadic.close ( ) :  void
Polyadic.dependsOn ( Graph graph ) :  boolean
Polyadic.getBaseGraph ( ) :  Graph
Polyadic.getBulkUpdateHandler ( ) :  BulkUpdateHandler
Polyadic.getCapabilities ( ) :  Capabilities
Polyadic.getPrefixMapping ( ) :  PrefixMapping
Polyadic.getRequiredBaseGraph ( ) :  Graph
Polyadic.getSubGraphs ( ) :  List
Polyadic.getTransactionHandler ( ) :  TransactionHandler
Polyadic.Polyadic ( )
Polyadic.Polyadic ( Graph[ ] graphs )
Polyadic.Polyadic ( Iterator graphs )
Polyadic.removeGraph ( Graph graph ) :  void
Polyadic.setBaseGraph ( Graph graph ) :  void

cdk-1.4.0.jar, PolyadicPrefixMappingImpl.class
package com.hp.hpl.jena.graph.compose
PolyadicPrefixMappingImpl.equals ( PrefixMappingImpl other ) :  boolean
PolyadicPrefixMappingImpl.expandPrefix ( String prefixed ) :  String
PolyadicPrefixMappingImpl.getNsPrefixMap ( ) :  Map
PolyadicPrefixMappingImpl.getNsPrefixURI ( String prefix ) :  String
PolyadicPrefixMappingImpl.getNsURIPrefix ( String uri ) :  String
PolyadicPrefixMappingImpl.PolyadicPrefixMappingImpl ( Polyadic p )
PolyadicPrefixMappingImpl.qnameFor ( String uri ) :  String
PolyadicPrefixMappingImpl.removeNsPrefix ( String prefix ) :  PrefixMapping
PolyadicPrefixMappingImpl.sameAs ( PrefixMappingImpl other ) :  boolean
PolyadicPrefixMappingImpl.setNsPrefix ( String prefix, String uri ) :  PrefixMapping
PolyadicPrefixMappingImpl.setNsPrefixes ( Map other ) :  PrefixMapping
PolyadicPrefixMappingImpl.setNsPrefixes ( PrefixMapping other ) :  PrefixMapping
PolyadicPrefixMappingImpl.shortForm ( String uri ) :  String
PolyadicPrefixMappingImpl.toString ( ) :  String

cdk-1.4.0.jar, Polymorphic.class
package com.hp.hpl.jena.enhanced
Polymorphic.addView ( Polymorphic other ) :  void
Polymorphic.alreadyHasView ( Class t ) :  boolean
Polymorphic.asInternal ( Class t ) :  Object
Polymorphic.canSupport ( Class p1 ) [abstract] :  boolean
Polymorphic.convertTo ( Class p1 ) [abstract] :  Object
Polymorphic.equals ( Object p1 ) [abstract] :  boolean
Polymorphic.getPersonality ( ) [abstract] :  Personality
Polymorphic.isValid ( ) [abstract] :  boolean
Polymorphic.supports ( Class t ) :  boolean

cdk-1.4.0.jar, Position.class
package com.ibm.icu.text
Transliterator.Position.equals ( Object obj ) :  boolean
Transliterator.Position.set ( Transliterator.Position pos ) :  void
Transliterator.Position.toString ( ) :  String
Transliterator.Position.Transliterator.Position ( )
Transliterator.Position.Transliterator.Position ( int contextStart, int contextLimit, int start )
Transliterator.Position.Transliterator.Position ( int contextStart, int contextLimit, int start, int limit )
Transliterator.Position.Transliterator.Position ( Transliterator.Position pos )
Transliterator.Position.validate ( int length ) :  void
package org.openscience.cdk.renderer.elements
TextGroupElement.Position.valueOf ( String name ) [static] :  TextGroupElement.Position
TextGroupElement.Position.values ( ) [static] :  TextGroupElement.Position[ ]

cdk-1.4.0.jar, PosixParser.class
package org.apache.commons.cli
PosixParser.burstToken ( String token, boolean stopAtNonOption ) :  void
PosixParser.flatten ( Options options, String[ ] arguments, boolean stopAtNonOption ) :  String[ ]
PosixParser.PosixParser ( )

cdk-1.4.0.jar, PostFilter.class
package org.openscience.cdk.smsd.filters
PostFilter.filter ( List mappings ) [static] :  List
PostFilter.PostFilter ( )

cdk-1.4.0.jar, PredicatesFilter.class
package com.hp.hpl.jena.ontology
OntTools.PredicatesFilter.accept ( Object x0 ) :  boolean
OntTools.PredicatesFilter.accept ( Statement s ) :  boolean
OntTools.PredicatesFilter.OntTools.PredicatesFilter ( Collection preds )
OntTools.PredicatesFilter.OntTools.PredicatesFilter ( Property pred )
OntTools.PredicatesFilter.OntTools.PredicatesFilter ( Property[ ] preds )

cdk-1.4.0.jar, PrefixMapping.class
package com.hp.hpl.jena.shared
PrefixMapping.expandPrefix ( String p1 ) [abstract] :  String
PrefixMapping.getNsPrefixMap ( ) [abstract] :  Map
PrefixMapping.getNsPrefixURI ( String p1 ) [abstract] :  String
PrefixMapping.getNsURIPrefix ( String p1 ) [abstract] :  String
PrefixMapping.lock ( ) [abstract] :  PrefixMapping
PrefixMapping.qnameFor ( String p1 ) [abstract] :  String
PrefixMapping.removeNsPrefix ( String p1 ) [abstract] :  PrefixMapping
PrefixMapping.samePrefixMappingAs ( PrefixMapping p1 ) [abstract] :  boolean
PrefixMapping.setNsPrefix ( String p1, String p2 ) [abstract] :  PrefixMapping
PrefixMapping.setNsPrefixes ( Map p1 ) [abstract] :  PrefixMapping
PrefixMapping.setNsPrefixes ( PrefixMapping p1 ) [abstract] :  PrefixMapping
PrefixMapping.shortForm ( String p1 ) [abstract] :  String
PrefixMapping.withDefaultMappings ( PrefixMapping p1 ) [abstract] :  PrefixMapping

cdk-1.4.0.jar, PrefixMappingAssembler.class
package com.hp.hpl.jena.assembler.assemblers
PrefixMappingAssembler.getPrefixes ( Assembler a, Resource root, PrefixMapping result ) [static] :  PrefixMapping
PrefixMappingAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object
PrefixMappingAssembler.PrefixMappingAssembler ( )

cdk-1.4.0.jar, Print.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Print.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Print.getName ( ) :  String
Print.headAction ( Node[ ] args, int length, RuleContext context ) :  void
Print.Print ( )
Print.print ( Node[ ] args, int length, RuleContext context ) :  void

cdk-1.4.0.jar, PrintUtil.class
package com.hp.hpl.jena.util
PrintUtil.expandQname ( String uri ) [static] :  String
PrintUtil.init ( ) [static] :  void
PrintUtil.print ( Node node ) [static] :  String
PrintUtil.print ( Object obj ) [static] :  String
PrintUtil.print ( RDFNode node ) [static] :  String
PrintUtil.print ( Statement stmt ) [static] :  String
PrintUtil.print ( Triple triple ) [static] :  String
PrintUtil.print ( TriplePattern triple ) [static] :  String
PrintUtil.printIndent ( PrintWriter out, int indent ) [static] :  void
PrintUtil.printOut ( Iterator it ) [static] :  void
PrintUtil.PrintUtil ( )
PrintUtil.registerPrefix ( String prefix, String namespace ) [static] :  void
PrintUtil.registerPrefixMap ( Map map ) [static] :  void
PrintUtil.removePrefix ( String prefix ) [static] :  void
PrintUtil.removePrefixMap ( Map map ) [static] :  void

cdk-1.4.0.jar, ProcessedTriple.class
package com.hp.hpl.jena.mem.faster
ProcessedTriple.createApplyer ( Graph g ) :  Applyer
ProcessedTriple.hasNoVariables ( ) :  boolean
ProcessedTriple.ProcessedTriple ( QueryNode S, QueryNode P, QueryNode O )

cdk-1.4.0.jar, Product.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Product.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Product.getArgLength ( ) :  int
Product.getName ( ) :  String
Product.Product ( )

cdk-1.4.0.jar, Profile.class
package com.hp.hpl.jena.ontology
Profile.ALL_DIFFERENT ( ) [abstract] :  Resource
Profile.ALL_VALUES_FROM ( ) [abstract] :  Property
Profile.ANNOTATION_PROPERTY ( ) [abstract] :  Resource
Profile.BACKWARD_COMPATIBLE_WITH ( ) [abstract] :  Property
Profile.CARDINALITY ( ) [abstract] :  Property
Profile.CARDINALITY_Q ( ) [abstract] :  Property
Profile.CLASS ( ) [abstract] :  Resource
Profile.COMMENT ( ) [abstract] :  Property
Profile.COMPLEMENT_OF ( ) [abstract] :  Property
Profile.DATARANGE ( ) [abstract] :  Resource
Profile.DATATYPE_PROPERTY ( ) [abstract] :  Resource
Profile.DEPRECATED_CLASS ( ) [abstract] :  Resource
Profile.DEPRECATED_PROPERTY ( ) [abstract] :  Resource
Profile.DIFFERENT_FROM ( ) [abstract] :  Property
Profile.DISJOINT_WITH ( ) [abstract] :  Property
Profile.DISTINCT_MEMBERS ( ) [abstract] :  Property
Profile.DOMAIN ( ) [abstract] :  Property
Profile.EQUIVALENT_CLASS ( ) [abstract] :  Property
Profile.EQUIVALENT_PROPERTY ( ) [abstract] :  Property
Profile.FIRST ( ) [abstract] :  Property
Profile.FUNCTIONAL_PROPERTY ( ) [abstract] :  Resource
Profile.getAliasFor ( Resource p1 ) [abstract] :  Resource
Profile.getAnnotationProperties ( ) [abstract] :  Iterator
Profile.getAxiomTypes ( ) [abstract] :  Iterator
Profile.getClassDescriptionTypes ( ) [abstract] :  Iterator
Profile.getLabel ( ) [abstract] :  String
Profile.HAS_CLASS_Q ( ) [abstract] :  Property
Profile.HAS_VALUE ( ) [abstract] :  Property
Profile.hasAliasFor ( Resource p1 ) [abstract] :  boolean
Profile.IMPORTS ( ) [abstract] :  Property
Profile.INCOMPATIBLE_WITH ( ) [abstract] :  Property
Profile.INTERSECTION_OF ( ) [abstract] :  Property
Profile.INVERSE_FUNCTIONAL_PROPERTY ( ) [abstract] :  Resource
Profile.INVERSE_OF ( ) [abstract] :  Property
Profile.IS_DEFINED_BY ( ) [abstract] :  Property
Profile.isSupported ( Node p1, EnhGraph p2, Class p3 ) [abstract] :  boolean
Profile.LABEL ( ) [abstract] :  Property
Profile.LIST ( ) [abstract] :  Resource
Profile.listAliasesFor ( Resource p1 ) [abstract] :  Iterator
Profile.MAX_CARDINALITY ( ) [abstract] :  Property
Profile.MAX_CARDINALITY_Q ( ) [abstract] :  Property
Profile.MIN_CARDINALITY ( ) [abstract] :  Property
Profile.MIN_CARDINALITY_Q ( ) [abstract] :  Property
Profile.NAMESPACE ( ) [abstract] :  String
Profile.NIL ( ) [abstract] :  Resource
Profile.NOTHING ( ) [abstract] :  Resource
Profile.OBJECT_PROPERTY ( ) [abstract] :  Resource
Profile.ON_PROPERTY ( ) [abstract] :  Property
Profile.ONE_OF ( ) [abstract] :  Property
Profile.ONTOLOGY ( ) [abstract] :  Resource
Profile.ONTOLOGY_PROPERTY ( ) [abstract] :  Resource
Profile.PRIOR_VERSION ( ) [abstract] :  Property
Profile.PROPERTY ( ) [abstract] :  Resource
Profile.RANGE ( ) [abstract] :  Property
Profile.REST ( ) [abstract] :  Property
Profile.RESTRICTION ( ) [abstract] :  Resource
Profile.SAME_AS ( ) [abstract] :  Property
Profile.SAME_INDIVIDUAL_AS ( ) [abstract] :  Property
Profile.SEE_ALSO ( ) [abstract] :  Property
Profile.SOME_VALUES_FROM ( ) [abstract] :  Property
Profile.SUB_CLASS_OF ( ) [abstract] :  Property
Profile.SUB_PROPERTY_OF ( ) [abstract] :  Property
Profile.SYMMETRIC_PROPERTY ( ) [abstract] :  Resource
Profile.THING ( ) [abstract] :  Resource
Profile.TRANSITIVE_PROPERTY ( ) [abstract] :  Resource
Profile.UNION_OF ( ) [abstract] :  Property
Profile.VERSION_INFO ( ) [abstract] :  Property

cdk-1.4.0.jar, ProfileException.class
package com.hp.hpl.jena.ontology
ProfileException.ProfileException ( String element, Profile profile )

cdk-1.4.0.jar, ProfileRegistry.class
package com.hp.hpl.jena.ontology
ProfileRegistry.getInstance ( ) [static] :  ProfileRegistry
ProfileRegistry.getProfile ( String uri ) :  Profile
ProfileRegistry.registerProfile ( String uri, Profile profile ) :  void

cdk-1.4.0.jar, Property.class
package com.hp.hpl.jena.rdf.model
Property.getLocalName ( ) [abstract] :  String
Property.getNameSpace ( ) [abstract] :  String
Property.getOrdinal ( ) [abstract] :  int
Property.isProperty ( ) [abstract] :  boolean

cdk-1.4.0.jar, PropertyNotFoundException.class
package com.hp.hpl.jena.shared
PropertyNotFoundException.PropertyNotFoundException ( Property p )

cdk-1.4.0.jar, PropertyRequiredException.class
package com.hp.hpl.jena.assembler.exceptions
PropertyRequiredException.getProperty ( ) :  Resource
PropertyRequiredException.PropertyRequiredException ( Resource root, Property property )

cdk-1.4.0.jar, PubchemFingerprinter.class
package org.openscience.cdk.fingerprint
PubchemFingerprinter.decode ( String enc ) [static] :  BitSet
PubchemFingerprinter.getFingerprint ( IAtomContainer atomContainer ) :  BitSet
PubchemFingerprinter.getFingerprintAsBytes ( ) :  byte[ ]
PubchemFingerprinter.getSize ( ) :  int
PubchemFingerprinter.PubchemFingerprinter ( )

cdk-1.4.0.jar, PutBindings.class
package com.hp.hpl.jena.graph.query
StageElement.PutBindings.run ( Domain current ) :  void
StageElement.PutBindings.StageElement.PutBindings ( Pipe sink )

cdk-1.4.0.jar, qtest.class
package jena
qtest.main ( String[ ] args ) [static] :  void
qtest.qtest ( )

cdk-1.4.0.jar, QuadTo.class
package org.openscience.cdk.renderer.elements.path
QuadTo.points ( ) :  float[ ]
QuadTo.QuadTo ( Point2d cp, Point2d ep )

cdk-1.4.0.jar, QualifiedRestriction.class
package com.hp.hpl.jena.ontology
QualifiedRestriction.getHasClassQ ( ) [abstract] :  OntResource
QualifiedRestriction.hasHasClassQ ( DataRange p1 ) [abstract] :  boolean
QualifiedRestriction.hasHasClassQ ( OntClass p1 ) [abstract] :  boolean
QualifiedRestriction.removeHasClassQ ( DataRange p1 ) [abstract] :  void
QualifiedRestriction.removeHasClassQ ( OntClass p1 ) [abstract] :  void
QualifiedRestriction.setHasClassQ ( OntClass p1 ) [abstract] :  void

cdk-1.4.0.jar, Quaternion.class
package org.openscience.cdk.math
Quaternion.add ( Quaternion q ) :  Quaternion
Quaternion.div ( Quaternion q ) :  Quaternion
Quaternion.fromRotationMatrix ( Matrix m ) [static] :  Quaternion
Quaternion.mag ( ) :  double
Quaternion.mag_sq ( ) :  double
Quaternion.mul ( double v ) :  Quaternion
Quaternion.mul ( Quaternion q ) :  Quaternion
Quaternion.negate ( ) :  Quaternion
Quaternion.normalize ( ) :  Quaternion
Quaternion.Quaternion ( )
Quaternion.Quaternion ( double a, double b, double c, double d )
Quaternion.Quaternion ( double latitude, double longitude, double angle )
Quaternion.Quaternion ( Vector axis, double angle )
Quaternion.sqrt ( ) :  Quaternion
Quaternion.sub ( Quaternion q ) :  Quaternion
Quaternion.toRotationMatrix ( ) :  Matrix
Quaternion.toString ( ) :  String

cdk-1.4.0.jar, query.class
package jena
query.invokeCmd ( String className, String[ ] args ) [static] :  void
query.main ( String[ ] args ) [static] :  void
query.query ( )

cdk-1.4.0.jar, Query.class
package com.hp.hpl.jena.graph.query
Query.addConstraint ( Expression e ) :  Query
Query.addMatch ( Node s, Node p, Node o ) :  Query
Query.addMatch ( Triple t ) :  Query
Query.args ( ) :  NamedGraphMap
Query.executeBindings ( Graph g, List stages, Node[ ] results ) :  ExtendedIterator
Query.executeBindings ( Graph g, Node[ ] results ) :  ExtendedIterator
Query.executeBindings ( List outStages, NamedGraphMap args, Node[ ] nodes ) :  ExtendedIterator
Query.executeBindings ( NamedGraphMap args, Node[ ] nodes ) :  ExtendedIterator
Query.getConstraints ( ) :  ExpressionSet
Query.getPattern ( ) :  List
Query.getSorter ( ) :  TripleSorter
Query.getVariableCount ( ) :  int
Query.Query ( )
Query.Query ( Graph pattern )
Query.setTripleSorter ( TripleSorter ts ) :  void

cdk-1.4.0.jar, QueryCompiler.class
package org.openscience.cdk.smsd.algorithm.vflib.query
QueryCompiler.compile ( ) :  IQuery
QueryCompiler.QueryCompiler ( IAtomContainer molecule, boolean shouldMatchBonds )
QueryCompiler.QueryCompiler ( IQueryAtomContainer molecule )

cdk-1.4.0.jar, QueryHandler.class
package com.hp.hpl.jena.graph.query
QueryHandler.containsNode ( Node p1 ) [abstract] :  boolean
QueryHandler.objectsFor ( Node p1, Node p2 ) [abstract] :  ExtendedIterator
QueryHandler.patternStage ( Mapping p1, ExpressionSet p2, Triple[ ] p3 ) [abstract] :  Stage
QueryHandler.predicatesFor ( Node p1, Node p2 ) [abstract] :  ExtendedIterator
QueryHandler.prepareBindings ( Query p1, Node[ ] p2 ) [abstract] :  BindingQueryPlan
QueryHandler.prepareTree ( Graph p1 ) [abstract] :  TreeQueryPlan
QueryHandler.subjectsFor ( Node p1, Node p2 ) [abstract] :  ExtendedIterator

cdk-1.4.0.jar, QueryMapper.class
package com.hp.hpl.jena.util
QueryMapper.getGraph ( ) :  Graph
QueryMapper.getQuery ( ) :  Query
QueryMapper.getVariables ( ) :  Node[ ]
QueryMapper.QueryMapper ( Model m, Resource[ ] variables )
QueryMapper.toQueryGraph ( Model m ) :  Graph
QueryMapper.toQueryNode ( RDFNode rn ) :  Node
QueryMapper.toQueryTriple ( Statement s ) :  Triple
QueryMapper.toQueryVariables ( Resource[ ] vars ) :  Node[ ]

cdk-1.4.0.jar, QueryNode.class
package com.hp.hpl.jena.graph.query
QueryNode.classify ( QueryNodeFactory f, Mapping map, Set recent, Node n ) [static] :  QueryNode
QueryNode.finder ( Domain d ) :  Node
QueryNode.isFrozen ( ) :  boolean
QueryNode.match ( Domain d, Node x ) :  boolean
QueryNode.matchOrBind ( Domain p1, Node p2 ) [abstract] :  boolean
QueryNode.mustMatch ( ) :  boolean
QueryNode.QueryNode ( Node node )
QueryNode.QueryNode ( Node node, int index )
QueryNode.toString ( ) :  String

cdk-1.4.0.jar, QueryNodeFactory.class
package com.hp.hpl.jena.graph.query
QueryNodeFactory.createAny ( ) [abstract] :  QueryNode
QueryNodeFactory.createArray ( int p1 ) [abstract] :  QueryTriple[ ]
QueryNodeFactory.createBind ( Node p1, int p2 ) [abstract] :  QueryNode
QueryNodeFactory.createBound ( Node p1, int p2 ) [abstract] :  QueryNode
QueryNodeFactory.createFixed ( Node p1 ) [abstract] :  QueryNode
QueryNodeFactory.createJustBound ( Node p1, int p2 ) [abstract] :  QueryNode
QueryNodeFactory.createTriple ( QueryNode p1, QueryNode p2, QueryNode p3 ) [abstract] :  QueryTriple

cdk-1.4.0.jar, QueryNodeFactoryBase.class
package com.hp.hpl.jena.graph.query
QueryNodeFactoryBase.createAny ( ) :  QueryNode
QueryNodeFactoryBase.createArray ( int size ) :  QueryTriple[ ]
QueryNodeFactoryBase.createBind ( Node node, int i ) :  QueryNode
QueryNodeFactoryBase.createBound ( Node node, int i ) :  QueryNode
QueryNodeFactoryBase.createFixed ( Node n ) :  QueryNode
QueryNodeFactoryBase.createJustBound ( Node node, int i ) :  QueryNode
QueryNodeFactoryBase.createTriple ( QueryNode S, QueryNode P, QueryNode O ) :  QueryTriple
QueryNodeFactoryBase.QueryNodeFactoryBase ( )

cdk-1.4.0.jar, QueryProcessor.class
package org.openscience.cdk.smsd.algorithm.mcgregor
QueryProcessor.getBondNumA ( ) :  int
QueryProcessor.getCTab1 ( ) :  List
QueryProcessor.getCTab2 ( ) :  List
QueryProcessor.getNeighborBondNumA ( ) :  int
QueryProcessor.process ( IAtomContainer query, IAtomContainer target, List unmapped_atoms_molA, List mapped_atoms, int counter ) :  void
QueryProcessor.process ( int setNumA, int setNumB, List i_bond_setA, List i_bond_setB, List unmapped_atoms_molA, List new_Mapping, int counter ) :  void
QueryProcessor.process ( IQueryAtomContainer query, IAtomContainer target, List unmapped_atoms_molA, List mapped_atoms, int counter ) :  void
QueryProcessor.QueryProcessor ( List cTab1Copy, List cTab2Copy, String[ ] signArray, int neighbor_bondnum_A, int set_bondnum_A, List i_bond_neighborsA, List c_bond_neighborsA, int mappingSize, List i_bond_setA, List c_bond_setA )

cdk-1.4.0.jar, QueryStageException.class
package com.hp.hpl.jena.shared
QueryStageException.QueryStageException ( Throwable cause )

cdk-1.4.0.jar, QueryTriple.class
package com.hp.hpl.jena.graph.query
QueryTriple.classify ( QueryNodeFactory f, Mapping m, Triple t ) [static] :  QueryTriple
QueryTriple.classify ( QueryNodeFactory f, Mapping m, Triple[ ] t ) [static] :  QueryTriple[ ]
QueryTriple.createApplyer ( Graph g ) :  Applyer
QueryTriple.createMatcher ( ) :  Matcher
QueryTriple.QueryTriple ( QueryNode S, QueryNode P, QueryNode O )
QueryTriple.toString ( ) :  String

cdk-1.4.0.jar, Quotient.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Quotient.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Quotient.getArgLength ( ) :  int
Quotient.getName ( ) :  String
Quotient.Quotient ( )

cdk-1.4.0.jar, RandCache.class
package com.hp.hpl.jena.util.cache
RandCache.clear ( ) :  void
RandCache.forgetStats ( ) :  void
RandCache.get ( Object key ) :  Object
RandCache.getEnabled ( ) :  boolean
RandCache.getGets ( ) :  long
RandCache.getHits ( ) :  long
RandCache.getPuts ( ) :  long
RandCache.makeSpace ( ) :  void
RandCache.put ( Object key, Object value ) :  void
RandCache.setEnabled ( boolean enabled ) :  boolean

cdk-1.4.0.jar, RandomOrderGraph.class
package com.hp.hpl.jena.shared
RandomOrderGraph.createDefaultGraph ( ) [static] :  Graph
RandomOrderGraph.createDefaultModel ( ) [static] :  Model
RandomOrderGraph.find ( Node s, Node p, Node o ) :  ExtendedIterator
RandomOrderGraph.find ( TripleMatch m ) :  ExtendedIterator
RandomOrderGraph.RandomOrderGraph ( Graph base )
RandomOrderGraph.RandomOrderGraph ( int bufsz, Graph base )

cdk-1.4.0.jar, RandomOrderIterator.class
package com.hp.hpl.jena.util.iterator
RandomOrderIterator.hasNext ( ) :  boolean
RandomOrderIterator.next ( ) :  Object
RandomOrderIterator.RandomOrderIterator ( int sz, Iterator base )
RandomOrderIterator.remove ( ) :  void

cdk-1.4.0.jar, RangeDateRule.class
package com.ibm.icu.util
RangeDateRule.add ( Date start, DateRule rule ) :  void *DEPRECATED*
RangeDateRule.add ( DateRule rule ) :  void *DEPRECATED*
RangeDateRule.firstAfter ( Date start ) :  Date *DEPRECATED*
RangeDateRule.firstBetween ( Date start, Date end ) :  Date *DEPRECATED*
RangeDateRule.isBetween ( Date start, Date end ) :  boolean *DEPRECATED*
RangeDateRule.isOn ( Date date ) :  boolean *DEPRECATED*
RangeDateRule.RangeDateRule ( ) *DEPRECATED*

cdk-1.4.0.jar, RangeValueIterator.class
package com.ibm.icu.util
RangeValueIterator.next ( RangeValueIterator.Element p1 ) [abstract] :  boolean
RangeValueIterator.reset ( ) [abstract] :  void

cdk-1.4.0.jar, RasmolColors.class
package org.openscience.cdk.renderer.color
RasmolColors.getAtomColor ( IAtom atom ) :  Color
RasmolColors.getAtomColor ( IAtom atom, Color defaultColor ) :  Color
RasmolColors.RasmolColors ( )

cdk-1.4.0.jar, RawCollationKey.class
package com.ibm.icu.text
RawCollationKey.compareTo ( Object rhs ) :  int *DEPRECATED*
RawCollationKey.RawCollationKey ( )
RawCollationKey.RawCollationKey ( byte[ ] bytes )
RawCollationKey.RawCollationKey ( byte[ ] bytesToAdopt, int size )
RawCollationKey.RawCollationKey ( int capacity )

cdk-1.4.0.jar, RCAction.class
package jena
rdfcat.RCAction.run ( rdfcat p1 ) [abstract] :  void

cdk-1.4.0.jar, RCCommandLine.class
package jena
rdfcat.RCCommandLine.getItems ( ) :  Iterator
rdfcat.RCCommandLine.handleUnrecognizedArg ( String argStr ) :  void
rdfcat.RCCommandLine.ignoreArgument ( String argStr ) :  boolean
rdfcat.RCCommandLine.rdfcat.RCCommandLine ( rdfcat p1 )
rdfcat.RCCommandLine.xendProcessing ( String argStr ) :  boolean

cdk-1.4.0.jar, RDBModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
RDBModelAssembler.consGraph ( IDBConnection c, String name, ReificationStyle style, boolean fresh ) :  GraphRDB
RDBModelAssembler.consModel ( IDBConnection c, String name, ReificationStyle style, boolean fresh ) :  Model
RDBModelAssembler.getConnection ( Assembler a, Resource root ) :  ConnectionDescription
RDBModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode mode ) :  Model
RDBModelAssembler.openModel ( Assembler a, Resource root, Content initial, Mode mode ) :  Model
RDBModelAssembler.openModel ( Resource root, ConnectionDescription c, String name, ReificationStyle style, Content initial, Mode mode ) :  Model
RDBModelAssembler.RDBModelAssembler ( )

cdk-1.4.0.jar, RDF.class
package com.hp.hpl.jena.vocabulary
RDF.getURI ( ) [static] :  String
RDF.li ( int i ) [static] :  Property
RDF.property ( String local ) [static] :  Property
RDF.RDF ( )
RDF.resource ( String local ) [static] :  Resource

cdk-1.4.0.jar, rdfcat.class
package jena
rdfcat.addIncludes ( Model inModel, List queue ) :  void
rdfcat.expectInput ( String lang ) :  void
rdfcat.getCheckedLanguage ( String shortLang ) [static] :  String
rdfcat.getExpectedInput ( ) :  String
rdfcat.getOutputStream ( ) :  OutputStream
rdfcat.getURL ( RDFNode n ) :  String
rdfcat.go ( String[ ] args ) :  void
rdfcat.main ( String[ ] args ) [static] :  void
rdfcat.makeUnabbreviateMap ( ) [static] :  Map
rdfcat.rdfcat ( )
rdfcat.readInput ( String inputName ) :  void
rdfcat.setInclude ( boolean incl ) :  void
rdfcat.setOutput ( String lang ) :  void
rdfcat.setRemoveIncludeStatements ( boolean f ) :  void
rdfcat.usage ( ) :  void

cdk-1.4.0.jar, RDFCollection.class
package com.hp.hpl.jena.rdf.arp.states
RDFCollection.abort ( ) :  void
RDFCollection.RDFCollection ( WantsObjectFrameI s, AbsXMLContext x )
RDFCollection.startElement ( String x0, String x1, String x2, Attributes x3 ) :  FrameI

cdk-1.4.0.jar, rdfcompare.class
package jena
rdfcompare.main ( String[ ] args ) [static] :  void
rdfcompare.rdfcompare ( )
rdfcompare.read ( Model model, String in, String lang ) [static] :  void
rdfcompare.usage ( ) [static] :  void

cdk-1.4.0.jar, rdfcopy.class
package jena
rdfcopy.main ( String[ ] args ) [static] :  void
rdfcopy.rdfcopy ( )
rdfcopy.read ( Model model, String in, String lang ) [static] :  void
rdfcopy.usage ( ) [static] :  void

cdk-1.4.0.jar, RDFDatatype.class
package com.hp.hpl.jena.datatypes
RDFDatatype.cannonicalise ( Object p1 ) [abstract] :  Object
RDFDatatype.extendedTypeDefinition ( ) [abstract] :  Object
RDFDatatype.getHashCode ( LiteralLabel p1 ) [abstract] :  int
RDFDatatype.getJavaClass ( ) [abstract] :  Class
RDFDatatype.getURI ( ) [abstract] :  String
RDFDatatype.isEqual ( LiteralLabel p1, LiteralLabel p2 ) [abstract] :  boolean
RDFDatatype.isValid ( String p1 ) [abstract] :  boolean
RDFDatatype.isValidLiteral ( LiteralLabel p1 ) [abstract] :  boolean
RDFDatatype.isValidValue ( Object p1 ) [abstract] :  boolean
RDFDatatype.normalizeSubType ( Object p1, RDFDatatype p2 ) [abstract] :  RDFDatatype
RDFDatatype.parse ( String p1 ) [abstract] :  Object
RDFDatatype.unparse ( Object p1 ) [abstract] :  String

cdk-1.4.0.jar, RDFErrorHandler.class
package com.hp.hpl.jena.rdf.model
RDFErrorHandler.error ( Exception p1 ) [abstract] :  void
RDFErrorHandler.fatalError ( Exception p1 ) [abstract] :  void
RDFErrorHandler.warning ( Exception p1 ) [abstract] :  void

cdk-1.4.0.jar, RDFList.class
package com.hp.hpl.jena.rdf.model
RDFList.add ( RDFNode p1 ) [abstract] :  void
RDFList.append ( Iterator p1 ) [abstract] :  RDFList
RDFList.append ( RDFList p1 ) [abstract] :  RDFList
RDFList.apply ( RDFList.ApplyFn p1 ) [abstract] :  void
RDFList.asJavaList ( ) [abstract] :  List
RDFList.concatenate ( Iterator p1 ) [abstract] :  void
RDFList.concatenate ( RDFList p1 ) [abstract] :  void
RDFList.cons ( RDFNode p1 ) [abstract] :  RDFList
RDFList.contains ( RDFNode p1 ) [abstract] :  boolean
RDFList.copy ( ) [abstract] :  RDFList
RDFList.get ( int p1 ) [abstract] :  RDFNode
RDFList.getHead ( ) [abstract] :  RDFNode
RDFList.getStrict ( ) [abstract] :  boolean
RDFList.getTail ( ) [abstract] :  RDFList
RDFList.getValidityErrorMessage ( ) [abstract] :  String
RDFList.indexOf ( RDFNode p1 ) [abstract] :  int
RDFList.indexOf ( RDFNode p1, int p2 ) [abstract] :  int
RDFList.isEmpty ( ) [abstract] :  boolean
RDFList.isValid ( ) [abstract] :  boolean
RDFList.iterator ( ) [abstract] :  ExtendedIterator
RDFList.mapWith ( Map1 p1 ) [abstract] :  ExtendedIterator
RDFList.reduce ( RDFList.ReduceFn p1, Object p2 ) [abstract] :  Object
RDFList.remove ( RDFNode p1 ) [abstract] :  RDFList
RDFList.removeAll ( ) [abstract] :  void *DEPRECATED*
RDFList.removeHead ( ) [abstract] :  RDFList
RDFList.removeList ( ) [abstract] :  void
RDFList.replace ( int p1, RDFNode p2 ) [abstract] :  RDFNode
RDFList.sameListAs ( RDFList p1 ) [abstract] :  boolean
RDFList.setHead ( RDFNode p1 ) [abstract] :  RDFNode
RDFList.setStrict ( boolean p1 ) [abstract] :  void
RDFList.setTail ( RDFList p1 ) [abstract] :  RDFList
RDFList.size ( ) [abstract] :  int
RDFList.with ( RDFNode p1 ) [abstract] :  RDFList

cdk-1.4.0.jar, RDFNode.class
package com.hp.hpl.jena.rdf.model
RDFNode.as ( Class p1 ) [abstract] :  RDFNode
RDFNode.canAs ( Class p1 ) [abstract] :  boolean
RDFNode.inModel ( Model p1 ) [abstract] :  RDFNode
RDFNode.isAnon ( ) [abstract] :  boolean
RDFNode.isLiteral ( ) [abstract] :  boolean
RDFNode.isResource ( ) [abstract] :  boolean
RDFNode.isURIResource ( ) [abstract] :  boolean
RDFNode.toString ( ) [abstract] :  String
RDFNode.visitWith ( RDFVisitor p1 ) [abstract] :  Object

cdk-1.4.0.jar, rdfparse.class
package jena
rdfparse.main ( String[ ] args ) [static] :  void
rdfparse.rdfparse ( )
rdfparse.runTests ( boolean internetTest ) [static] :  void

cdk-1.4.0.jar, RDFRDBException.class
package com.hp.hpl.jena.db
RDFRDBException.RDFRDBException ( String message )
RDFRDBException.RDFRDBException ( String message, Exception e )

cdk-1.4.0.jar, RDFReader.class
package com.hp.hpl.jena.rdf.model
RDFReader.read ( Model p1, InputStream p2, String p3 ) [abstract] :  void
RDFReader.read ( Model p1, Reader p2, String p3 ) [abstract] :  void
RDFReader.read ( Model p1, String p2 ) [abstract] :  void
RDFReader.setErrorHandler ( RDFErrorHandler p1 ) [abstract] :  RDFErrorHandler
RDFReader.setProperty ( String p1, Object p2 ) [abstract] :  Object

cdk-1.4.0.jar, RDFReaderF.class
package com.hp.hpl.jena.rdf.model
RDFReaderF.getReader ( ) [abstract] :  RDFReader
RDFReaderF.getReader ( String p1 ) [abstract] :  RDFReader
RDFReaderF.setReaderClassName ( String p1, String p2 ) [abstract] :  String

cdk-1.4.0.jar, RDFS.class
package com.hp.hpl.jena.vocabulary
RDFS.getURI ( ) [static] :  String
RDFS.property ( String local ) [static] :  Property
RDFS.RDFS ( )
RDFS.resource ( String local ) [static] :  Resource

cdk-1.4.0.jar, RDFSFBRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSFBRuleReasoner.getGraphCapabilities ( ) :  Capabilities
RDFSFBRuleReasoner.loadRules ( ) [static] :  List
RDFSFBRuleReasoner.RDFSFBRuleReasoner ( ReasonerFactory parent )

cdk-1.4.0.jar, RDFSFBRuleReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSFBRuleReasonerFactory.create ( Resource configuration ) :  Reasoner
RDFSFBRuleReasonerFactory.getCapabilities ( ) :  Model
RDFSFBRuleReasonerFactory.getURI ( ) :  String
RDFSFBRuleReasonerFactory.RDFSFBRuleReasonerFactory ( )
RDFSFBRuleReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, RDFSForwardRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSForwardRuleReasoner.getGraphCapabilities ( ) :  Capabilities
RDFSForwardRuleReasoner.loadRules ( ) [static] :  List
RDFSForwardRuleReasoner.RDFSForwardRuleReasoner ( ReasonerFactory parent )

cdk-1.4.0.jar, RDFSRuleInfGraph.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSRuleInfGraph.RDFSRuleInfGraph ( Reasoner reasoner, List rules, Graph schema )
RDFSRuleInfGraph.RDFSRuleInfGraph ( Reasoner reasoner, List rules, Graph schema, Graph data )
RDFSRuleInfGraph.validate ( ) :  ValidityReport

cdk-1.4.0.jar, RDFSRuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSRuleReasoner.bind ( Graph data ) :  InfGraph
RDFSRuleReasoner.bindSchema ( Graph tbox ) :  Reasoner
RDFSRuleReasoner.doSetParameter ( Property parameter, Object value ) :  boolean
RDFSRuleReasoner.getGraphCapabilities ( ) :  Capabilities
RDFSRuleReasoner.loadRulesLevel ( String level ) [static] :  List
RDFSRuleReasoner.RDFSRuleReasoner ( FBRuleInfGraph schemaGraph, ReasonerFactory factory )
RDFSRuleReasoner.RDFSRuleReasoner ( ReasonerFactory factory, Resource configuration )
RDFSRuleReasoner.RDFSRuleReasoner ( ReasonerFactory parent )

cdk-1.4.0.jar, RDFSRuleReasonerFactory.class
package com.hp.hpl.jena.reasoner.rulesys
RDFSRuleReasonerFactory.create ( Resource configuration ) :  Reasoner
RDFSRuleReasonerFactory.getCapabilities ( ) :  Model
RDFSRuleReasonerFactory.getURI ( ) :  String
RDFSRuleReasonerFactory.RDFSRuleReasonerFactory ( )
RDFSRuleReasonerFactory.theInstance ( ) [static] :  ReasonerFactory

cdk-1.4.0.jar, RDFSyntax.class
package com.hp.hpl.jena.vocabulary
RDFSyntax.getURI ( ) [static] :  String
RDFSyntax.RDFSyntax ( )

cdk-1.4.0.jar, RDFTest.class
package com.hp.hpl.jena.vocabulary
RDFTest.getURI ( ) [static] :  String
RDFTest.RDFTest ( )

cdk-1.4.0.jar, RDFVisitor.class
package com.hp.hpl.jena.rdf.model
RDFVisitor.visitBlank ( Resource p1, AnonId p2 ) [abstract] :  Object
RDFVisitor.visitLiteral ( Literal p1 ) [abstract] :  Object
RDFVisitor.visitURI ( Resource p1, String p2 ) [abstract] :  Object

cdk-1.4.0.jar, RDFWriter.class
package com.hp.hpl.jena.rdf.model
RDFWriter.setErrorHandler ( RDFErrorHandler p1 ) [abstract] :  RDFErrorHandler
RDFWriter.setProperty ( String p1, Object p2 ) [abstract] :  Object
RDFWriter.write ( Model p1, OutputStream p2, String p3 ) [abstract] :  void
RDFWriter.write ( Model p1, Writer p2, String p3 ) [abstract] :  void

cdk-1.4.0.jar, RDFWriterF.class
package com.hp.hpl.jena.rdf.model
RDFWriterF.getWriter ( ) [abstract] :  RDFWriter
RDFWriterF.getWriter ( String p1 ) [abstract] :  RDFWriter
RDFWriterF.setWriterClassName ( String p1, String p2 ) [abstract] :  String

cdk-1.4.0.jar, RDFXMLWriterI.class
package com.hp.hpl.jena.xmloutput
RDFXMLWriterI.setProperty ( String p1, Object p2 ) [abstract] :  Object

cdk-1.4.0.jar, ReadAction.class
package jena
rdfcat.ReadAction.rdfcat.ReadAction ( rdfcat uri, String lang, String p3 )
rdfcat.ReadAction.run ( rdfcat rc ) :  void

cdk-1.4.0.jar, ReadFailureHandler.class
package com.hp.hpl.jena.ontology
OntDocumentManager.ReadFailureHandler.handleFailedRead ( String p1, Model p2, Exception p3 ) [abstract] :  void

cdk-1.4.0.jar, ReadHook.class
package com.hp.hpl.jena.ontology
OntDocumentManager.ReadHook.afterRead ( Model p1, String p2, OntDocumentManager p3 ) [abstract] :  void
OntDocumentManager.ReadHook.beforeRead ( Model p1, String p2, OntDocumentManager p3 ) [abstract] :  String

cdk-1.4.0.jar, Reasoner.class
package com.hp.hpl.jena.reasoner
Reasoner.addDescription ( Model p1, Resource p2 ) [abstract] :  void
Reasoner.bind ( Graph p1 ) [abstract] :  InfGraph
Reasoner.bindSchema ( Graph p1 ) [abstract] :  Reasoner
Reasoner.bindSchema ( Model p1 ) [abstract] :  Reasoner
Reasoner.getGraphCapabilities ( ) [abstract] :  Capabilities
Reasoner.getReasonerCapabilities ( ) [abstract] :  Model
Reasoner.setDerivationLogging ( boolean p1 ) [abstract] :  void
Reasoner.setParameter ( Property p1, Object p2 ) [abstract] :  void
Reasoner.supportsProperty ( Property p1 ) [abstract] :  boolean

cdk-1.4.0.jar, ReasonerClashException.class
package com.hp.hpl.jena.assembler.exceptions
ReasonerClashException.ReasonerClashException ( Resource root )

cdk-1.4.0.jar, ReasonerException.class
package com.hp.hpl.jena.reasoner
ReasonerException.ReasonerException ( String msg )
ReasonerException.ReasonerException ( String msg, Throwable cause )

cdk-1.4.0.jar, ReasonerFactory.class
package com.hp.hpl.jena.reasoner
ReasonerFactory.create ( Resource p1 ) [abstract] :  Reasoner
ReasonerFactory.getCapabilities ( ) [abstract] :  Model
ReasonerFactory.getURI ( ) [abstract] :  String

cdk-1.4.0.jar, ReasonerFactoryAssembler.class
package com.hp.hpl.jena.assembler.assemblers
ReasonerFactoryAssembler.getReasoner ( Resource root ) :  Reasoner
ReasonerFactoryAssembler.getReasonerFactory ( Resource root ) [static] :  ReasonerFactory
ReasonerFactoryAssembler.getReasonerFactoryByURL ( Resource root, Resource reasonerURL ) [static] :  ReasonerFactory
ReasonerFactoryAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object
ReasonerFactoryAssembler.ReasonerFactoryAssembler ( )

cdk-1.4.0.jar, ReasonerRegistry.class
package com.hp.hpl.jena.reasoner
ReasonerRegistry.create ( String uri, Resource configuration ) :  Reasoner
ReasonerRegistry.getAllDescriptions ( ) :  Model
ReasonerRegistry.getDescription ( String uri ) :  Resource
ReasonerRegistry.getFactory ( String uri ) :  ReasonerFactory
ReasonerRegistry.getOWLMicroReasoner ( ) [static] :  Reasoner
ReasonerRegistry.getOWLMiniReasoner ( ) [static] :  Reasoner
ReasonerRegistry.getOWLReasoner ( ) [static] :  Reasoner
ReasonerRegistry.getRDFSReasoner ( ) [static] :  Reasoner
ReasonerRegistry.getRDFSSimpleReasoner ( ) [static] :  Reasoner
ReasonerRegistry.getTransitiveReasoner ( ) [static] :  Reasoner
ReasonerRegistry.makeDirect ( Node node ) [static] :  Node
ReasonerRegistry.makeDirect ( String uri ) [static] :  String
ReasonerRegistry.register ( ReasonerFactory factory ) :  void
ReasonerRegistry.register ( String reasonerUri, ReasonerFactory factory ) :  void
ReasonerRegistry.theRegistry ( ) [static] :  ReasonerRegistry

cdk-1.4.0.jar, ReasonerVocabulary.class
package com.hp.hpl.jena.vocabulary
ReasonerVocabulary.getJenaReasonerNS ( ) [static] :  String
ReasonerVocabulary.getRBNamespace ( ) [static] :  String
ReasonerVocabulary.jenaReasonerProperty ( String localName ) [static] :  Property
ReasonerVocabulary.ReasonerVocabulary ( )
ReasonerVocabulary.ruleReasonerProperty ( String localName ) [static] :  Property

cdk-1.4.0.jar, ReconstructionTest.class
package signature.simple
ReconstructionTest.bowtieaneTest ( ) :  void
ReconstructionTest.petersensGraphTest ( ) :  void
ReconstructionTest.reconstruct ( SimpleGraph graph ) :  void
ReconstructionTest.ReconstructionTest ( )

cdk-1.4.0.jar, RectangleElement.class
package org.openscience.cdk.renderer.elements
RectangleElement.accept ( IRenderingVisitor visitor ) :  void
RectangleElement.RectangleElement ( double xCoord, double yCoord, double width, double height, boolean filled, Color color )
RectangleElement.RectangleElement ( double xCoord1, double yCoord1, double xCoord2, double yCoord2, Color color )

cdk-1.4.0.jar, ReduceFn.class
package com.hp.hpl.jena.rdf.model
RDFList.ReduceFn.reduce ( RDFNode p1, Object p2 ) [abstract] :  Object

cdk-1.4.0.jar, Regex.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Regex.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Regex.getArgLength ( ) :  int
Regex.getName ( ) :  String
Regex.getString ( Node n, RuleContext context ) :  String
Regex.Regex ( )

cdk-1.4.0.jar, RegexpTree.class
package com.hp.hpl.jena.graph.query.regexptrees
RegexpTree.equals ( Object p1 ) [abstract] :  boolean
RegexpTree.hashCode ( ) [abstract] :  int
RegexpTree.RegexpTree ( )
RegexpTree.toString ( ) [abstract] :  String

cdk-1.4.0.jar, RegexpTreeGenerator.class
package com.hp.hpl.jena.graph.query.regexptrees
RegexpTreeGenerator.getAlternatives ( List p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getAnySingle ( ) [abstract] :  RegexpTree
RegexpTreeGenerator.getBackReference ( int p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getClass ( String p1, boolean p2 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getEndOfLine ( ) [abstract] :  RegexpTree
RegexpTreeGenerator.getNothing ( ) [abstract] :  RegexpTree
RegexpTreeGenerator.getOneOrMore ( RegexpTree p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getOptional ( RegexpTree p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getParen ( RegexpTree p1, int p2 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getSequence ( List p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getStartOfLine ( ) [abstract] :  RegexpTree
RegexpTreeGenerator.getText ( char p1 ) [abstract] :  RegexpTree
RegexpTreeGenerator.getZeroOrMore ( RegexpTree p1 ) [abstract] :  RegexpTree

cdk-1.4.0.jar, Regression.class
package com.hp.hpl.jena.regression
Regression.doTest ( Model m1, Model m2, Model m3, Model m4 ) [static] :  void
Regression.error ( String testName, int testNum ) :  void
Regression.error ( String testName, int testNum, Exception e ) :  void
Regression.error ( String testName, int testNum, long v ) :  void
Regression.getErrors ( ) :  boolean
Regression.Regression ( )
Regression.setErrors ( boolean b ) :  boolean
Regression.test ( Model m1, Model m2, Model m3, Model m4 ) :  void
Regression.test1 ( Model m ) :  void
Regression.test10 ( Model m ) :  void
Regression.test11 ( Model m1, Model m2 ) :  void
Regression.test12 ( Model m ) :  void
Regression.test13 ( Model m ) :  void
Regression.test14 ( Model m ) :  void
Regression.test15 ( Model m ) :  void
Regression.test16 ( Model m ) :  void
Regression.test17 ( Model m ) :  void
Regression.test18 ( Model m ) :  void
Regression.test19 ( Model m1, Model m2 ) :  void
Regression.test2 ( Model m ) :  void
Regression.test20 ( Model m ) :  void
Regression.test3 ( Model m ) :  void
Regression.test4 ( Model m ) :  void
Regression.test5 ( Model m ) :  void
Regression.test6 ( Model m ) :  void
Regression.test7 ( Model m1, Model m2 ) :  void
Regression.test8 ( Model m ) :  void
Regression.test9 ( Model m ) :  void
Regression.test97 ( Model m ) :  void
Regression.test99 ( Model m ) :  void
Regression.testAlt ( Model m, Alt alt1, Alt alt2, Alt alt3, Alt alt4, String test, int n ) :  void
Regression.testBag ( Model m, Bag bag1, Bag bag2, Bag bag3, String test, int n ) :  void
Regression.testContainer ( Model m, Container cont1, Container cont2, String test, int n ) :  void
Regression.testResource ( Model m, Resource r, String test, int n, int numProps ) :  void
Regression.testSeq ( Model m, Seq seq1, Seq seq2, Seq seq3, Seq seq4, Seq seq5, Seq seq6, Seq seq7, String test, int n ) :  void

cdk-1.4.0.jar, ReificationStyle.class
package com.hp.hpl.jena.shared
ReificationStyle.conceals ( ) :  boolean
ReificationStyle.intercepts ( ) :  boolean
ReificationStyle.ReificationStyle ( boolean intercept, boolean conceal )
ReificationStyle.toString ( ) :  String

cdk-1.4.0.jar, ReifiedStatement.class
package com.hp.hpl.jena.rdf.model
ReifiedStatement.getStatement ( ) [abstract] :  Statement

cdk-1.4.0.jar, Reifier.class
package com.hp.hpl.jena.graph
Reifier.allNodes ( ) [abstract] :  ExtendedIterator
Reifier.allNodes ( Triple p1 ) [abstract] :  ExtendedIterator
Reifier.close ( ) [abstract] :  void
Reifier.find ( TripleMatch p1 ) [abstract] :  ExtendedIterator
Reifier.findEither ( TripleMatch p1, boolean p2 ) [abstract] :  ExtendedIterator
Reifier.findExposed ( TripleMatch p1 ) [abstract] :  ExtendedIterator
Reifier.getParentGraph ( ) [abstract] :  Graph
Reifier.getStyle ( ) [abstract] :  ReificationStyle
Reifier.handledAdd ( Triple p1 ) [abstract] :  boolean
Reifier.handledRemove ( Triple p1 ) [abstract] :  boolean
Reifier.hasTriple ( Node p1 ) [abstract] :  boolean
Reifier.hasTriple ( Triple p1 ) [abstract] :  boolean
Reifier.reifyAs ( Node p1, Triple p2 ) [abstract] :  Node
Reifier.remove ( Node p1, Triple p2 ) [abstract] :  void
Reifier.remove ( Triple p1 ) [abstract] :  void
Reifier.size ( ) [abstract] :  int

cdk-1.4.0.jar, RelativeURIException.class
package com.hp.hpl.jena.n3
RelativeURIException.RelativeURIException ( String msg )

cdk-1.4.0.jar, Remove.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Remove.getName ( ) :  String
Remove.headAction ( Node[ ] args, int length, RuleContext context ) :  void
Remove.isMonotonic ( ) :  boolean
Remove.Remove ( )

cdk-1.4.0.jar, RendererModel.class
package org.openscience.cdk.renderer
RendererModel.addCDKChangeListener ( ICDKChangeListener listener ) :  void
RendererModel.fireChange ( ) :  void
RendererModel.get ( Class paramType ) :  Object
RendererModel.getClipboardContent ( ) :  IAtomContainer
RendererModel.getDefault ( Class param ) :  Object
RendererModel.getExternalSelectedPart ( ) :  IAtomContainer
RendererModel.getHighlightedAtom ( ) :  IAtom
RendererModel.getHighlightedBond ( ) :  IBond
RendererModel.getMerge ( ) :  Map
RendererModel.getNotification ( ) :  boolean
RendererModel.getParameter ( Class param ) :  IGeneratorParameter
RendererModel.getRenderingParameters ( ) :  List
RendererModel.getSelection ( ) :  IChemObjectSelection
RendererModel.getToolTipText ( IAtom atom ) :  String
RendererModel.getToolTipTextMap ( ) :  Map
RendererModel.hasParameter ( Class param ) :  boolean
RendererModel.registerParameters ( IGenerator generator ) :  void
RendererModel.removeCDKChangeListener ( ICDKChangeListener listener ) :  void
RendererModel.RendererModel ( )
RendererModel.set ( Class paramType, Object value ) :  void
RendererModel.setClipboardContent ( IAtomContainer content ) :  void
RendererModel.setExternalSelectedPart ( IAtomContainer externalSelectedPart ) :  void
RendererModel.setHighlightedAtom ( IAtom highlightedAtom ) :  void
RendererModel.setHighlightedBond ( IBond highlightedBond ) :  void
RendererModel.setNotification ( boolean notification ) :  void
RendererModel.setSelection ( IChemObjectSelection selection ) :  void
RendererModel.setToolTipTextMap ( Map map ) :  void

cdk-1.4.0.jar, Repeated.class
package com.hp.hpl.jena.graph.query.regexptrees
Repeated.getOperand ( ) :  RegexpTree
Repeated.Repeated ( RegexpTree operand )

cdk-1.4.0.jar, Replaceable.class
package com.ibm.icu.text
Replaceable.char32At ( int p1 ) [abstract] :  int
Replaceable.charAt ( int p1 ) [abstract] :  char
Replaceable.copy ( int p1, int p2, int p3 ) [abstract] :  void
Replaceable.getChars ( int p1, int p2, char[ ] p3, int p4 ) [abstract] :  void
Replaceable.hasMetaData ( ) [abstract] :  boolean
Replaceable.length ( ) [abstract] :  int
Replaceable.replace ( int p1, int p2, char[ ] p3, int p4, int p5 ) [abstract] :  void
Replaceable.replace ( int p1, int p2, String p3 ) [abstract] :  void

cdk-1.4.0.jar, ReplaceableString.class
package com.ibm.icu.text
ReplaceableString.char32At ( int offset ) :  int
ReplaceableString.charAt ( int offset ) :  char
ReplaceableString.copy ( int start, int limit, int dest ) :  void
ReplaceableString.getChars ( int srcStart, int srcLimit, char[ ] dst, int dstStart ) :  void
ReplaceableString.hasMetaData ( ) :  boolean
ReplaceableString.length ( ) :  int
ReplaceableString.replace ( int start, int limit, char[ ] chars, int charsStart, int charsLen ) :  void
ReplaceableString.replace ( int start, int limit, String text ) :  void
ReplaceableString.ReplaceableString ( )
ReplaceableString.ReplaceableString ( String str )
ReplaceableString.ReplaceableString ( StringBuffer buf )
ReplaceableString.substring ( int start, int limit ) :  String
ReplaceableString.toString ( ) :  String

cdk-1.4.0.jar, Replacement.class
package jena
schemagen.Replacement.schemagen.Replacement ( schemagen pattern, Pattern sub, String p3 )

cdk-1.4.0.jar, Report.class
package com.hp.hpl.jena.reasoner
ValidityReport.Report.getDescription ( ) :  String
ValidityReport.Report.getExtension ( ) :  Object
ValidityReport.Report.getType ( ) :  String
ValidityReport.Report.isError ( ) :  boolean
ValidityReport.Report.toString ( ) :  String
ValidityReport.Report.ValidityReport.Report ( boolean error, String type, String description )
ValidityReport.Report.ValidityReport.Report ( boolean error, String type, String description, Object extension )

cdk-1.4.0.jar, ResIterator.class
package com.hp.hpl.jena.rdf.model
ResIterator.nextResource ( ) [abstract] :  Resource

cdk-1.4.0.jar, ResolvingProperties.class
package net.sf.jnati.config
ResolvingProperties.get ( Object key ) :  Object
ResolvingProperties.getProperty ( String key ) :  String
ResolvingProperties.put ( Object key, Object value ) :  Object
ResolvingProperties.ResolvingProperties ( )
ResolvingProperties.ResolvingProperties ( Map params )
ResolvingProperties.ResolvingProperties ( ResolvingProperties defaults )
ResolvingProperties.ResolvingProperties ( ResolvingProperties defaults, Map params )

cdk-1.4.0.jar, Resource.class
package com.hp.hpl.jena.rdf.model
Resource.abort ( ) [abstract] :  Resource
Resource.addLiteral ( Property p1, boolean p2 ) [abstract] :  Resource
Resource.addLiteral ( Property p1, char p2 ) [abstract] :  Resource
Resource.addLiteral ( Property p1, double p2 ) [abstract] :  Resource
Resource.addLiteral ( Property p1, float p2 ) [abstract] :  Resource
Resource.addLiteral ( Property p1, long p2 ) [abstract] :  Resource
Resource.addLiteral ( Property p1, Object p2 ) [abstract] :  Resource
Resource.addProperty ( Property p1, RDFNode p2 ) [abstract] :  Resource
Resource.addProperty ( Property p1, String p2 ) [abstract] :  Resource
Resource.addProperty ( Property p1, String p2, RDFDatatype p3 ) [abstract] :  Resource
Resource.addProperty ( Property p1, String p2, String p3 ) [abstract] :  Resource
Resource.begin ( ) [abstract] :  Resource
Resource.commit ( ) [abstract] :  Resource
Resource.equals ( Object p1 ) [abstract] :  boolean
Resource.getId ( ) [abstract] :  AnonId
Resource.getLocalName ( ) [abstract] :  String
Resource.getModel ( ) [abstract] :  Model
Resource.getNameSpace ( ) [abstract] :  String
Resource.getProperty ( Property p1 ) [abstract] :  Statement
Resource.getRequiredProperty ( Property p1 ) [abstract] :  Statement
Resource.getURI ( ) [abstract] :  String
Resource.hasLiteral ( Property p1, boolean p2 ) [abstract] :  boolean
Resource.hasLiteral ( Property p1, char p2 ) [abstract] :  boolean
Resource.hasLiteral ( Property p1, double p2 ) [abstract] :  boolean
Resource.hasLiteral ( Property p1, float p2 ) [abstract] :  boolean
Resource.hasLiteral ( Property p1, long p2 ) [abstract] :  boolean
Resource.hasLiteral ( Property p1, Object p2 ) [abstract] :  boolean
Resource.hasProperty ( Property p1 ) [abstract] :  boolean
Resource.hasProperty ( Property p1, RDFNode p2 ) [abstract] :  boolean
Resource.hasProperty ( Property p1, String p2 ) [abstract] :  boolean
Resource.hasProperty ( Property p1, String p2, String p3 ) [abstract] :  boolean
Resource.hasURI ( String p1 ) [abstract] :  boolean
Resource.listProperties ( ) [abstract] :  StmtIterator
Resource.listProperties ( Property p1 ) [abstract] :  StmtIterator
Resource.removeAll ( Property p1 ) [abstract] :  Resource
Resource.removeProperties ( ) [abstract] :  Resource
Resource.toString ( ) [abstract] :  String

cdk-1.4.0.jar, ResourceF.class
package com.hp.hpl.jena.rdf.model
ResourceF.createResource ( Resource p1 ) [abstract] :  Resource

cdk-1.4.0.jar, ResourceFactory.class
package com.hp.hpl.jena.rdf.model
ResourceFactory.createPlainLiteral ( String string ) [static] :  Literal
ResourceFactory.createProperty ( String namespace, String localName ) [static] :  Property
ResourceFactory.createProperty ( String uriref ) [static] :  Property
ResourceFactory.createResource ( ) [static] :  Resource
ResourceFactory.createResource ( String uriref ) [static] :  Resource
ResourceFactory.createStatement ( Resource subject, Property predicate, RDFNode object ) [static] :  Statement
ResourceFactory.createTypedLiteral ( Object value ) [static] :  Literal
ResourceFactory.createTypedLiteral ( String string, RDFDatatype dType ) [static] :  Literal
ResourceFactory.getInstance ( ) [static] :  ResourceFactory.Interface
ResourceFactory.setInstance ( ResourceFactory.Interface newInstance ) [static] :  ResourceFactory.Interface

cdk-1.4.0.jar, ResourceRequiredException.class
package com.hp.hpl.jena.rdf.model
ResourceRequiredException.ResourceRequiredException ( Node n )
ResourceRequiredException.ResourceRequiredException ( RDFNode n )

cdk-1.4.0.jar, ResourceUtils.class
package com.hp.hpl.jena.util
ResourceUtils.maximalLowerElements ( Collection resources, Property rel, boolean inverse ) [static] :  List
ResourceUtils.maximalLowerElements ( Iterator resources, Property rel, boolean inverse ) [static] :  List
ResourceUtils.partition ( List l, Property p ) [static] :  List
ResourceUtils.reachableClosure ( Resource root ) [static] :  Model
ResourceUtils.removeEquiv ( List l, Property p, Resource ref ) [static] :  List
ResourceUtils.renameResource ( Resource old, String uri ) [static] :  Resource
ResourceUtils.ResourceUtils ( )

cdk-1.4.0.jar, ResTestObjF.class
package com.hp.hpl.jena.regression
Regression.ResTestObjF.createResource ( Resource r ) :  Resource
Regression.ResTestObjF.Regression.ResTestObjF ( )

cdk-1.4.0.jar, Restriction.class
package com.hp.hpl.jena.ontology
Restriction.asAllValuesFromRestriction ( ) [abstract] :  AllValuesFromRestriction
Restriction.asCardinalityRestriction ( ) [abstract] :  CardinalityRestriction
Restriction.asHasValueRestriction ( ) [abstract] :  HasValueRestriction
Restriction.asMaxCardinalityRestriction ( ) [abstract] :  MaxCardinalityRestriction
Restriction.asMinCardinalityRestriction ( ) [abstract] :  MinCardinalityRestriction
Restriction.asSomeValuesFromRestriction ( ) [abstract] :  SomeValuesFromRestriction
Restriction.convertToAllValuesFromRestriction ( Resource p1 ) [abstract] :  AllValuesFromRestriction
Restriction.convertToCardinalityRestriction ( int p1 ) [abstract] :  CardinalityRestriction
Restriction.convertToHasValueRestriction ( RDFNode p1 ) [abstract] :  HasValueRestriction
Restriction.convertToMaxCardinalityRestriction ( int p1 ) [abstract] :  MaxCardinalityRestriction
Restriction.convertToMinCardinalityRestriction ( int p1 ) [abstract] :  MinCardinalityRestriction
Restriction.convertToSomeValuesFromRestriction ( Resource p1 ) [abstract] :  SomeValuesFromRestriction
Restriction.getOnProperty ( ) [abstract] :  OntProperty
Restriction.isAllValuesFromRestriction ( ) [abstract] :  boolean
Restriction.isCardinalityRestriction ( ) [abstract] :  boolean
Restriction.isHasValueRestriction ( ) [abstract] :  boolean
Restriction.isMaxCardinalityRestriction ( ) [abstract] :  boolean
Restriction.isMinCardinalityRestriction ( ) [abstract] :  boolean
Restriction.isSomeValuesFromRestriction ( ) [abstract] :  boolean
Restriction.onProperty ( Property p1 ) [abstract] :  boolean
Restriction.removeOnProperty ( Property p1 ) [abstract] :  void
Restriction.setOnProperty ( Property p1 ) [abstract] :  void

cdk-1.4.0.jar, ResultSet.class
package com.hp.hpl.jena.vocabulary
ResultSet.getURI ( ) [static] :  String
ResultSet.ResultSet ( )

cdk-1.4.0.jar, RETERuleInfGraph.class
package com.hp.hpl.jena.reasoner.rulesys
RETERuleInfGraph.instantiateRuleEngine ( List rules ) :  void
RETERuleInfGraph.performAdd ( Triple t ) :  void
RETERuleInfGraph.performDelete ( Triple t ) :  void
RETERuleInfGraph.RETERuleInfGraph ( Reasoner reasoner, Graph schema )
RETERuleInfGraph.RETERuleInfGraph ( Reasoner reasoner, List rules, Graph schema )
RETERuleInfGraph.RETERuleInfGraph ( Reasoner reasoner, List rules, Graph schema, Graph data )

cdk-1.4.0.jar, Rewrite.class
package com.hp.hpl.jena.graph.query
Rewrite.contains ( Expression L, String content, String modifiers ) [static] :  Expression
Rewrite.endsWith ( Expression L, String content, String modifiers ) [static] :  Expression
Rewrite.front ( String s ) [static] :  String
Rewrite.getPattern ( Expression E ) [static] :  PatternLiteral
Rewrite.iOnly ( String modifiers ) [static] :  boolean
Rewrite.isContains ( PatternLiteral pattern ) [static] :  boolean
Rewrite.isEndsWith ( PatternLiteral pattern ) [static] :  boolean
Rewrite.isStartsWith ( PatternLiteral pattern ) [static] :  boolean
Rewrite.notSpecial ( String pattern ) [static] :  boolean
Rewrite.Rewrite ( )
Rewrite.rewriteStringMatch ( Expression e ) [static] :  Expression
Rewrite.startsWith ( Expression L, String content, String modifiers ) [static] :  Expression

cdk-1.4.0.jar, RGraph.class
package org.openscience.cdk.isomorphism.mcss
RGraph.setStart ( long start ) :  void
RGraph.setTimeout ( long timeout ) :  void

cdk-1.4.0.jar, RGroup.class
package org.openscience.cdk.isomorphism.matchers
RGroup.getFirstAttachmentPoint ( ) :  IAtom
RGroup.getGroup ( ) :  IAtomContainer
RGroup.getSecondAttachmentPoint ( ) :  IAtom
RGroup.makeLabel ( int rgroupNum ) [static] :  String
RGroup.RGroup ( )
RGroup.setFirstAttachmentPoint ( IAtom firstAttachmentPoint ) :  void
RGroup.setGroup ( IAtomContainer group ) :  void
RGroup.setSecondAttachmentPoint ( IAtom secondAttachmentPoint ) :  void

cdk-1.4.0.jar, RGroupList.class
package org.openscience.cdk.isomorphism.matchers
RGroupList.equals ( Object obj ) :  boolean
RGroupList.getOccurrence ( ) :  String
RGroupList.getRequiredRGroupNumber ( ) :  int
RGroupList.getRGroupNumber ( ) :  int
RGroupList.getRGroups ( ) :  List
RGroupList.hashCode ( ) :  int
RGroupList.isRestH ( ) :  boolean
RGroupList.isValidOccurrenceSyntax ( String occ ) [static] :  boolean
RGroupList.matchOccurence ( int maxAttachments ) :  List
RGroupList.RGroupList ( int rGroupNumber )
RGroupList.RGroupList ( int rGroupNumber, boolean restH, String occurrence, int requiredRGroupNumber )
RGroupList.setOccurrence ( String occurrence ) :  void
RGroupList.setRequiredRGroupNumber ( int rGroupNumberImplicated ) :  void
RGroupList.setRestH ( boolean restH ) :  void
RGroupList.setRGroupNumber ( int rGroupNumber ) :  void
RGroupList.setRGroups ( List rGroups ) :  void

cdk-1.4.0.jar, RGroupQuery.class
package org.openscience.cdk.isomorphism.matchers
RGroupQuery.areRootAtomsDefined ( ) :  boolean
RGroupQuery.areSubstituentsDefined ( ) :  boolean
RGroupQuery.getAllConfigurations ( ) :  List
RGroupQuery.getAllRgroupQueryAtoms ( ) :  List
RGroupQuery.getAtomContainerCount ( ) :  int
RGroupQuery.getRGroupDefinitions ( ) :  Map
RGroupQuery.getRgroupQueryAtoms ( Integer rgroupNumber ) :  List
RGroupQuery.getRootAttachmentPoints ( ) :  Map
RGroupQuery.getRootStructure ( ) :  IAtomContainer
RGroupQuery.getSubstituents ( ) :  List
RGroupQuery.isValidRgroupQueryLabel ( String Rxx ) [static] :  boolean
RGroupQuery.RGroupQuery ( )
RGroupQuery.setRGroupDefinitions ( Map rGroupDefinitions ) :  void
RGroupQuery.setRootAttachmentPoints ( Map rootAttachmentPoints ) :  void
RGroupQuery.setRootStructure ( IAtomContainer rootStructure ) :  void

cdk-1.4.0.jar, RGroupQueryFormat.class
package org.openscience.cdk.io.formats
RGroupQueryFormat.getFormatName ( ) :  String
RGroupQueryFormat.getInstance ( ) [static] :  IResourceFormat
RGroupQueryFormat.getMIMEType ( ) :  String
RGroupQueryFormat.getNameExtensions ( ) :  String[ ]
RGroupQueryFormat.getPreferredNameExtension ( ) :  String
RGroupQueryFormat.getReaderClassName ( ) :  String
RGroupQueryFormat.getRequiredDataFeatures ( ) :  int
RGroupQueryFormat.getSupportedDataFeatures ( ) :  int
RGroupQueryFormat.getWriterClassName ( ) :  String
RGroupQueryFormat.isXMLBased ( ) :  boolean
RGroupQueryFormat.matches ( int lineNumber, String line ) :  boolean

cdk-1.4.0.jar, RGroupQueryReader.class
package org.openscience.cdk.io
RGroupQueryReader.accepts ( Class classObject ) :  boolean
RGroupQueryReader.close ( ) :  void
RGroupQueryReader.getFormat ( ) :  IResourceFormat
RGroupQueryReader.read ( IChemObject object ) :  IChemObject
RGroupQueryReader.RGroupQueryReader ( )
RGroupQueryReader.RGroupQueryReader ( InputStream in )
RGroupQueryReader.RGroupQueryReader ( Reader in )
RGroupQueryReader.setReader ( InputStream input ) :  void
RGroupQueryReader.setReader ( Reader input ) :  void

cdk-1.4.0.jar, RGroupQueryWriter.class
package org.openscience.cdk.io
RGroupQueryWriter.accepts ( Class classObject ) :  boolean
RGroupQueryWriter.close ( ) :  void
RGroupQueryWriter.getFormat ( ) :  IResourceFormat
RGroupQueryWriter.RGroupQueryWriter ( )
RGroupQueryWriter.RGroupQueryWriter ( Writer out )
RGroupQueryWriter.setWriter ( OutputStream output ) :  void
RGroupQueryWriter.setWriter ( Writer out ) :  void
RGroupQueryWriter.write ( IChemObject object ) :  void

cdk-1.4.0.jar, RingElement.class
package org.openscience.cdk.renderer.elements
RingElement.accept ( IRenderingVisitor v ) :  void
RingElement.RingElement ( double x, double y, double radius, Color color )

cdk-1.4.0.jar, RingFilter.class
package org.openscience.cdk.smsd.ring
RingFilter.filterAtoms ( IAtomContainer molecule, Collection atoms ) :  void
RingFilter.filterAtoms ( int atomLimit, Collection rings, Collection atoms ) :  void
RingFilter.RingFilter ( AtomMatcher filter, RingFinder finder )

cdk-1.4.0.jar, RingFinder.class
package org.openscience.cdk.smsd.ring
RingFinder.findRings ( IAtomContainer p1 ) [abstract] :  Collection
RingFinder.getRingSet ( IAtomContainer p1 ) [abstract] :  IRingSet

cdk-1.4.0.jar, RingGenerator.class
package org.openscience.cdk.renderer.generators
RingGenerator.generateRingElements ( IBond bond, IRing ring, RendererModel model ) :  IRenderingElement
RingGenerator.getParameters ( ) :  List
RingGenerator.RingGenerator ( )

cdk-1.4.0.jar, RingPlacer.class
package org.openscience.cdk.layout
RingPlacer.placeRing ( IRing ring, Point2d ringCenter, double bondLength, Map startAngles ) :  void

cdk-1.4.0.jar, RingProportion.class
package org.openscience.cdk.renderer.generators
RingGenerator.RingProportion.getDefault ( ) :  Double
RingGenerator.RingProportion.getDefault ( ) :  Object
RingGenerator.RingProportion.RingGenerator.RingProportion ( )

cdk-1.4.0.jar, rset.class
package jena
rset.main ( String[ ] args ) [static] :  void
rset.rset ( )

cdk-1.4.0.jar, RSIterator.class
package com.hp.hpl.jena.rdf.model
RSIterator.nextRS ( ) [abstract] :  ReifiedStatement

cdk-1.4.0.jar, RSS.class
package com.hp.hpl.jena.vocabulary
RSS.getURI ( ) [static] :  String
RSS.RSS ( )

cdk-1.4.0.jar, Rule.class
package com.hp.hpl.jena.reasoner.rulesys
Rule.bodyLength ( ) :  int
Rule.cloneRule ( ) :  Rule
Rule.equals ( Object o ) :  boolean
Rule.getBody ( ) :  ClauseEntry[ ]
Rule.getBodyElement ( int n ) :  ClauseEntry
Rule.getHead ( ) :  ClauseEntry[ ]
Rule.getHeadElement ( int n ) :  ClauseEntry
Rule.getName ( ) :  String
Rule.getNumVars ( ) :  int
Rule.hashCode ( ) :  int
Rule.headLength ( ) :  int
Rule.instantiate ( BindingEnvironment env ) :  Rule
Rule.isAxiom ( ) :  boolean
Rule.isBackward ( ) :  boolean
Rule.isMonotonic ( ) :  boolean
Rule.parseRule ( String source ) [static] :  Rule
Rule.parseRules ( Rule.Parser parser ) [static] :  List
Rule.parseRules ( String source ) [static] :  List
Rule.Rule ( List head, List body )
Rule.Rule ( String name, ClauseEntry[ ] head, ClauseEntry[ ] body )
Rule.Rule ( String name, List head, List body )
Rule.rulesFromURL ( String uri ) [static] :  List
Rule.rulesParserFromReader ( BufferedReader src ) [static] :  Rule.Parser
Rule.sameAs ( Object o ) :  boolean
Rule.setBackward ( boolean flag ) :  void
Rule.setNumVars ( int n ) :  void
Rule.toShortString ( ) :  String
Rule.toString ( ) :  String

cdk-1.4.0.jar, RuleBasedBreakIterator.class
package com.ibm.icu.text
RuleBasedBreakIterator.clone ( ) :  Object
RuleBasedBreakIterator.current ( ) :  int
RuleBasedBreakIterator.equals ( Object that ) :  boolean
RuleBasedBreakIterator.first ( ) :  int
RuleBasedBreakIterator.following ( int offset ) :  int
RuleBasedBreakIterator.getInstanceFromCompiledRules ( InputStream is ) [static] :  RuleBasedBreakIterator *DEPRECATED*
RuleBasedBreakIterator.getRuleStatus ( ) :  int *DEPRECATED*
RuleBasedBreakIterator.getRuleStatusVec ( int[ ] fillInArray ) :  int *DEPRECATED*
RuleBasedBreakIterator.getText ( ) :  CharacterIterator
RuleBasedBreakIterator.hashCode ( ) :  int
RuleBasedBreakIterator.isBoundary ( int offset ) :  boolean
RuleBasedBreakIterator.last ( ) :  int
RuleBasedBreakIterator.next ( ) :  int
RuleBasedBreakIterator.next ( int n ) :  int
RuleBasedBreakIterator.preceding ( int offset ) :  int
RuleBasedBreakIterator.previous ( ) :  int
RuleBasedBreakIterator.RuleBasedBreakIterator ( )
RuleBasedBreakIterator.RuleBasedBreakIterator ( String description )
RuleBasedBreakIterator.setText ( CharacterIterator newText ) :  void
RuleBasedBreakIterator.toString ( ) :  String

cdk-1.4.0.jar, RuleBasedBreakIterator_New.class
package com.ibm.icu.text
RuleBasedBreakIterator_New.checkOffset ( int offset, CharacterIterator text ) [static] :  void
RuleBasedBreakIterator_New.clone ( ) :  Object
RuleBasedBreakIterator_New.current ( ) :  int
RuleBasedBreakIterator_New.dump ( ) :  void
RuleBasedBreakIterator_New.equals ( Object that ) :  boolean
RuleBasedBreakIterator_New.first ( ) :  int
RuleBasedBreakIterator_New.following ( int offset ) :  int
RuleBasedBreakIterator_New.getInstanceFromCompiledRules ( InputStream is ) [static] :  RuleBasedBreakIterator
RuleBasedBreakIterator_New.getRuleStatus ( ) :  int *DEPRECATED*
RuleBasedBreakIterator_New.getRuleStatusVec ( int[ ] fillInArray ) :  int *DEPRECATED*
RuleBasedBreakIterator_New.getText ( ) :  CharacterIterator
RuleBasedBreakIterator_New.hashCode ( ) :  int
RuleBasedBreakIterator_New.isBoundary ( int offset ) :  boolean
RuleBasedBreakIterator_New.last ( ) :  int
RuleBasedBreakIterator_New.next ( ) :  int
RuleBasedBreakIterator_New.next ( int n ) :  int
RuleBasedBreakIterator_New.preceding ( int offset ) :  int
RuleBasedBreakIterator_New.previous ( ) :  int
RuleBasedBreakIterator_New.setText ( CharacterIterator newText ) :  void
RuleBasedBreakIterator_New.toString ( ) :  String

cdk-1.4.0.jar, RuleBasedBreakIterator_Old.class
package com.ibm.icu.text
RuleBasedBreakIterator_Old.checkOffset ( int offset, CharacterIterator text ) [static] :  void
RuleBasedBreakIterator_Old.clone ( ) :  Object
RuleBasedBreakIterator_Old.current ( ) :  int
RuleBasedBreakIterator_Old.debugDumpTables ( ) :  void
RuleBasedBreakIterator_Old.debugPrintln ( String s ) [static] :  void
RuleBasedBreakIterator_Old.equals ( Object that ) :  boolean
RuleBasedBreakIterator_Old.first ( ) :  int
RuleBasedBreakIterator_Old.following ( int offset ) :  int
RuleBasedBreakIterator_Old.getRuleStatus ( ) :  int *DEPRECATED*
RuleBasedBreakIterator_Old.getRuleStatusVec ( int[ ] fillInArray ) :  int *DEPRECATED*
RuleBasedBreakIterator_Old.getText ( ) :  CharacterIterator
RuleBasedBreakIterator_Old.handleNext ( ) :  int
RuleBasedBreakIterator_Old.handlePrevious ( ) :  int
RuleBasedBreakIterator_Old.hashCode ( ) :  int
RuleBasedBreakIterator_Old.isBoundary ( int offset ) :  boolean
RuleBasedBreakIterator_Old.last ( ) :  int
RuleBasedBreakIterator_Old.lookupBackwardState ( int state, int category ) :  int
RuleBasedBreakIterator_Old.lookupCategory ( char c ) :  int
RuleBasedBreakIterator_Old.lookupState ( int state, int category ) :  int
RuleBasedBreakIterator_Old.makeBuilder ( ) :  RuleBasedBreakIterator_Old.Builder
RuleBasedBreakIterator_Old.next ( ) :  int
RuleBasedBreakIterator_Old.next ( int n ) :  int
RuleBasedBreakIterator_Old.preceding ( int offset ) :  int
RuleBasedBreakIterator_Old.previous ( ) :  int
RuleBasedBreakIterator_Old.RuleBasedBreakIterator_Old ( String description )
RuleBasedBreakIterator_Old.setText ( CharacterIterator newText ) :  void
RuleBasedBreakIterator_Old.toString ( ) :  String
RuleBasedBreakIterator_Old.writeSwappedInt ( int x, DataOutputStream out, boolean littleEndian ) :  void
RuleBasedBreakIterator_Old.writeSwappedShort ( short x, DataOutputStream out, boolean littleEndian ) :  void
RuleBasedBreakIterator_Old.writeTablesToFile ( FileOutputStream file, boolean littleEndian ) :  void

cdk-1.4.0.jar, RuleBasedCollator.class
package com.ibm.icu.text
RuleBasedCollator.clone ( ) :  Object
RuleBasedCollator.compare ( String source, String target ) :  int
RuleBasedCollator.equals ( Object obj ) :  boolean
RuleBasedCollator.getCollationElementIterator ( CharacterIterator source ) :  CollationElementIterator
RuleBasedCollator.getCollationElementIterator ( String source ) :  CollationElementIterator
RuleBasedCollator.getCollationElementIterator ( UCharacterIterator source ) :  CollationElementIterator
RuleBasedCollator.getCollationKey ( String source ) :  CollationKey
RuleBasedCollator.getContractionsAndExpansions ( UnicodeSet contractions, UnicodeSet expansions, boolean addPrefixes ) :  void *DEPRECATED*
RuleBasedCollator.getNumericCollation ( ) :  boolean
RuleBasedCollator.getRawCollationKey ( String source, RawCollationKey key ) :  RawCollationKey
RuleBasedCollator.getRules ( ) :  String
RuleBasedCollator.getRules ( boolean fullrules ) :  String
RuleBasedCollator.getTailoredSet ( ) :  UnicodeSet
RuleBasedCollator.getUCAVersion ( ) :  VersionInfo
RuleBasedCollator.getVariableTop ( ) :  int
RuleBasedCollator.getVersion ( ) :  VersionInfo
RuleBasedCollator.hashCode ( ) :  int
RuleBasedCollator.isAlternateHandlingShifted ( ) :  boolean
RuleBasedCollator.isCaseLevel ( ) :  boolean
RuleBasedCollator.isFrenchCollation ( ) :  boolean
RuleBasedCollator.isHiraganaQuaternary ( ) :  boolean
RuleBasedCollator.isLowerCaseFirst ( ) :  boolean
RuleBasedCollator.isUpperCaseFirst ( ) :  boolean
RuleBasedCollator.RuleBasedCollator ( String rules )
RuleBasedCollator.setAlternateHandlingDefault ( ) :  void
RuleBasedCollator.setAlternateHandlingShifted ( boolean shifted ) :  void
RuleBasedCollator.setCaseFirstDefault ( ) :  void
RuleBasedCollator.setCaseLevel ( boolean flag ) :  void
RuleBasedCollator.setCaseLevelDefault ( ) :  void
RuleBasedCollator.setDecompositionDefault ( ) :  void
RuleBasedCollator.setFrenchCollation ( boolean flag ) :  void
RuleBasedCollator.setFrenchCollationDefault ( ) :  void
RuleBasedCollator.setHiraganaQuaternary ( boolean flag ) :  void
RuleBasedCollator.setHiraganaQuaternaryDefault ( ) :  void
RuleBasedCollator.setLowerCaseFirst ( boolean lowerfirst ) :  void
RuleBasedCollator.setNumericCollation ( boolean flag ) :  void
RuleBasedCollator.setNumericCollationDefault ( ) :  void
RuleBasedCollator.setStrength ( int newStrength ) :  void
RuleBasedCollator.setStrengthDefault ( ) :  void
RuleBasedCollator.setUpperCaseFirst ( boolean upperfirst ) :  void
RuleBasedCollator.setVariableTop ( int varTop ) :  void
RuleBasedCollator.setVariableTop ( String varTop ) :  int

cdk-1.4.0.jar, RuleBasedNumberFormat.class
package com.ibm.icu.text
RuleBasedNumberFormat.clone ( ) :  Object
RuleBasedNumberFormat.equals ( Object that ) :  boolean
RuleBasedNumberFormat.format ( BigDecimal number, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
RuleBasedNumberFormat.format ( BigDecimal number, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
RuleBasedNumberFormat.format ( BigInteger number, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
RuleBasedNumberFormat.format ( double number, String ruleSet ) :  String
RuleBasedNumberFormat.format ( double number, StringBuffer toAppendTo, FieldPosition ignore ) :  StringBuffer
RuleBasedNumberFormat.format ( long number, String ruleSet ) :  String
RuleBasedNumberFormat.format ( long number, StringBuffer toAppendTo, FieldPosition ignore ) :  StringBuffer
RuleBasedNumberFormat.getDefaultRuleSetName ( ) :  String *DEPRECATED*
RuleBasedNumberFormat.getRuleSetDisplayName ( String ruleSetName ) :  String *DEPRECATED*
RuleBasedNumberFormat.getRuleSetDisplayName ( String ruleSetName, ULocale locale ) :  String *DEPRECATED*
RuleBasedNumberFormat.getRuleSetDisplayNameLocales ( ) :  ULocale[ ] *DEPRECATED*
RuleBasedNumberFormat.getRuleSetDisplayNames ( ) :  String[ ] *DEPRECATED*
RuleBasedNumberFormat.getRuleSetDisplayNames ( ULocale locale ) :  String[ ] *DEPRECATED*
RuleBasedNumberFormat.getRuleSetNames ( ) :  String[ ]
RuleBasedNumberFormat.lenientParseEnabled ( ) :  boolean
RuleBasedNumberFormat.parse ( String text, ParsePosition parsePosition ) :  Number
RuleBasedNumberFormat.RuleBasedNumberFormat ( int format )
RuleBasedNumberFormat.RuleBasedNumberFormat ( Locale locale, int format )
RuleBasedNumberFormat.RuleBasedNumberFormat ( String description )
RuleBasedNumberFormat.RuleBasedNumberFormat ( String description, Locale locale )
RuleBasedNumberFormat.RuleBasedNumberFormat ( String description, String[ ][ ] localizations ) *DEPRECATED*
RuleBasedNumberFormat.RuleBasedNumberFormat ( String description, String[ ][ ] localizations, ULocale locale ) *DEPRECATED*
RuleBasedNumberFormat.RuleBasedNumberFormat ( String description, ULocale locale ) *DEPRECATED*
RuleBasedNumberFormat.RuleBasedNumberFormat ( ULocale locale, int format ) *DEPRECATED*
RuleBasedNumberFormat.setDefaultRuleSet ( String ruleSetName ) :  void
RuleBasedNumberFormat.setLenientParseMode ( boolean enabled ) :  void
RuleBasedNumberFormat.toString ( ) :  String

cdk-1.4.0.jar, RuleContext.class
package com.hp.hpl.jena.reasoner.rulesys
RuleContext.add ( Triple p1 ) [abstract] :  void
RuleContext.contains ( Node p1, Node p2, Node p3 ) [abstract] :  boolean
RuleContext.contains ( Triple p1 ) [abstract] :  boolean
RuleContext.find ( Node p1, Node p2, Node p3 ) [abstract] :  ClosableIterator
RuleContext.getEnv ( ) [abstract] :  BindingEnvironment
RuleContext.getGraph ( ) [abstract] :  InfGraph
RuleContext.getRule ( ) [abstract] :  Rule
RuleContext.remove ( Triple p1 ) [abstract] :  void
RuleContext.setRule ( Rule p1 ) [abstract] :  void
RuleContext.silentAdd ( Triple p1 ) [abstract] :  void

cdk-1.4.0.jar, RuleDerivation.class
package com.hp.hpl.jena.reasoner.rulesys
RuleDerivation.equals ( Object other ) :  boolean
RuleDerivation.getConclusion ( ) :  Triple
RuleDerivation.getMatches ( ) :  List
RuleDerivation.getRule ( ) :  Rule
RuleDerivation.printTrace ( PrintWriter out, boolean bindings ) :  void
RuleDerivation.printTrace ( PrintWriter out, boolean bindings, int indent, HashSet seen ) :  void
RuleDerivation.RuleDerivation ( Rule rule, Triple conclusion, List matches, InfGraph infGraph )
RuleDerivation.toString ( ) :  String

cdk-1.4.0.jar, RuleMap.class
package jena
RuleMap.loadRules ( BufferedReader src, Map prefixes ) [static] :  List
RuleMap.loadRules ( String filename, Map prefixes ) [static] :  List
RuleMap.main ( String[ ] args ) [static] :  void
RuleMap.RuleMap ( )

cdk-1.4.0.jar, RuleMode.class
package com.hp.hpl.jena.reasoner.rulesys
GenericRuleReasoner.RuleMode.GenericRuleReasoner.RuleMode ( String name )
GenericRuleReasoner.RuleMode.toString ( ) :  String

cdk-1.4.0.jar, RulePreprocessHook.class
package com.hp.hpl.jena.reasoner.rulesys
RulePreprocessHook.needsRerun ( FBRuleInfGraph p1, Triple p2 ) [abstract] :  boolean
RulePreprocessHook.run ( FBRuleInfGraph p1, Finder p2, Graph p3 ) [abstract] :  void

cdk-1.4.0.jar, RuleReasoner.class
package com.hp.hpl.jena.reasoner.rulesys
RuleReasoner.getRules ( ) [abstract] :  List
RuleReasoner.setRules ( List p1 ) [abstract] :  void

cdk-1.4.0.jar, RuleSet.class
package com.hp.hpl.jena.assembler
RuleSet.create ( List rules ) [static] :  RuleSet
RuleSet.create ( String ruleString ) [static] :  RuleSet
RuleSet.equals ( Object other ) :  boolean
RuleSet.getRules ( ) :  List
RuleSet.hashCode ( ) :  int
RuleSet.RuleSet ( List rules )

cdk-1.4.0.jar, RuleSetAssembler.class
package com.hp.hpl.jena.assembler.assemblers
RuleSetAssembler.addRules ( List result, Assembler a, Resource root ) [static] :  List
RuleSetAssembler.createRuleSet ( Assembler a, Resource root ) [static] :  RuleSet
RuleSetAssembler.open ( Assembler a, Resource root, Mode irrelevant ) :  Object
RuleSetAssembler.RuleSetAssembler ( )

cdk-1.4.0.jar, RulesetNotFoundException.class
package com.hp.hpl.jena.shared
RulesetNotFoundException.getURI ( ) :  String
RulesetNotFoundException.RulesetNotFoundException ( String uri )

cdk-1.4.0.jar, RuleStore.class
package com.hp.hpl.jena.reasoner.rulesys
FBRuleInfGraph.RuleStore.FBRuleInfGraph.RuleStore ( List rawRules, Object fRuleStore, List bRules )

cdk-1.4.0.jar, RunValuatorSet.class
package com.hp.hpl.jena.graph.query
StageElement.RunValuatorSet.run ( Domain current ) :  void
StageElement.RunValuatorSet.StageElement.RunValuatorSet ( ValuatorSet s, StageElement next )

cdk-1.4.0.jar, SAX2Model.class
package com.hp.hpl.jena.rdf.arp
SAX2Model.close ( ) :  void
SAX2Model.create ( String base, Model m ) [static] :  SAX2Model
SAX2Model.create ( String base, Model m, String lang ) [static] :  SAX2Model
SAX2Model.SAX2Model ( String base, Model m, String lang )
SAX2Model.setErrorHandler ( RDFErrorHandler errHandler ) :  RDFErrorHandler
SAX2Model.setProperty ( String str, Object value ) :  Object
SAX2Model.startPrefixMapping ( String prefix, String uri ) :  void

cdk-1.4.0.jar, SAX2RDF.class
package com.hp.hpl.jena.rdf.arp
SAX2RDF.create ( String base ) [static] :  SAX2RDF
SAX2RDF.create ( String base, String lang ) [static] :  SAX2RDF
SAX2RDF.getHandlers ( ) :  ARPHandlers
SAX2RDF.getOptions ( ) :  ARPOptions
SAX2RDF.installHandlers ( XMLReader rdr, XMLHandler sax2rdf ) [static] :  void
SAX2RDF.setHandlersWith ( ARPHandlers handlers ) :  void
SAX2RDF.setOptionsWith ( ARPOptions opts ) :  void
SAX2RDF.startPrefixMapping ( String prefix, String uri ) :  void

cdk-1.4.0.jar, Scale.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.Scale.BasicSceneGenerator.Scale ( )
BasicSceneGenerator.Scale.getDefault ( ) :  Double
BasicSceneGenerator.Scale.getDefault ( ) :  Object

cdk-1.4.0.jar, schemagen.class
package jena
schemagen.abort ( String msg, Exception e ) :  void
schemagen.addReplacementPattern ( String key, String replacement ) :  void
schemagen.asLegalJavaID ( String s, boolean cap ) :  String
schemagen.closeOutput ( ) :  void
schemagen.determineConfigRoot ( ) :  void
schemagen.determineLanguage ( ) :  void
schemagen.determineNamespaceURI ( ) :  String
schemagen.filter ( Resource r ) :  boolean
schemagen.formatComment ( String comment ) :  String
schemagen.getAllValues ( Object option ) :  List
schemagen.getClassName ( ) :  String
schemagen.getComment ( Resource r ) :  String
schemagen.getDefaultPrefixNamespace ( ) :  String
schemagen.getImports ( ) :  String
schemagen.getOntologyElementNamespace ( ) :  String
schemagen.getOpt ( Object option ) :  OptionDefinition
schemagen.getOptionNamespace ( ) :  String
schemagen.getResource ( Object option ) :  Resource
schemagen.getUCValueName ( Resource r ) :  String
schemagen.getValue ( Object option ) :  String
schemagen.getValueName ( Resource r, String disambiguator ) :  String
schemagen.go ( String[ ] args ) :  void
schemagen.guessNamespace ( ) :  String
schemagen.hasComment ( Resource r ) :  boolean
schemagen.hasResourceValue ( Object option ) :  boolean
schemagen.hasValue ( Object option ) :  boolean
schemagen.includeSource ( ) :  boolean
schemagen.indentTo ( int i, StringBuffer buf ) :  int
schemagen.isIncluded ( Resource r ) :  boolean
schemagen.isTrue ( Object option ) :  boolean
schemagen.main ( String[ ] args ) [static] :  void
schemagen.noComments ( ) :  boolean
schemagen.pop ( int n ) :  void
schemagen.processFooter ( ) :  void
schemagen.processHeader ( ) :  void
schemagen.processInput ( ) :  void
schemagen.schemagen ( )
schemagen.selectIndividuals ( ) :  ExtendedIterator
schemagen.selectInput ( ) :  void
schemagen.selectOutput ( ) :  void
schemagen.setGlobalReplacements ( ) :  void
schemagen.sorted ( ExtendedIterator i ) :  ExtendedIterator
schemagen.sorted ( List members ) :  ExtendedIterator
schemagen.substitute ( String sIn ) :  String
schemagen.urlCheck ( String uriOrFile ) :  String
schemagen.usage ( ) :  void
schemagen.useOntology ( ) :  boolean
schemagen.write ( int indentLevel, String s ) :  void
schemagen.writeAnnotationProperties ( ) :  void
schemagen.writeClassClose ( ) :  void
schemagen.writeClassDeclaration ( ) :  void
schemagen.writeClasses ( ) :  void
schemagen.writeDatatypeProperties ( ) :  void
schemagen.writeIndividuals ( ) :  void
schemagen.writeInitialDeclarations ( ) :  void
schemagen.writeln ( int indent ) :  void
schemagen.writeln ( int indent, String s ) :  void
schemagen.writeModelDeclaration ( ) :  void
schemagen.writeNamespace ( ) :  void
schemagen.writeObjectProperties ( ) :  void
schemagen.writeOntClasses ( ) :  void
schemagen.writeOntIndividuals ( ) :  void
schemagen.writeProperties ( ) :  void
schemagen.writeRDFClasses ( ) :  void
schemagen.writeRDFIndividuals ( ) :  void
schemagen.writeRDFProperties ( boolean useOntProperty ) :  void
schemagen.writeSource ( ) :  void
schemagen.writeValue ( Resource r, String template, String valueClass, String creator, String disambiguator ) :  void

cdk-1.4.0.jar, SDFToSignatures.class
package signature.chemistry
SDFToSignatures.main ( String[ ] args ) [static] :  void
SDFToSignatures.SDFToSignatures ( )

cdk-1.4.0.jar, SearchIterator.class
package com.ibm.icu.text
SearchIterator.first ( ) :  int
SearchIterator.following ( int position ) :  int
SearchIterator.getBreakIterator ( ) :  BreakIterator
SearchIterator.getIndex ( ) [abstract] :  int
SearchIterator.getMatchedText ( ) :  String
SearchIterator.getMatchLength ( ) :  int
SearchIterator.getMatchStart ( ) :  int
SearchIterator.getTarget ( ) :  CharacterIterator
SearchIterator.handleNext ( int p1 ) [abstract] :  int
SearchIterator.handlePrevious ( int p1 ) [abstract] :  int
SearchIterator.isOverlapping ( ) :  boolean
SearchIterator.last ( ) :  int
SearchIterator.next ( ) :  int
SearchIterator.preceding ( int position ) :  int
SearchIterator.previous ( ) :  int
SearchIterator.reset ( ) :  void
SearchIterator.SearchIterator ( CharacterIterator target, BreakIterator breaker )
SearchIterator.setBreakIterator ( BreakIterator breakiter ) :  void
SearchIterator.setIndex ( int position ) :  void
SearchIterator.setMatchLength ( int length ) :  void
SearchIterator.setOverlapping ( boolean allowOverlap ) :  void
SearchIterator.setTarget ( CharacterIterator text ) :  void

cdk-1.4.0.jar, Selector.class
package com.hp.hpl.jena.rdf.model
Selector.getObject ( ) [abstract] :  RDFNode
Selector.getPredicate ( ) [abstract] :  Property
Selector.getSubject ( ) [abstract] :  Resource
Selector.isSimple ( ) [abstract] :  boolean
Selector.test ( Statement p1 ) [abstract] :  boolean

cdk-1.4.0.jar, Seq.class
package com.hp.hpl.jena.rdf.model
Seq.add ( int p1, boolean p2 ) [abstract] :  Seq
Seq.add ( int p1, char p2 ) [abstract] :  Seq
Seq.add ( int p1, double p2 ) [abstract] :  Seq
Seq.add ( int p1, float p2 ) [abstract] :  Seq
Seq.add ( int p1, long p2 ) [abstract] :  Seq
Seq.add ( int p1, Object p2 ) [abstract] :  Seq
Seq.add ( int p1, RDFNode p2 ) [abstract] :  Seq
Seq.add ( int p1, String p2 ) [abstract] :  Seq
Seq.add ( int p1, String p2, String p3 ) [abstract] :  Seq
Seq.getAlt ( int p1 ) [abstract] :  Alt
Seq.getBag ( int p1 ) [abstract] :  Bag
Seq.getBoolean ( int p1 ) [abstract] :  boolean
Seq.getByte ( int p1 ) [abstract] :  byte
Seq.getChar ( int p1 ) [abstract] :  char
Seq.getDouble ( int p1 ) [abstract] :  double
Seq.getFloat ( int p1 ) [abstract] :  float
Seq.getInt ( int p1 ) [abstract] :  int
Seq.getLanguage ( int p1 ) [abstract] :  String
Seq.getLiteral ( int p1 ) [abstract] :  Literal
Seq.getLong ( int p1 ) [abstract] :  long
Seq.getObject ( int p1 ) [abstract] :  RDFNode
Seq.getObject ( int p1, ObjectF p2 ) [abstract] :  Object *DEPRECATED*
Seq.getResource ( int p1 ) [abstract] :  Resource
Seq.getResource ( int p1, ResourceF p2 ) [abstract] :  Resource
Seq.getSeq ( int p1 ) [abstract] :  Seq
Seq.getShort ( int p1 ) [abstract] :  short
Seq.getString ( int p1 ) [abstract] :  String
Seq.indexOf ( boolean p1 ) [abstract] :  int
Seq.indexOf ( char p1 ) [abstract] :  int
Seq.indexOf ( double p1 ) [abstract] :  int
Seq.indexOf ( float p1 ) [abstract] :  int
Seq.indexOf ( long p1 ) [abstract] :  int
Seq.indexOf ( Object p1 ) [abstract] :  int
Seq.indexOf ( RDFNode p1 ) [abstract] :  int
Seq.indexOf ( String p1 ) [abstract] :  int
Seq.indexOf ( String p1, String p2 ) [abstract] :  int
Seq.remove ( int p1 ) [abstract] :  Seq
Seq.set ( int p1, boolean p2 ) [abstract] :  Seq
Seq.set ( int p1, char p2 ) [abstract] :  Seq
Seq.set ( int p1, double p2 ) [abstract] :  Seq
Seq.set ( int p1, float p2 ) [abstract] :  Seq
Seq.set ( int p1, long p2 ) [abstract] :  Seq
Seq.set ( int p1, Object p2 ) [abstract] :  Seq
Seq.set ( int p1, RDFNode p2 ) [abstract] :  Seq
Seq.set ( int p1, String p2 ) [abstract] :  Seq
Seq.set ( int p1, String p2, String p3 ) [abstract] :  Seq

cdk-1.4.0.jar, SeqIndexBoundsException.class
package com.hp.hpl.jena.rdf.model
SeqIndexBoundsException.SeqIndexBoundsException ( int limit, int index )

cdk-1.4.0.jar, Sequence.class
package com.hp.hpl.jena.graph.query.regexptrees
Sequence.create ( List operands ) [static] :  RegexpTree
Sequence.equals ( Object other ) :  boolean
Sequence.hashCode ( ) :  int
Sequence.Sequence ( RegexpTree[ ] operands )
Sequence.toString ( ) :  String

cdk-1.4.0.jar, SetBunch.class
package com.hp.hpl.jena.mem
SetBunch.add ( Triple t ) :  void
SetBunch.app ( Domain d, StageElement next, MatchOrBind s ) :  void
SetBunch.contains ( Triple t ) :  boolean
SetBunch.containsBySameValueAs ( Triple t ) :  boolean
SetBunch.equalsObjectOK ( Triple t ) [static] :  boolean
SetBunch.iterator ( ) :  ExtendedIterator
SetBunch.iterator ( HashCommon.NotifyEmpty container ) :  ExtendedIterator
SetBunch.remove ( Triple t ) :  void
SetBunch.SetBunch ( TripleBunch b )
SetBunch.size ( ) :  int
SetBunch.slowContains ( Triple t ) :  boolean

cdk-1.4.0.jar, SetupDatabase.class
package com.hp.hpl.jena.assembler.acceptance
AllAccept.SetupDatabase.AllAccept.SetupDatabase ( Test tests )
AllAccept.SetupDatabase.setUp ( ) :  void

cdk-1.4.0.jar, Shape.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.Shape.valueOf ( String name ) [static] :  BasicAtomGenerator.Shape
BasicAtomGenerator.Shape.values ( ) [static] :  BasicAtomGenerator.Shape[ ]

cdk-1.4.0.jar, ShowAromaticity.class
package org.openscience.cdk.renderer.generators
RingGenerator.ShowAromaticity.getDefault ( ) :  Boolean
RingGenerator.ShowAromaticity.getDefault ( ) :  Object
RingGenerator.ShowAromaticity.RingGenerator.ShowAromaticity ( )

cdk-1.4.0.jar, ShowEndCarbons.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.ShowEndCarbons.BasicAtomGenerator.ShowEndCarbons ( )
BasicAtomGenerator.ShowEndCarbons.getDefault ( ) :  Boolean
BasicAtomGenerator.ShowEndCarbons.getDefault ( ) :  Object

cdk-1.4.0.jar, ShowExplicitHydrogens.class
package org.openscience.cdk.renderer.generators
BasicAtomGenerator.ShowExplicitHydrogens.BasicAtomGenerator.ShowExplicitHydrogens ( )
BasicAtomGenerator.ShowExplicitHydrogens.getDefault ( ) :  Boolean
BasicAtomGenerator.ShowExplicitHydrogens.getDefault ( ) :  Object

cdk-1.4.0.jar, ShowMoleculeTitle.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.ShowMoleculeTitle.BasicSceneGenerator.ShowMoleculeTitle ( )
BasicSceneGenerator.ShowMoleculeTitle.getDefault ( ) :  Boolean
BasicSceneGenerator.ShowMoleculeTitle.getDefault ( ) :  Object

cdk-1.4.0.jar, ShowTooltip.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.ShowTooltip.BasicSceneGenerator.ShowTooltip ( )
BasicSceneGenerator.ShowTooltip.getDefault ( ) :  Boolean
BasicSceneGenerator.ShowTooltip.getDefault ( ) :  Object

cdk-1.4.0.jar, SignatureQuotientGraph.class
package org.openscience.cdk.signature
SignatureQuotientGraph.isConnected ( int index1, int index2 ) :  boolean
SignatureQuotientGraph.SignatureQuotientGraph ( IAtomContainer atomContainer )
SignatureQuotientGraph.SignatureQuotientGraph ( IAtomContainer atomContainer, int height )

cdk-1.4.0.jar, SignatureReactionCanoniser.class
package org.openscience.cdk.smsd.labelling
SignatureReactionCanoniser.getCanonicalReaction ( IReaction reaction ) :  IReaction
SignatureReactionCanoniser.SignatureReactionCanoniser ( )

cdk-1.4.0.jar, SignatureViewer.class
package signature.display
SignatureViewer.actionPerformed ( ActionEvent e ) :  void
SignatureViewer.main ( String[ ] args ) [static] :  void
SignatureViewer.SignatureViewer ( )

cdk-1.4.0.jar, SilentAddI.class
package com.hp.hpl.jena.reasoner.rulesys
SilentAddI.silentAdd ( Triple p1 ) [abstract] :  void

cdk-1.4.0.jar, SimpleApplyer.class
package com.hp.hpl.jena.graph.query
QueryTriple.SimpleApplyer.applyToTriples ( Domain d, Matcher m, StageElement next ) :  void
QueryTriple.SimpleApplyer.find ( Domain d ) :  Iterator
QueryTriple.SimpleApplyer.QueryTriple.SimpleApplyer ( Graph g, QueryTriple qt )

cdk-1.4.0.jar, SimpleBasisSet.class
package org.openscience.cdk.math.qm
SimpleBasisSet.SimpleBasisSet ( IAtom[ ] atoms )

cdk-1.4.0.jar, SimpleCycle.class
package org.openscience.cdk.ringsearch.cyclebasis
SimpleCycle.checkConsistency ( ) :  boolean

cdk-1.4.0.jar, SimpleCycleBasis.class
package org.openscience.cdk.ringsearch.cyclebasis
SimpleCycleBasis.printIncidenceMatrix ( ) :  void

cdk-1.4.0.jar, SimpleDateFormat.class
package com.ibm.icu.text
SimpleDateFormat.applyLocalizedPattern ( String pattern ) :  void
SimpleDateFormat.applyPattern ( String pattern ) :  void
SimpleDateFormat.clone ( ) :  Object
SimpleDateFormat.equals ( Object obj ) :  boolean
SimpleDateFormat.format ( Calendar cal, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
SimpleDateFormat.get2DigitYearStart ( ) :  Date
SimpleDateFormat.getDateFormatSymbols ( ) :  DateFormatSymbols
SimpleDateFormat.getSymbols ( ) :  DateFormatSymbols
SimpleDateFormat.hashCode ( ) :  int
SimpleDateFormat.matchString ( String text, int start, int field, String[ ] data, Calendar cal ) :  int
SimpleDateFormat.parse ( String text, Calendar cal, ParsePosition parsePos ) :  void
SimpleDateFormat.set2DigitYearStart ( Date startDate ) :  void
SimpleDateFormat.setDateFormatSymbols ( DateFormatSymbols newFormatSymbols ) :  void
SimpleDateFormat.SimpleDateFormat ( )
SimpleDateFormat.SimpleDateFormat ( String pattern )
SimpleDateFormat.SimpleDateFormat ( String pattern, DateFormatSymbols formatData )
SimpleDateFormat.SimpleDateFormat ( String pattern, DateFormatSymbols formatData, ULocale loc )
SimpleDateFormat.SimpleDateFormat ( String pattern, Locale loc )
SimpleDateFormat.SimpleDateFormat ( String pattern, ULocale loc ) *DEPRECATED*
SimpleDateFormat.subFormat ( char ch, int count, int beginOffset, FieldPosition pos, DateFormatSymbols formatData, Calendar cal ) :  String
SimpleDateFormat.subFormat ( StringBuffer buf, char ch, int count, int beginOffset, FieldPosition pos, Calendar cal ) :  void
SimpleDateFormat.subParse ( String text, int start, char ch, int count, boolean obeyCount, boolean allowNegative, boolean[ ] ambiguousYear, Calendar cal ) :  int
SimpleDateFormat.toLocalizedPattern ( ) :  String
SimpleDateFormat.toPattern ( ) :  String
SimpleDateFormat.zeroPaddingNumber ( long value, int minDigits, int maxDigits ) :  String
SimpleDateFormat.zeroPaddingNumber ( StringBuffer buf, int value, int minDigits, int maxDigits ) :  void

cdk-1.4.0.jar, SimpleDateRule.class
package com.ibm.icu.util
SimpleDateRule.firstAfter ( Date start ) :  Date *DEPRECATED*
SimpleDateRule.firstBetween ( Date start, Date end ) :  Date *DEPRECATED*
SimpleDateRule.isBetween ( Date start, Date end ) :  boolean *DEPRECATED*
SimpleDateRule.isOn ( Date date ) :  boolean *DEPRECATED*
SimpleDateRule.SimpleDateRule ( int month, int dayOfMonth ) *DEPRECATED*
SimpleDateRule.SimpleDateRule ( int month, int dayOfMonth, int dayOfWeek, boolean after ) *DEPRECATED*

cdk-1.4.0.jar, SimpleGenerator.class
package com.hp.hpl.jena.graph.query.regexptrees
SimpleGenerator.getAlternatives ( List operands ) :  RegexpTree
SimpleGenerator.getAnySingle ( ) :  RegexpTree
SimpleGenerator.getBackReference ( int n ) :  RegexpTree
SimpleGenerator.getClass ( String chars, boolean reject ) :  RegexpTree
SimpleGenerator.getEndOfLine ( ) :  RegexpTree
SimpleGenerator.getNothing ( ) :  RegexpTree
SimpleGenerator.getOneOrMore ( RegexpTree d ) :  RegexpTree
SimpleGenerator.getOptional ( RegexpTree d ) :  RegexpTree
SimpleGenerator.getParen ( RegexpTree operand, int index ) :  RegexpTree
SimpleGenerator.getSequence ( List operands ) :  RegexpTree
SimpleGenerator.getStartOfLine ( ) :  RegexpTree
SimpleGenerator.getText ( char ch ) :  RegexpTree
SimpleGenerator.getZeroOrMore ( RegexpTree d ) :  RegexpTree
SimpleGenerator.SimpleGenerator ( )

cdk-1.4.0.jar, SimpleGraph.class
package signature.simple
SimpleGraph.degree ( int vertexIndex ) :  int
SimpleGraph.getConnected ( int vertexIndex ) :  int[ ]
SimpleGraph.getVertexCount ( ) :  int
SimpleGraph.isConnected ( int i, int j ) :  boolean
SimpleGraph.makeEdge ( int a, int b ) :  void
SimpleGraph.SimpleGraph ( )
SimpleGraph.SimpleGraph ( SimpleGraph graph, int[ ] permutation )
SimpleGraph.SimpleGraph ( String graphString )
SimpleGraph.toString ( ) :  String

cdk-1.4.0.jar, SimpleGraphBuilder.class
package signature.simple
SimpleGraphBuilder.fromTree ( ColoredTree tree ) :  SimpleGraph
SimpleGraphBuilder.makeEdge ( int vertexIndex1, int vertexIndex2, String a, String b, String edgeLabel ) :  void
SimpleGraphBuilder.makeGraph ( ) :  void
SimpleGraphBuilder.makeVertex ( String label ) :  void
SimpleGraphBuilder.SimpleGraphBuilder ( )

cdk-1.4.0.jar, SimpleGraphFactory.class
package signature.simple
SimpleGraphFactory.make26Fullerene ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeAdamantane ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeBowtieane ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeCuneane ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeDiSpiroOctane ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeDoubleBridgedPentagon ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeFourRegularExample ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeNapthalene ( ) [static] :  SimpleGraph
SimpleGraphFactory.makePappusGraph ( ) [static] :  SimpleGraph
SimpleGraphFactory.makePetersensGraph ( ) [static] :  SimpleGraph
SimpleGraphFactory.makePrism ( int size ) [static] :  SimpleGraph
SimpleGraphFactory.makeSandwich ( int size ) [static] :  SimpleGraph
SimpleGraphFactory.makeSpiroPentagons ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeSquareQuotientGraph ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeThreeFourFiveTwisted ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeTietzesGraph ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeTricycloPropaIndene ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeTruncatedTetrahedron ( ) [static] :  SimpleGraph
SimpleGraphFactory.makeTwistane ( ) [static] :  SimpleGraph
SimpleGraphFactory.SimpleGraphFactory ( )

cdk-1.4.0.jar, SimpleGraphPermutor.class
package signature.simple
SimpleGraphPermutor.next ( ) :  Object
SimpleGraphPermutor.next ( ) :  SimpleGraph
SimpleGraphPermutor.remove ( ) :  void
SimpleGraphPermutor.SimpleGraphPermutor ( SimpleGraph graph )

cdk-1.4.0.jar, SimpleGraphSignature.class
package signature.simple
SimpleGraphSignature.getVertexCount ( ) :  int
SimpleGraphSignature.signatureForVertex ( int vertexIndex ) :  AbstractVertexSignature
SimpleGraphSignature.signatureStringForVertex ( int vertexIndex ) :  String
SimpleGraphSignature.signatureStringForVertex ( int vertexIndex, int height ) :  String
SimpleGraphSignature.SimpleGraphSignature ( SimpleGraph graph )
SimpleGraphSignature.toCanonicalString ( ) :  String

cdk-1.4.0.jar, SimpleGraphTest.class
package signature.simple
SimpleGraphTest.signatureFromString ( String string ) :  SimpleGraphSignature
SimpleGraphTest.signatureHeightTest ( ) :  void
SimpleGraphTest.SimpleGraphTest ( )
SimpleGraphTest.testChain ( ) :  void
SimpleGraphTest.testColoredTreeRoundtrip ( ) :  void
SimpleGraphTest.testVertexCount ( ) :  void

cdk-1.4.0.jar, SimpleHoliday.class
package com.ibm.icu.util
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, int dayOfWeek, String name ) *DEPRECATED*
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, int dayOfWeek, String name, int startYear ) *DEPRECATED*
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, int dayOfWeek, String name, int startYear, int endYear ) *DEPRECATED*
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, String name ) *DEPRECATED*
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, String name, int startYear ) *DEPRECATED*
SimpleHoliday.SimpleHoliday ( int month, int dayOfMonth, String name, int startYear, int endYear ) *DEPRECATED*

cdk-1.4.0.jar, SimpleNumberFormatFactory.class
package com.ibm.icu.text
NumberFormat.SimpleNumberFormatFactory.getSupportedLocaleNames ( ) :  Set
NumberFormat.SimpleNumberFormatFactory.NumberFormat.SimpleNumberFormatFactory ( Locale locale )
NumberFormat.SimpleNumberFormatFactory.NumberFormat.SimpleNumberFormatFactory ( Locale locale, boolean visible )
NumberFormat.SimpleNumberFormatFactory.NumberFormat.SimpleNumberFormatFactory ( ULocale locale ) *DEPRECATED*
NumberFormat.SimpleNumberFormatFactory.NumberFormat.SimpleNumberFormatFactory ( ULocale locale, boolean visible ) *DEPRECATED*
NumberFormat.SimpleNumberFormatFactory.visible ( ) :  boolean

cdk-1.4.0.jar, SimpleQueryEngine.class
package com.hp.hpl.jena.graph.query
SimpleQueryEngine.cons ( Triple pattern, Object cons ) [static] :  SimpleQueryEngine.Cons
SimpleQueryEngine.executeBindings ( List outStages, NamedGraphMap args, Node[ ] nodes ) :  ExtendedIterator
SimpleQueryEngine.SimpleQueryEngine ( List pattern, TripleSorter sorter, ExpressionSet constraints )
SimpleQueryEngine.SimpleQueryEngine ( NamedTripleBunches triples, TripleSorter ts, ExpressionSet constraint ) *DEPRECATED*

cdk-1.4.0.jar, SimpleQueryHandler.class
package com.hp.hpl.jena.graph.query
SimpleQueryHandler.containsNode ( Node n ) :  boolean
SimpleQueryHandler.objectsFor ( Graph g, Node s, Node p ) [static] :  ExtendedIterator
SimpleQueryHandler.objectsFor ( Node s, Node p ) :  ExtendedIterator
SimpleQueryHandler.patternStage ( Mapping map, ExpressionSet constraints, Triple[ ] t ) :  Stage
SimpleQueryHandler.predicatesFor ( Graph g, Node s, Node o ) [static] :  ExtendedIterator
SimpleQueryHandler.predicatesFor ( Node s, Node o ) :  ExtendedIterator
SimpleQueryHandler.prepareBindings ( Query q, Node[ ] variables ) :  BindingQueryPlan
SimpleQueryHandler.prepareTree ( Graph pattern ) :  TreeQueryPlan
SimpleQueryHandler.SimpleQueryHandler ( Graph graph )
SimpleQueryHandler.subjectsFor ( Graph g, Node p, Node o ) [static] :  ExtendedIterator
SimpleQueryHandler.subjectsFor ( Node p, Node o ) :  ExtendedIterator

cdk-1.4.0.jar, SimpleQueryPlan.class
package com.hp.hpl.jena.graph.query
SimpleQueryPlan.executeBindings ( ) :  ExtendedIterator
SimpleQueryPlan.SimpleQueryPlan ( Graph graph, Query query, Node[ ] variables )

cdk-1.4.0.jar, SimpleQuotientGraph.class
package signature.simple
SimpleQuotientGraph.isConnected ( int i, int j ) :  boolean
SimpleQuotientGraph.SimpleQuotientGraph ( SimpleGraph graph )
SimpleQuotientGraph.SimpleQuotientGraph ( SimpleGraph graph, int height )

cdk-1.4.0.jar, SimpleQuotientGraphTest.class
package signature.simple
SimpleQuotientGraphTest.adamantaneTest ( ) :  void
SimpleQuotientGraphTest.bowtieaneQuotientGraphTest ( ) :  void
SimpleQuotientGraphTest.check3Regularity ( SimpleGraph graph ) :  void
SimpleQuotientGraphTest.check4Regularity ( SimpleGraph graph ) :  void
SimpleQuotientGraphTest.checkParameters ( SimpleQuotientGraph qGraph, int expectedVertexCount, int expectedEdgeCount, int expectedLoopEdgeCount ) :  void
SimpleQuotientGraphTest.cubeTest ( ) :  void
SimpleQuotientGraphTest.cuneaneTest ( ) :  void
SimpleQuotientGraphTest.diSpiroOctaneQuotientGraphTest ( ) :  void
SimpleQuotientGraphTest.doubleBridgedPentagonTest ( ) :  void
SimpleQuotientGraphTest.draw ( SimpleQuotientGraph quotientGraph ) :  void
SimpleQuotientGraphTest.fourRegularExampleTest ( ) :  void
SimpleQuotientGraphTest.fullerene26Test ( ) :  void
SimpleQuotientGraphTest.hexagonalSandwichTest ( ) :  void
SimpleQuotientGraphTest.napthaleneTest ( ) :  void
SimpleQuotientGraphTest.pappusGraphTest ( ) :  void
SimpleQuotientGraphTest.pentagonalPrismTest ( ) :  void
SimpleQuotientGraphTest.pentagonalSandwichTest ( ) :  void
SimpleQuotientGraphTest.petersensGraphTest ( ) :  void
SimpleQuotientGraphTest.SimpleQuotientGraphTest ( )
SimpleQuotientGraphTest.spiroPentagonTest ( ) :  void
SimpleQuotientGraphTest.squareQuotientGraphTest ( ) :  void
SimpleQuotientGraphTest.squareSandwichTest ( ) :  void
SimpleQuotientGraphTest.threeFourFiveTwistedGraphTest ( ) :  void
SimpleQuotientGraphTest.tietzesGraphTest ( ) :  void
SimpleQuotientGraphTest.triangleSandwichTest ( ) :  void
SimpleQuotientGraphTest.triangularPrismTest ( ) :  void
SimpleQuotientGraphTest.tricycloPropaIndeneQuotientGraphTest ( ) :  void
SimpleQuotientGraphTest.truncatedTetrahedronTest ( ) :  void
SimpleQuotientGraphTest.twistaneTest ( ) :  void

cdk-1.4.0.jar, SimpleSelector.class
package com.hp.hpl.jena.rdf.model
SimpleSelector.getObject ( ) :  RDFNode
SimpleSelector.getPredicate ( ) :  Property
SimpleSelector.getSubject ( ) :  Resource
SimpleSelector.isSimple ( ) :  boolean
SimpleSelector.selects ( Statement s ) :  boolean
SimpleSelector.SimpleSelector ( )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, boolean object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, char object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, double object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, float object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, long object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, Object object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, RDFNode object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, String object )
SimpleSelector.SimpleSelector ( Resource subject, Property predicate, String object, String language )
SimpleSelector.test ( Statement s ) :  boolean

cdk-1.4.0.jar, SimpleTimeZone.class
package com.ibm.icu.util
SimpleTimeZone.getDSTSavings ( ) :  int
SimpleTimeZone.setDSTSavings ( int millisSavedDuringDST ) :  void
SimpleTimeZone.setEndRule ( int month, int dayOfMonth, int dayOfWeek, int time, boolean after ) :  void
SimpleTimeZone.setEndRule ( int month, int dayOfMonth, int time ) :  void
SimpleTimeZone.setEndRule ( int month, int dayOfWeekInMonth, int dayOfWeek, int time ) :  void
SimpleTimeZone.setRawOffset ( int offsetMillis ) :  void *DEPRECATED*
SimpleTimeZone.setStartRule ( int month, int dayOfMonth, int dayOfWeek, int time, boolean after ) :  void
SimpleTimeZone.setStartRule ( int month, int dayOfMonth, int time ) :  void
SimpleTimeZone.setStartRule ( int month, int dayOfWeekInMonth, int dayOfWeek, int time ) :  void
SimpleTimeZone.setStartYear ( int year ) :  void
SimpleTimeZone.SimpleTimeZone ( int rawOffset, String ID )
SimpleTimeZone.SimpleTimeZone ( int rawOffset, String ID, int startMonth, int startDay, int startDayOfWeek, int startTime, int endMonth, int endDay, int endDayOfWeek, int endTime )
SimpleTimeZone.SimpleTimeZone ( int rawOffset, String ID, int startMonth, int startDay, int startDayOfWeek, int startTime, int endMonth, int endDay, int endDayOfWeek, int endTime, int dstSavings )
SimpleTimeZone.SimpleTimeZone ( SimpleTimeZone tz )

cdk-1.4.0.jar, SimpleTreeQueryPlan.class
package com.hp.hpl.jena.graph.query
SimpleTreeQueryPlan.executeTree ( ) :  Graph
SimpleTreeQueryPlan.getRoots ( Graph pattern ) [static] :  Set
SimpleTreeQueryPlan.SimpleTreeQueryPlan ( Graph target, Graph pattern )

cdk-1.4.0.jar, SimpleTripleSorter.class
package com.hp.hpl.jena.graph.query
SimpleTripleSorter.accept ( Triple t ) :  void
SimpleTripleSorter.bc ( Node n, Node other ) :  int
SimpleTripleSorter.bind ( Node n ) :  void
SimpleTripleSorter.bind ( Triple t ) :  void
SimpleTripleSorter.bindingCount ( Node n, Triple o ) :  int
SimpleTripleSorter.bindingCount ( Triple t ) :  int
SimpleTripleSorter.bindingCount ( Triple t, Triple other ) :  int
SimpleTripleSorter.findLightest ( List candidates ) :  List
SimpleTripleSorter.findMostBinding ( List candidates ) :  Triple
SimpleTripleSorter.SimpleTripleSorter ( )
SimpleTripleSorter.SimpleTripleSorter ( Triple[ ] triples )
SimpleTripleSorter.sort ( ) :  Triple[ ]
SimpleTripleSorter.sort ( Triple[ ] ts ) :  Triple[ ]
SimpleTripleSorter.weight ( Node n ) :  int
SimpleTripleSorter.weight ( Triple t ) :  int

cdk-1.4.0.jar, SimpleVertexSignature.class
package signature.simple
SimpleVertexSignature.getConnected ( int vertexIndex ) :  int[ ]
SimpleVertexSignature.getEdgeLabel ( int vertexIndex, int otherVertexIndex ) :  String
SimpleVertexSignature.getIntLabel ( int vertexIndex ) :  int
SimpleVertexSignature.getVertexSymbol ( int vertexIndex ) :  String
SimpleVertexSignature.SimpleVertexSignature ( int rootVertexIndex, int height, SimpleGraph graph )
SimpleVertexSignature.SimpleVertexSignature ( int rootVertexIndex, SimpleGraph graph )

cdk-1.4.0.jar, SingleMapping.class
package org.openscience.cdk.smsd.algorithm.single
SingleMapping.getOverLaps ( IAtomContainer source, IAtomContainer target, boolean removeHydrogen ) :  List
SingleMapping.getOverLaps ( IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen ) :  List
SingleMapping.SingleMapping ( )

cdk-1.4.0.jar, SingleMappingHandler.class
package org.openscience.cdk.smsd.algorithm.single
SingleMappingHandler.getAllAtomMapping ( ) :  List
SingleMappingHandler.getAllMapping ( ) :  List
SingleMappingHandler.getFirstAtomMapping ( ) :  Map
SingleMappingHandler.getFirstMapping ( ) :  Map
SingleMappingHandler.searchMCS ( boolean bondTypeMatch ) :  void
SingleMappingHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
SingleMappingHandler.set ( MolHandler source, MolHandler target ) :  void
SingleMappingHandler.SingleMappingHandler ( boolean removeH )

cdk-1.4.0.jar, SingletonIterator.class
package com.hp.hpl.jena.util.iterator
SingletonIterator.hasNext ( ) :  boolean
SingletonIterator.next ( ) :  Object
SingletonIterator.SingletonIterator ( Object element )

cdk-1.4.0.jar, SlotValuator.class
package com.hp.hpl.jena.graph.query
SlotValuator.evalBool ( IndexValues iv ) :  boolean
SlotValuator.evalObject ( IndexValues iv ) :  Object
SlotValuator.SlotValuator ( int index )

cdk-1.4.0.jar, SmallGraphMem.class
package com.hp.hpl.jena.mem
SmallGraphMem.clear ( ) :  void
SmallGraphMem.createTripleStore ( ) :  TripleStore
SmallGraphMem.destroy ( ) :  void
SmallGraphMem.getBulkUpdateHandler ( ) :  BulkUpdateHandler
SmallGraphMem.graphBaseContains ( Triple t ) :  boolean
SmallGraphMem.graphBaseFind ( TripleMatch m ) :  ExtendedIterator
SmallGraphMem.graphBaseSize ( ) :  int
SmallGraphMem.performAdd ( Triple t ) :  void
SmallGraphMem.performDelete ( Triple t ) :  void
SmallGraphMem.SmallGraphMem ( )
SmallGraphMem.SmallGraphMem ( ReificationStyle style )

cdk-1.4.0.jar, SMARTSQueryTool.class
package org.openscience.cdk.smiles.smarts
SMARTSQueryTool.setQueryCacheSize ( int maxEntries ) :  void

cdk-1.4.0.jar, SmilesGenerator.class
package org.openscience.cdk.smiles
SmilesGenerator.createChiralSMILES ( IAtomContainer molecule, boolean[ ] doubleBondConfiguration ) :  String
SmilesGenerator.createSMILES ( IAtomContainer molecule ) :  String
SmilesGenerator.createSMILES ( IAtomContainer molecule, boolean chiral, boolean[ ] doubleBondConfiguration ) :  String
SmilesGenerator.createSMILESWithoutCheckForMultipleMolecules ( IAtomContainer molecule, boolean chiral, boolean[ ] doubleBondConfiguration ) :  String
SmilesGenerator.SmilesGenerator ( boolean useAromaticityFlag )

cdk-1.4.0.jar, SmilesParser.class
package org.openscience.cdk.smiles
SmilesParser.isPreservingAromaticity ( ) :  boolean
SmilesParser.setPreservingAromaticity ( boolean preservingAromaticity ) :  void

cdk-1.4.0.jar, SmilesReactionCanoniser.class
package org.openscience.cdk.smsd.labelling
SmilesReactionCanoniser.getCanonicalReaction ( IReaction reaction ) :  IReaction
SmilesReactionCanoniser.SmilesReactionCanoniser ( )

cdk-1.4.0.jar, SMILESReader.class
package org.openscience.cdk.io
SMILESReader.SMILESReader ( Reader input, IChemObjectBuilder builder )

cdk-1.4.0.jar, SMILESWriter.class
package org.openscience.cdk.io
SMILESWriter.customizeJob ( ) :  void
SMILESWriter.getIOSettings ( ) :  IOSetting[ ]

cdk-1.4.0.jar, SMSDNormalizer.class
package org.openscience.cdk.normalize
SMSDNormalizer.aromatizeMolecule ( IAtomContainer mol ) [static] :  void
SMSDNormalizer.convertExplicitToImplicitHydrogens ( IAtomContainer atomContainer ) [static] :  IAtomContainer
SMSDNormalizer.getExplicitHydrogenCount ( IAtomContainer atomContainer, IAtom atom ) [static] :  int
SMSDNormalizer.getHydrogenCount ( IAtomContainer atomContainer, IAtom atom ) [static] :  int
SMSDNormalizer.getImplicitHydrogenCount ( IAtomContainer atomContainer, IAtom atom ) [static] :  int
SMSDNormalizer.makeDeepCopy ( IAtomContainer container ) [static] :  IMolecule
SMSDNormalizer.percieveAtomTypesAndConfigureAtoms ( IAtomContainer container ) [static] :  void
SMSDNormalizer.removeHydrogensAndPreserveAtomID ( IAtomContainer atomContainer ) [static] :  IAtomContainer
SMSDNormalizer.SMSDNormalizer ( )

cdk-1.4.0.jar, SomeValuesFromRestriction.class
package com.hp.hpl.jena.ontology
SomeValuesFromRestriction.getSomeValuesFrom ( ) [abstract] :  Resource
SomeValuesFromRestriction.hasSomeValuesFrom ( Resource p1 ) [abstract] :  boolean
SomeValuesFromRestriction.removeSomeValuesFrom ( Resource p1 ) [abstract] :  void
SomeValuesFromRestriction.setSomeValuesFrom ( Resource p1 ) [abstract] :  void

cdk-1.4.0.jar, sparql.class
package jena
sparql.main ( String[ ] args ) [static] :  void
sparql.sparql ( )

cdk-1.4.0.jar, SquarePlanarShape.class
package org.openscience.cdk.stereo
StereoTool.SquarePlanarShape.valueOf ( String name ) [static] :  StereoTool.SquarePlanarShape
StereoTool.SquarePlanarShape.values ( ) [static] :  StereoTool.SquarePlanarShape[ ]

cdk-1.4.0.jar, Stage.class
package com.hp.hpl.jena.graph.query
Stage.close ( ) :  void
Stage.connectFrom ( Stage s ) :  Stage
Stage.deliver ( Pipe p1 ) [abstract] :  Pipe
Stage.initial ( int count ) [static] :  Stage
Stage.isClosed ( ) :  boolean
Stage.markClosed ( ) :  void
Stage.Stage ( )

cdk-1.4.0.jar, StageElement.class
package com.hp.hpl.jena.graph.query
StageElement.run ( Domain p1 ) [abstract] :  void
StageElement.StageElement ( )

cdk-1.4.0.jar, StandardValidityReport.class
package com.hp.hpl.jena.reasoner
StandardValidityReport.add ( boolean error, String type, String description ) :  void
StandardValidityReport.add ( boolean error, String type, String description, Object extension ) :  void
StandardValidityReport.add ( ValidityReport.Report report ) :  void
StandardValidityReport.getReports ( ) :  Iterator
StandardValidityReport.isClean ( ) :  boolean
StandardValidityReport.isValid ( ) :  boolean
StandardValidityReport.size ( ) :  int
StandardValidityReport.StandardValidityReport ( )

cdk-1.4.0.jar, StartOfLine.class
package com.hp.hpl.jena.graph.query.regexptrees
StartOfLine.equals ( Object x ) :  boolean
StartOfLine.hashCode ( ) :  int
StartOfLine.StartOfLine ( )
StartOfLine.toString ( ) :  String

cdk-1.4.0.jar, StartStateRDForDescription.class
package com.hp.hpl.jena.rdf.arp.states
StartStateRDForDescription.abort ( ) :  void
StartStateRDForDescription.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
StartStateRDForDescription.StartStateRDForDescription ( XMLHandler handler, AbsXMLContext x )

cdk-1.4.0.jar, Statement.class
package com.hp.hpl.jena.rdf.model
Statement.changeLiteralObject ( boolean p1 ) [abstract] :  Statement
Statement.changeLiteralObject ( char p1 ) [abstract] :  Statement
Statement.changeLiteralObject ( double p1 ) [abstract] :  Statement
Statement.changeLiteralObject ( float p1 ) [abstract] :  Statement
Statement.changeLiteralObject ( int p1 ) [abstract] :  Statement
Statement.changeLiteralObject ( long p1 ) [abstract] :  Statement
Statement.changeObject ( RDFNode p1 ) [abstract] :  Statement
Statement.changeObject ( String p1 ) [abstract] :  Statement
Statement.changeObject ( String p1, boolean p2 ) [abstract] :  Statement
Statement.changeObject ( String p1, String p2 ) [abstract] :  Statement
Statement.changeObject ( String p1, String p2, boolean p3 ) [abstract] :  Statement
Statement.createReifiedStatement ( ) [abstract] :  ReifiedStatement
Statement.createReifiedStatement ( String p1 ) [abstract] :  ReifiedStatement
Statement.equals ( Object p1 ) [abstract] :  boolean
Statement.getAlt ( ) [abstract] :  Alt
Statement.getBag ( ) [abstract] :  Bag
Statement.getBoolean ( ) [abstract] :  boolean
Statement.getByte ( ) [abstract] :  byte
Statement.getChar ( ) [abstract] :  char
Statement.getDouble ( ) [abstract] :  double
Statement.getFloat ( ) [abstract] :  float
Statement.getInt ( ) [abstract] :  int
Statement.getLanguage ( ) [abstract] :  String
Statement.getLiteral ( ) [abstract] :  Literal
Statement.getLong ( ) [abstract] :  long
Statement.getModel ( ) [abstract] :  Model
Statement.getObject ( ) [abstract] :  RDFNode
Statement.getObject ( ObjectF p1 ) [abstract] :  Object *DEPRECATED*
Statement.getPredicate ( ) [abstract] :  Property
Statement.getProperty ( Property p1 ) [abstract] :  Statement
Statement.getResource ( ) [abstract] :  Resource
Statement.getResource ( ResourceF p1 ) [abstract] :  Resource
Statement.getSeq ( ) [abstract] :  Seq
Statement.getShort ( ) [abstract] :  short
Statement.getStatementProperty ( Property p1 ) [abstract] :  Statement
Statement.getString ( ) [abstract] :  String
Statement.getSubject ( ) [abstract] :  Resource
Statement.hashCode ( ) [abstract] :  int
Statement.hasWellFormedXML ( ) [abstract] :  boolean
Statement.isReified ( ) [abstract] :  boolean
Statement.listReifiedStatements ( ) [abstract] :  RSIterator
Statement.remove ( ) [abstract] :  Statement
Statement.removeReification ( ) [abstract] :  void

cdk-1.4.0.jar, StatementBoundary.class
package com.hp.hpl.jena.rdf.model
StatementBoundary.asTripleBoundary ( Model p1 ) [abstract] :  TripleBoundary
StatementBoundary.stopAt ( Statement p1 ) [abstract] :  boolean

cdk-1.4.0.jar, StatementBoundaryBase.class
package com.hp.hpl.jena.rdf.model
StatementBoundaryBase.asTripleBoundary ( Model m ) :  TripleBoundary
StatementBoundaryBase.continueWith ( Statement s ) :  boolean
StatementBoundaryBase.convert ( Model s, StatementBoundary b ) [static] :  TripleBoundary
StatementBoundaryBase.StatementBoundaryBase ( )
StatementBoundaryBase.stopAt ( Statement s ) :  boolean

cdk-1.4.0.jar, StatementHandler.class
package com.hp.hpl.jena.rdf.arp
StatementHandler.statement ( AResource p1, AResource p2, ALiteral p3 ) [abstract] :  void
StatementHandler.statement ( AResource p1, AResource p2, AResource p3 ) [abstract] :  void

cdk-1.4.0.jar, StatementListener.class
package com.hp.hpl.jena.rdf.listeners
StatementListener.addedStatement ( Statement s ) :  void
StatementListener.addedStatements ( List statements ) :  void
StatementListener.addedStatements ( Model m ) :  void
StatementListener.addedStatements ( Statement[ ] statements ) :  void
StatementListener.addedStatements ( StmtIterator statements ) :  void
StatementListener.notifyEvent ( Model m, Object event ) :  void
StatementListener.removedStatement ( Statement s ) :  void
StatementListener.removedStatements ( List statements ) :  void
StatementListener.removedStatements ( Model m ) :  void
StatementListener.removedStatements ( Statement[ ] statements ) :  void
StatementListener.removedStatements ( StmtIterator statements ) :  void
StatementListener.StatementListener ( )

cdk-1.4.0.jar, StatementTripleBoundary.class
package com.hp.hpl.jena.rdf.model
StatementTripleBoundary.asTripleBoundary ( Model ignored ) :  TripleBoundary
StatementTripleBoundary.StatementTripleBoundary ( TripleBoundary tb )
StatementTripleBoundary.stopAt ( Statement s ) :  boolean

cdk-1.4.0.jar, Stereo.class
package org.openscience.cdk.interfaces
IBond.Stereo.valueOf ( String name ) [static] :  IBond.Stereo
IBond.Stereo.values ( ) [static] :  IBond.Stereo[ ]
ITetrahedralChirality.Stereo.valueOf ( String name ) [static] :  ITetrahedralChirality.Stereo
ITetrahedralChirality.Stereo.values ( ) [static] :  ITetrahedralChirality.Stereo[ ]

cdk-1.4.0.jar, StereoClass.class
package org.openscience.cdk.stereo
StereoTool.StereoClass.valueOf ( String name ) [static] :  StereoTool.StereoClass
StereoTool.StereoClass.values ( ) [static] :  StereoTool.StereoClass[ ]

cdk-1.4.0.jar, StereoTool.class
package org.openscience.cdk.stereo
StereoTool.allCoplanar ( Vector3d planeNormal, Point3d pointInPlane, Point3d[ ] points ) [static] :  boolean
StereoTool.getHandedness ( IAtom baseAtomA, IAtom baseAtomB, IAtom baseAtomC, IAtom apexAtom ) [static] :  StereoTool.TetrahedralSign
StereoTool.getNormal ( Point3d ptA, Point3d ptB, Point3d ptC ) [static] :  Vector3d
StereoTool.getSquarePlanarShape ( IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD ) [static] :  StereoTool.SquarePlanarShape
StereoTool.getStereo ( IAtom atom1, IAtom atom2, IAtom atom3, IAtom atom4 ) [static] :  ITetrahedralChirality.Stereo
StereoTool.isColinear ( Point3d ptA, Point3d ptB, Point3d ptC ) [static] :  boolean
StereoTool.isOctahedral ( IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF, IAtom atomG ) [static] :  boolean
StereoTool.isSquarePlanar ( IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD ) [static] :  boolean
StereoTool.isTrigonalBipyramidal ( IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF ) [static] :  boolean
StereoTool.signedDistanceToPlane ( Vector3d planeNormal, Point3d pointInPlane, Point3d point ) [static] :  double
StereoTool.StereoTool ( )

cdk-1.4.0.jar, StmtIterator.class
package com.hp.hpl.jena.rdf.model
StmtIterator.nextStatement ( ) [abstract] :  Statement

cdk-1.4.0.jar, StoreTripleIterator.class
package com.hp.hpl.jena.mem
StoreTripleIterator.remove ( ) :  void
StoreTripleIterator.StoreTripleIterator ( Graph toNotify, Iterator it, NodeToTriplesMapBase X, NodeToTriplesMapBase A, NodeToTriplesMapBase B )

cdk-1.4.0.jar, StrConcat.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
StrConcat.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
StrConcat.getArgLength ( ) :  int
StrConcat.getName ( ) :  String
StrConcat.lex ( Node n, RuleContext context ) :  String
StrConcat.StrConcat ( )

cdk-1.4.0.jar, StringCharacterIterator.class
package com.ibm.icu.text
StringCharacterIterator.clone ( ) :  Object *DEPRECATED*
StringCharacterIterator.current ( ) :  char *DEPRECATED*
StringCharacterIterator.equals ( Object obj ) :  boolean *DEPRECATED*
StringCharacterIterator.first ( ) :  char *DEPRECATED*
StringCharacterIterator.getBeginIndex ( ) :  int *DEPRECATED*
StringCharacterIterator.getEndIndex ( ) :  int *DEPRECATED*
StringCharacterIterator.getIndex ( ) :  int *DEPRECATED*
StringCharacterIterator.hashCode ( ) :  int *DEPRECATED*
StringCharacterIterator.last ( ) :  char *DEPRECATED*
StringCharacterIterator.next ( ) :  char *DEPRECATED*
StringCharacterIterator.previous ( ) :  char *DEPRECATED*
StringCharacterIterator.setIndex ( int p ) :  char *DEPRECATED*
StringCharacterIterator.setText ( String text ) :  void *DEPRECATED*
StringCharacterIterator.StringCharacterIterator ( String text ) *DEPRECATED*
StringCharacterIterator.StringCharacterIterator ( String text, int begin, int end, int pos ) *DEPRECATED*
StringCharacterIterator.StringCharacterIterator ( String text, int pos ) *DEPRECATED*

cdk-1.4.0.jar, StringComparator.class
package com.ibm.icu.text
UTF16.StringComparator.compare ( Object a, Object b ) :  int
UTF16.StringComparator.getCodePointCompare ( ) :  boolean
UTF16.StringComparator.getIgnoreCase ( ) :  boolean
UTF16.StringComparator.getIgnoreCaseOption ( ) :  int
UTF16.StringComparator.setCodePointCompare ( boolean flag ) :  void
UTF16.StringComparator.setIgnoreCase ( boolean ignorecase, int foldcaseoption ) :  void
UTF16.StringComparator.UTF16.StringComparator ( )
UTF16.StringComparator.UTF16.StringComparator ( boolean codepointcompare, boolean ignorecase, int foldcaseoption )

cdk-1.4.0.jar, StringPrep.class
package com.ibm.icu.text
StringPrep.prepare ( UCharacterIterator src, int options ) :  StringBuffer
StringPrep.StringPrep ( InputStream inputStream )

cdk-1.4.0.jar, StringPrepParseException.class
package com.ibm.icu.text
StringPrepParseException.equals ( Object other ) :  boolean
StringPrepParseException.StringPrepParseException ( String message, int error )
StringPrepParseException.StringPrepParseException ( String message, int error, String rules, int pos )
StringPrepParseException.StringPrepParseException ( String message, int error, String rules, int pos, int lineNumber )
StringPrepParseException.toString ( ) :  String

cdk-1.4.0.jar, StringSearch.class
package com.ibm.icu.text
StringSearch.getCollator ( ) :  RuleBasedCollator
StringSearch.getIndex ( ) :  int
StringSearch.getPattern ( ) :  String
StringSearch.handleNext ( int start ) :  int
StringSearch.handlePrevious ( int start ) :  int
StringSearch.isCanonical ( ) :  boolean
StringSearch.reset ( ) :  void
StringSearch.setCanonical ( boolean allowCanonical ) :  void
StringSearch.setCollator ( RuleBasedCollator collator ) :  void
StringSearch.setIndex ( int position ) :  void
StringSearch.setPattern ( String pattern ) :  void
StringSearch.setTarget ( CharacterIterator text ) :  void
StringSearch.StringSearch ( String pattern, CharacterIterator target, Locale locale )
StringSearch.StringSearch ( String pattern, CharacterIterator target, RuleBasedCollator collator )
StringSearch.StringSearch ( String pattern, CharacterIterator target, RuleBasedCollator collator, BreakIterator breakiter )
StringSearch.StringSearch ( String pattern, CharacterIterator target, ULocale locale ) *DEPRECATED*
StringSearch.StringSearch ( String pattern, String target )

cdk-1.4.0.jar, StringTokenizer.class
package com.ibm.icu.util
StringTokenizer.countTokens ( ) :  int
StringTokenizer.hasMoreElements ( ) :  boolean
StringTokenizer.hasMoreTokens ( ) :  boolean
StringTokenizer.nextElement ( ) :  Object
StringTokenizer.nextToken ( ) :  String
StringTokenizer.nextToken ( String delim ) :  String
StringTokenizer.nextToken ( UnicodeSet delim ) :  String
StringTokenizer.StringTokenizer ( String str )
StringTokenizer.StringTokenizer ( String str, String delim )
StringTokenizer.StringTokenizer ( String str, String delim, boolean returndelims )
StringTokenizer.StringTokenizer ( String str, UnicodeSet delim )
StringTokenizer.StringTokenizer ( String str, UnicodeSet delim, boolean returndelims )

cdk-1.4.0.jar, SubstituteLoggerFactory.class
package org.slf4j.helpers
SubstituteLoggerFactory.getLogger ( String name ) :  Logger
SubstituteLoggerFactory.getLoggerNameList ( ) :  List
SubstituteLoggerFactory.SubstituteLoggerFactory ( )

cdk-1.4.0.jar, Sum.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Sum.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Sum.getArgLength ( ) :  int
Sum.getName ( ) :  String
Sum.Sum ( )

cdk-1.4.0.jar, SymbolTable.class
package com.ibm.icu.text
SymbolTable.lookup ( String p1 ) [abstract] :  char[ ]
SymbolTable.lookupMatcher ( int p1 ) [abstract] :  UnicodeMatcher
SymbolTable.parseReference ( String p1, ParsePosition p2, int p3 ) [abstract] :  String

cdk-1.4.0.jar, SymmetryClass.class
package signature
SymmetryClass.addIndex ( int vertexIndex ) :  void
SymmetryClass.compareTo ( Object x0 ) :  int
SymmetryClass.compareTo ( SymmetryClass o ) :  int
SymmetryClass.getMinimal ( int vertexIndex, List used ) :  int
SymmetryClass.getSignatureString ( ) :  String
SymmetryClass.hasSignature ( String otherSignatureString ) :  boolean
SymmetryClass.iterator ( ) :  Iterator
SymmetryClass.size ( ) :  int
SymmetryClass.SymmetryClass ( String signatureString )
SymmetryClass.toString ( ) :  String

cdk-1.4.0.jar, SyntaxError.class
package com.hp.hpl.jena.shared
SyntaxError.SyntaxError ( String message )

cdk-1.4.0.jar, SyntaxException.class
package com.hp.hpl.jena.graph.query.regexptrees
PerlPatternParser.SyntaxException.PerlPatternParser.SyntaxException ( String message )

cdk-1.4.0.jar, SystemOutLoggingTool.class
package org.openscience.cdk.tools
SystemOutLoggingTool.create ( Class sourceClass ) [static] :  ILoggingTool
SystemOutLoggingTool.debug ( Object object ) :  void
SystemOutLoggingTool.debug ( Object object, Object[ ] objects ) :  void
SystemOutLoggingTool.dumpClasspath ( ) :  void
SystemOutLoggingTool.dumpSystemProperties ( ) :  void
SystemOutLoggingTool.error ( Object object ) :  void
SystemOutLoggingTool.error ( Object object, Object[ ] objects ) :  void
SystemOutLoggingTool.fatal ( Object object ) :  void
SystemOutLoggingTool.info ( Object object ) :  void
SystemOutLoggingTool.info ( Object object, Object[ ] objects ) :  void
SystemOutLoggingTool.isDebugEnabled ( ) :  boolean
SystemOutLoggingTool.setDebugEnabled ( boolean enabled ) :  void
SystemOutLoggingTool.setStackLength ( int length ) :  void
SystemOutLoggingTool.SystemOutLoggingTool ( Class classInst )
SystemOutLoggingTool.warn ( Object object ) :  void
SystemOutLoggingTool.warn ( Object object, Object[ ] objects ) :  void

cdk-1.4.0.jar, SystemType.class
package net.sf.jnati
SystemType.equals ( Object obj ) :  boolean
SystemType.get ( String name ) [static] :  SystemType
SystemType.getName ( ) :  String
SystemType.hashCode ( ) :  int
SystemType.isFreeBsd ( ) :  boolean
SystemType.isLinux ( ) :  boolean
SystemType.isMac ( ) :  boolean
SystemType.isUnknown ( ) :  boolean
SystemType.isWindows ( ) :  boolean
SystemType.toString ( ) :  String

cdk-1.4.0.jar, SystemTyper.class
package net.sf.jnati
SystemTyper.detectPlatform ( ) :  SystemType
SystemTyper.getDefaultInstance ( ) [static] :  SystemTyper
SystemTyper.main ( String[ ] args ) [static] :  void
SystemTyper.SystemTyper ( String filename )

cdk-1.4.0.jar, Table.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Table.getName ( ) :  String
Table.headAction ( Node[ ] args, int length, RuleContext context ) :  void
Table.Table ( )

cdk-1.4.0.jar, TableAll.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
TableAll.getName ( ) :  String
TableAll.headAction ( Node[ ] args, int length, RuleContext context ) :  void
TableAll.TableAll ( )

cdk-1.4.0.jar, TargetProcessor.class
package org.openscience.cdk.smsd.algorithm.mcgregor
TargetProcessor.getBondNumB ( ) :  int
TargetProcessor.getCTab1 ( ) :  List
TargetProcessor.getCTab2 ( ) :  List
TargetProcessor.getNeighborBondNumB ( ) :  int
TargetProcessor.process ( IAtomContainer target, List unmapped_atoms_molB, int mappingSize, List i_bond_setB, List c_bond_setB, List mapped_atoms, int counter ) :  void
TargetProcessor.process ( int setNumB, List unmapped_atoms_molB, int newMapingSize, List i_bond_setB, List c_bond_setB, List new_Mapping, int counter, List new_i_bond_setB, List new_c_bond_setB ) :  void
TargetProcessor.TargetProcessor ( List cTab1Copy, List cTab2Copy, String[ ] signArray, int neighbor_bondnum_B, int set_bondnum_B, List iBondNeighborsB, List cBondNeighborsB, int newNeighborNumA, List newINeighborsA, List newCNeighborsA )

cdk-1.4.0.jar, TargetProperties.class
package org.openscience.cdk.smsd.algorithm.vflib.builder
TargetProperties.countNeighbors ( IAtom atom ) :  Integer
TargetProperties.getAtom ( int j ) :  IAtom
TargetProperties.getAtomCount ( ) :  int
TargetProperties.getBond ( IAtom atom1, IAtom atom2 ) :  IBond
TargetProperties.getNeighbors ( IAtom atom ) :  List
TargetProperties.TargetProperties ( IAtomContainer container )

cdk-1.4.0.jar, TestCaseBasic.class
package com.hp.hpl.jena.regression
TestCaseBasic.empty ( Model m ) :  void
TestCaseBasic.soaktest ( ) :  void
TestCaseBasic.test0 ( ) :  void
TestCaseBasic.test1 ( ) :  void
TestCaseBasic.test10 ( ) :  void
TestCaseBasic.test11 ( ) :  void
TestCaseBasic.test12 ( ) :  void
TestCaseBasic.test13 ( ) :  void
TestCaseBasic.test14 ( ) :  void
TestCaseBasic.test15 ( ) :  void
TestCaseBasic.test16 ( ) :  void
TestCaseBasic.test17 ( ) :  void
TestCaseBasic.test18 ( ) :  void
TestCaseBasic.test19 ( ) :  void
TestCaseBasic.test2 ( ) :  void
TestCaseBasic.test3 ( ) :  void
TestCaseBasic.test4 ( ) :  void
TestCaseBasic.test5 ( ) :  void
TestCaseBasic.test6 ( ) :  void
TestCaseBasic.test7 ( ) :  void
TestCaseBasic.test8 ( ) :  void
TestCaseBasic.test9 ( ) :  void
TestCaseBasic.test97 ( ) :  void
TestCaseBasic.TestCaseBasic ( String name )
TestCaseBasic.testMatch ( ) :  void
TestCaseBasic.testNTripleReader ( ) :  void
TestCaseBasic.testReaderInterface ( ) :  void

cdk-1.4.0.jar, TestColoredTreePanel.class
package signature.display
TestColoredTreePanel.dummyTest ( ) :  void
TestColoredTreePanel.main ( String[ ] args ) [static] :  void
TestColoredTreePanel.makeColoredTree ( String signatureString ) [static] :  ColoredTree
TestColoredTreePanel.TestColoredTreePanel ( )

cdk-1.4.0.jar, TestDatabaseModes.class
package com.hp.hpl.jena.assembler.acceptance
TestDatabaseModes.TestDatabaseModes ( String name )
TestDatabaseModes.testRDBModelCreatedWhenMissing ( ) :  void
TestDatabaseModes.testRDBModelFailsIfExists ( ) :  void
TestDatabaseModes.testRDBModelFailsIfMissing ( ) :  void
TestDatabaseModes.testRDBModelOpenedWhenExists ( ) :  void

cdk-1.4.0.jar, TestException.class
package com.hp.hpl.jena.util.junit
TestException.TestException ( )
TestException.TestException ( String msg )
TestException.TestException ( String msg, Throwable cause )
TestException.TestException ( Throwable cause )

cdk-1.4.0.jar, TestFactoryManifest.class
package com.hp.hpl.jena.util.junit
TestFactoryManifest.getTestSuite ( ) :  TestSuite
TestFactoryManifest.makeTest ( Resource p1, Resource p2, String p3, Resource p4, Resource p5 ) [abstract] :  Test
TestFactoryManifest.process ( String filename ) :  TestSuite
TestFactoryManifest.processManifestItem ( Resource manifest, Resource item, String testName, Resource action, Resource result ) :  boolean
TestFactoryManifest.TestFactoryManifest ( )

cdk-1.4.0.jar, TestInputStreamFactory.class
package com.hp.hpl.jena.shared.wg
TestInputStreamFactory.fullyOpen ( String str ) :  InputStream
TestInputStreamFactory.getBase ( ) :  IRI
TestInputStreamFactory.getCreationJava ( ) :  String
TestInputStreamFactory.getMapBase ( ) :  IRI
TestInputStreamFactory.open ( IRI uri ) :  InputStream
TestInputStreamFactory.open ( String str ) :  InputStream
TestInputStreamFactory.openOutput ( String str ) :  OutputStream
TestInputStreamFactory.savable ( ) :  boolean
TestInputStreamFactory.TestInputStreamFactory ( IRI baseDir, IRI getBaseDir )
TestInputStreamFactory.TestInputStreamFactory ( IRI baseDir, String propDir )
TestInputStreamFactory.TestInputStreamFactory ( IRI baseDir, ZipFile zip )

cdk-1.4.0.jar, TestManifest.class
package com.hp.hpl.jena.vocabulary
TestManifest.getURI ( ) [static] :  String
TestManifest.TestManifest ( )

cdk-1.4.0.jar, TestManifestX.class
package com.hp.hpl.jena.vocabulary
TestManifestX.getURI ( ) [static] :  String
TestManifestX.TestManifestX ( )

cdk-1.4.0.jar, testMatch.class
package com.hp.hpl.jena.regression
testMatch.doTest ( GetModel gm1 ) [static] :  void
testMatch.error ( Exception e ) :  void
testMatch.getErrors ( ) :  boolean

cdk-1.4.0.jar, TestMultipleTrees.class
package signature.display
TestMultipleTrees.dummyTest ( ) :  void
TestMultipleTrees.main ( String[ ] args ) [static] :  void
TestMultipleTrees.makePanel ( JFrame f, String signature, int w, int h ) [static] :  void
TestMultipleTrees.TestMultipleTrees ( )

cdk-1.4.0.jar, testNTripleReader.class
package com.hp.hpl.jena.regression
testNTripleReader.doTest ( Model m1 ) [static] :  void
testNTripleReader.empty ( Model m ) :  void
testNTripleReader.error ( String test, int n ) :  void
testNTripleReader.getErrors ( ) :  boolean
testNTripleReader.testNTripleReader ( )

cdk-1.4.0.jar, testReaderInterface.class
package com.hp.hpl.jena.regression
testReaderInterface.doTest ( Model m1 ) [static] :  void
testReaderInterface.error ( String test, int n ) :  void
testReaderInterface.getErrors ( ) :  boolean
testReaderInterface.testReaderInterface ( )

cdk-1.4.0.jar, TestUtils.class
package com.hp.hpl.jena.util.junit
TestUtils.getLiteral ( Resource r, Property p ) [static] :  String
TestUtils.getLiteralOrURI ( Resource r, Property p ) [static] :  String
TestUtils.getResource ( Resource r, Property p ) [static] :  Resource
TestUtils.safeName ( String s ) [static] :  String
TestUtils.TestUtils ( )

cdk-1.4.0.jar, TetrahedralChirality.class
package org.openscience.cdk.stereo
TetrahedralChirality.getBuilder ( ) :  IChemObjectBuilder
TetrahedralChirality.getChiralAtom ( ) :  IAtom
TetrahedralChirality.getLigands ( ) :  IAtom[ ]
TetrahedralChirality.getStereo ( ) :  ITetrahedralChirality.Stereo
TetrahedralChirality.TetrahedralChirality ( IAtom chiralAtom, IAtom[ ] ligandAtoms, ITetrahedralChirality.Stereo chirality )
TetrahedralChirality.toString ( ) :  String

cdk-1.4.0.jar, TetrahedralSign.class
package org.openscience.cdk.stereo
StereoTool.TetrahedralSign.valueOf ( String name ) [static] :  StereoTool.TetrahedralSign
StereoTool.TetrahedralSign.values ( ) [static] :  StereoTool.TetrahedralSign[ ]

cdk-1.4.0.jar, Text.class
package com.hp.hpl.jena.graph.query.regexptrees
Text.create ( char ch ) [static] :  Text
Text.create ( String s ) [static] :  Text
Text.equals ( Object p1 ) [abstract] :  boolean
Text.getString ( ) [abstract] :  String
Text.hashCode ( ) [abstract] :  int
Text.Text ( )

cdk-1.4.0.jar, TextElement.class
package org.openscience.cdk.renderer.elements
TextElement.accept ( IRenderingVisitor visotor ) :  void
TextElement.TextElement ( double xCoord, double yCoord, String text, Color color )

cdk-1.4.0.jar, TextGroupElement.class
package org.openscience.cdk.renderer.elements
TextGroupElement.accept ( IRenderingVisitor v ) :  void
TextGroupElement.addChild ( String text, String subscript, TextGroupElement.Position position ) :  void
TextGroupElement.addChild ( String text, TextGroupElement.Position position ) :  void
TextGroupElement.TextGroupElement ( double x, double y, String text, Color color )

cdk-1.4.0.jar, TimeManager.class
package org.openscience.cdk.smsd.tools
TimeManager.getElapsedTimeInHours ( ) :  double
TimeManager.getElapsedTimeInMilliSeconds ( ) :  double
TimeManager.getElapsedTimeInMinutes ( ) :  double
TimeManager.getElapsedTimeInSeconds ( ) :  double
TimeManager.TimeManager ( )

cdk-1.4.0.jar, TimeOut.class
package org.openscience.cdk.smsd.global
TimeOut.getInstance ( ) [static] :  TimeOut
TimeOut.getTimeOut ( ) :  double
TimeOut.isTimeOutFlag ( ) :  boolean
TimeOut.setTimeOut ( double timeout ) :  void
TimeOut.setTimeOutFlag ( boolean timeOut ) :  void
TimeOut.TimeOut ( )

cdk-1.4.0.jar, TimeZone.class
package com.ibm.icu.util
TimeZone.clone ( ) :  Object
TimeZone.countEquivalentIDs ( String id ) [static] :  int
TimeZone.getAvailableIDs ( ) [static] :  String[ ]
TimeZone.getAvailableIDs ( int rawOffset ) [static] :  String[ ]
TimeZone.getAvailableIDs ( String country ) [static] :  String[ ]
TimeZone.getDefault ( ) [static] :  TimeZone
TimeZone.getDisplayName ( ) :  String
TimeZone.getDisplayName ( boolean daylight, int style ) :  String
TimeZone.getDisplayName ( boolean daylight, int style, Locale locale ) :  String
TimeZone.getDisplayName ( boolean daylight, int style, ULocale locale ) :  String *DEPRECATED*
TimeZone.getDisplayName ( Locale locale ) :  String
TimeZone.getDisplayName ( ULocale locale ) :  String *DEPRECATED*
TimeZone.getDSTSavings ( ) :  int
TimeZone.getEquivalentID ( String id, int index ) [static] :  String
TimeZone.getID ( ) :  String
TimeZone.getOffset ( int p1, int p2, int p3, int p4, int p5, int p6 ) [abstract] :  int
TimeZone.getOffset ( long date ) :  int
TimeZone.getOffset ( long date, boolean local, int[ ] offsets ) :  void
TimeZone.getRawOffset ( ) [abstract] :  int
TimeZone.getTimeZone ( String ID ) [static] :  TimeZone
TimeZone.hasSameRules ( TimeZone other ) :  boolean
TimeZone.inDaylightTime ( Date p1 ) [abstract] :  boolean
TimeZone.setDefault ( TimeZone tz ) [static] :  void
TimeZone.setID ( String ID ) :  void
TimeZone.setRawOffset ( int p1 ) [abstract] :  void
TimeZone.TimeZone ( )
TimeZone.useDaylightTime ( ) [abstract] :  boolean

cdk-1.4.0.jar, Token.class
package com.hp.hpl.jena.n3.turtle.parser
Token.getValue ( ) :  Object
Token.newToken ( int ofKind ) [static] :  Token
Token.newToken ( int ofKind, String image ) [static] :  Token
Token.Token ( )
Token.Token ( int kind )
Token.Token ( int kind, String image )
Token.toString ( ) :  String

cdk-1.4.0.jar, Tokenizer.class
package com.hp.hpl.jena.util
Tokenizer.hasMoreTokens ( ) :  boolean
Tokenizer.main ( String[ ] args ) [static] :  void
Tokenizer.nextToken ( ) :  String
Tokenizer.Tokenizer ( String str, String delim, String literalDelim, boolean returnDelims )

cdk-1.4.0.jar, TokenMgrError.class
package com.hp.hpl.jena.n3.turtle.parser
TokenMgrError.addEscapes ( String str ) [static] :  String
TokenMgrError.getMessage ( ) :  String
TokenMgrError.LexicalError ( boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, char curChar ) [static] :  String
TokenMgrError.TokenMgrError ( )
TokenMgrError.TokenMgrError ( boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, char curChar, int reason )
TokenMgrError.TokenMgrError ( String message, int reason )

cdk-1.4.0.jar, TowardsRingCenterProportion.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.TowardsRingCenterProportion.BasicBondGenerator.TowardsRingCenterProportion ( )
BasicBondGenerator.TowardsRingCenterProportion.getDefault ( ) :  Double
BasicBondGenerator.TowardsRingCenterProportion.getDefault ( ) :  Object

cdk-1.4.0.jar, TrackingTripleIterator.class
package com.hp.hpl.jena.mem
TrackingTripleIterator.next ( ) :  Object
TrackingTripleIterator.next ( ) :  Triple
TrackingTripleIterator.TrackingTripleIterator ( Iterator it )

cdk-1.4.0.jar, TransactionAbortedException.class
package com.hp.hpl.jena.assembler.exceptions
TransactionAbortedException.TransactionAbortedException ( Resource root, Throwable t )

cdk-1.4.0.jar, TransactionHandler.class
package com.hp.hpl.jena.graph
TransactionHandler.abort ( ) [abstract] :  void
TransactionHandler.begin ( ) [abstract] :  void
TransactionHandler.commit ( ) [abstract] :  void
TransactionHandler.executeInTransaction ( Command p1 ) [abstract] :  Object
TransactionHandler.transactionsSupported ( ) [abstract] :  boolean

cdk-1.4.0.jar, TransitiveEngine.class
package com.hp.hpl.jena.reasoner.transitiveReasoner
TransitiveEngine.add ( Triple t ) :  boolean
TransitiveEngine.cacheSubClassUtility ( Finder graph, transitiveReasoner.TransitiveGraphCache spCache, transitiveReasoner.TransitiveGraphCache scCache ) [static] :  boolean
TransitiveEngine.cacheSubPropUtility ( Finder graph, transitiveReasoner.TransitiveGraphCache spCache ) [static] :  boolean
TransitiveEngine.checkOccurance ( Node prop, Graph graph ) :  boolean
TransitiveEngine.delete ( Triple t ) :  boolean
TransitiveEngine.getFinder ( TriplePattern pattern, Finder continuation ) :  Finder
TransitiveEngine.getSubClassCache ( ) :  transitiveReasoner.TransitiveGraphCache
TransitiveEngine.getSubPropertyCache ( ) :  transitiveReasoner.TransitiveGraphCache
TransitiveEngine.insert ( Finder baseData, FGraph newData ) :  Finder
TransitiveEngine.setCaching ( boolean cacheSP, boolean cacheSC ) :  void
TransitiveEngine.TransitiveEngine ( transitiveReasoner.TransitiveEngine tengine )
TransitiveEngine.TransitiveEngine ( transitiveReasoner.TransitiveGraphCache subClassCache, transitiveReasoner.TransitiveGraphCache subPropertyCache )

cdk-1.4.0.jar, TransitiveGraphCache.class
package com.hp.hpl.jena.reasoner.transitiveReasoner
TransitiveGraphCache.addRelation ( Triple t ) :  void
TransitiveGraphCache.cacheAll ( Finder graph, Node predicate ) :  boolean
TransitiveGraphCache.clear ( ) :  void
TransitiveGraphCache.contains ( TriplePattern pattern ) :  boolean
TransitiveGraphCache.deepCopy ( ) :  transitiveReasoner.TransitiveGraphCache
TransitiveGraphCache.dump ( ) :  String
TransitiveGraphCache.find ( TriplePattern pattern ) :  ExtendedIterator
TransitiveGraphCache.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
TransitiveGraphCache.getClosedPredicate ( ) :  Node
TransitiveGraphCache.getDirectPredicate ( ) :  Node
TransitiveGraphCache.isSubject ( Node node ) :  boolean
TransitiveGraphCache.listAllSubjects ( ) :  ExtendedIterator
TransitiveGraphCache.removeRelation ( Triple t ) :  void
TransitiveGraphCache.setCaching ( boolean enable ) :  void
TransitiveGraphCache.TransitiveGraphCache ( Node directPredicate, Node closedPredicate )

cdk-1.4.0.jar, TransitiveInfGraph.class
package com.hp.hpl.jena.reasoner.transitiveReasoner
TransitiveInfGraph.find ( TriplePattern pattern ) :  ExtendedIterator
TransitiveInfGraph.findWithContinuation ( TriplePattern pattern, Finder continuation ) :  ExtendedIterator
TransitiveInfGraph.getCapabilities ( ) :  Capabilities
TransitiveInfGraph.getSchemaGraph ( ) :  Graph
TransitiveInfGraph.graphBaseFind ( Node subject, Node property, Node object ) :  ExtendedIterator
TransitiveInfGraph.performAdd ( Triple t ) :  void
TransitiveInfGraph.performDelete ( Triple t ) :  void
TransitiveInfGraph.prepare ( ) :  void
TransitiveInfGraph.TransitiveInfGraph ( Graph data, transitiveReasoner.TransitiveReasoner reasoner )

cdk-1.4.0.jar, TransitiveReasoner.class
package com.hp.hpl.jena.reasoner.transitiveReasoner
TransitiveReasoner.addDescription ( Model configSpec, Resource base ) :  void
TransitiveReasoner.bind ( Graph data ) :  InfGraph
TransitiveReasoner.bindSchema ( Graph tbox ) :  Reasoner
TransitiveReasoner.bindSchema ( Model tbox ) :  Reasoner
TransitiveReasoner.getGraphCapabilities ( ) :  Capabilities
TransitiveReasoner.getReasonerCapabilities ( ) :  Model
TransitiveReasoner.getSubClassCache ( ) :  transitiveReasoner.TransitiveGraphCache
TransitiveReasoner.getSubPropertyCache ( ) :  transitiveReasoner.TransitiveGraphCache
TransitiveReasoner.getTbox ( ) :  Finder
TransitiveReasoner.setDerivationLogging ( boolean logOn ) :  void
TransitiveReasoner.setParameter ( Property parameter, Object value ) :  void
TransitiveReasoner.supportsProperty ( Property property ) :  boolean
TransitiveReasoner.TransitiveReasoner ( )
TransitiveReasoner.TransitiveReasoner ( Finder tbox, transitiveReasoner.TransitiveGraphCache subClassCache, transitiveReasoner.TransitiveGraphCache subPropertyCache )

cdk-1.4.0.jar, TransitiveReasonerFactory.class
package com.hp.hpl.jena.reasoner.transitiveReasoner
TransitiveReasonerFactory.create ( Resource configuration ) :  Reasoner
TransitiveReasonerFactory.getCapabilities ( ) :  Model
TransitiveReasonerFactory.getURI ( ) :  String
TransitiveReasonerFactory.theInstance ( ) [static] :  ReasonerFactory
TransitiveReasonerFactory.TransitiveReasonerFactory ( )

cdk-1.4.0.jar, Transliterator.class
package com.ibm.icu.text
Transliterator.baseToRules ( boolean escapeUnprintable ) :  String
Transliterator.createFromRules ( String ID, String rules, int dir ) [static] :  Transliterator
Transliterator.filteredTransliterate ( Replaceable text, Transliterator.Position index, boolean incremental ) :  void
Transliterator.finishTransliteration ( Replaceable text, Transliterator.Position index ) :  void
Transliterator.getAvailableIDs ( ) [static] :  Enumeration
Transliterator.getAvailableSources ( ) [static] :  Enumeration
Transliterator.getAvailableTargets ( String source ) [static] :  Enumeration
Transliterator.getAvailableVariants ( String source, String target ) [static] :  Enumeration
Transliterator.getDisplayName ( String ID ) [static] :  String
Transliterator.getDisplayName ( String id, Locale inLocale ) [static] :  String
Transliterator.getDisplayName ( String id, ULocale inLocale ) [static] :  String *DEPRECATED*
Transliterator.getElements ( ) :  Transliterator[ ] *DEPRECATED*
Transliterator.getFilter ( ) :  UnicodeFilter
Transliterator.getID ( ) :  String
Transliterator.getInstance ( String ID ) [static] :  Transliterator
Transliterator.getInstance ( String ID, int dir ) [static] :  Transliterator
Transliterator.getInverse ( ) :  Transliterator
Transliterator.getMaximumContextLength ( ) :  int
Transliterator.getSourceSet ( ) :  UnicodeSet
Transliterator.getTargetSet ( ) :  UnicodeSet
Transliterator.handleGetSourceSet ( ) :  UnicodeSet
Transliterator.handleTransliterate ( Replaceable p1, Transliterator.Position p2, boolean p3 ) [abstract] :  void
Transliterator.registerClass ( String ID, Class transClass, String displayName ) [static] :  void
Transliterator.registerFactory ( String ID, Transliterator.Factory factory ) [static] :  void
Transliterator.registerInstance ( Transliterator trans ) [static] :  void
Transliterator.setFilter ( UnicodeFilter filter ) :  void
Transliterator.setID ( String id ) :  void
Transliterator.setMaximumContextLength ( int a ) :  void
Transliterator.toRules ( boolean escapeUnprintable ) :  String
Transliterator.transliterate ( Replaceable text ) :  void
Transliterator.transliterate ( Replaceable text, int start, int limit ) :  int
Transliterator.transliterate ( Replaceable text, Transliterator.Position index ) :  void
Transliterator.transliterate ( Replaceable text, Transliterator.Position index, int insertion ) :  void
Transliterator.transliterate ( Replaceable text, Transliterator.Position index, String insertion ) :  void
Transliterator.transliterate ( String text ) :  String
Transliterator.Transliterator ( String ID, UnicodeFilter filter )
Transliterator.unregister ( String ID ) [static] :  void

cdk-1.4.0.jar, TreeDrawer.class
package signature.display
TreeDrawer.makeImage ( ColoredTree coloredTree, File file, int w, int h ) [static] :  void
TreeDrawer.makeTreeImages ( List signatureStrings, String directoryPath, int w, int h ) [static] :  void
TreeDrawer.TreeDrawer ( )

cdk-1.4.0.jar, TreeLayout.class
package signature.display
DisplayableColoredTree.TreeLayout.DisplayableColoredTree.TreeLayout ( DisplayableColoredTree p1 )
DisplayableColoredTree.TreeLayout.layout ( DisplayableColoredTree.DrawNode node ) :  int
DisplayableColoredTree.TreeLayout.layoutTree ( DisplayableColoredTree.DrawNode root, int width, int height ) :  void

cdk-1.4.0.jar, TreeQueryPlan.class
package com.hp.hpl.jena.graph.query
TreeQueryPlan.executeTree ( ) [abstract] :  Graph

cdk-1.4.0.jar, Triple.class
package com.hp.hpl.jena.graph
Triple.asTriple ( ) :  Triple
Triple.create ( Node s, Node p, Node o ) [static] :  Triple
Triple.create ( PrefixMapping pm, String fact ) [static] :  Triple
Triple.create ( String fact ) [static] :  Triple
Triple.createMatch ( Node s, Node p, Node o ) [static] :  Triple
Triple.equals ( Object o ) :  boolean
Triple.getMatchObject ( ) :  Node
Triple.getMatchPredicate ( ) :  Node
Triple.getMatchSubject ( ) :  Node
Triple.getObject ( ) :  Node
Triple.getPredicate ( ) :  Node
Triple.getSubject ( ) :  Node
Triple.hashCode ( ) :  int
Triple.hashCode ( Node s, Node p, Node o ) [static] :  int
Triple.isConcrete ( ) :  boolean
Triple.matches ( Node s, Node p, Node o ) :  boolean
Triple.matches ( Triple other ) :  boolean
Triple.objectMatches ( Node o ) :  boolean
Triple.predicateMatches ( Node p ) :  boolean
Triple.sameAs ( Node s, Node p, Node o ) :  boolean
Triple.subjectMatches ( Node s ) :  boolean
Triple.toString ( ) :  String
Triple.toString ( PrefixMapping pm ) :  String
Triple.Triple ( Node s, Node p, Node o )

cdk-1.4.0.jar, TripleBoundary.class
package com.hp.hpl.jena.graph
TripleBoundary.stopAt ( Triple p1 ) [abstract] :  boolean

cdk-1.4.0.jar, TripleBunch.class
package com.hp.hpl.jena.mem
TripleBunch.add ( Triple p1 ) [abstract] :  void
TripleBunch.app ( Domain p1, StageElement p2, MatchOrBind p3 ) [abstract] :  void
TripleBunch.contains ( Triple p1 ) [abstract] :  boolean
TripleBunch.containsBySameValueAs ( Triple p1 ) [abstract] :  boolean
TripleBunch.iterator ( ) [abstract] :  ExtendedIterator
TripleBunch.iterator ( HashCommon.NotifyEmpty p1 ) [abstract] :  ExtendedIterator
TripleBunch.remove ( Triple p1 ) [abstract] :  void
TripleBunch.size ( ) [abstract] :  int

cdk-1.4.0.jar, TripleCache.class
package com.hp.hpl.jena.graph
TripleCache.get ( Node s, Node p, Node o ) :  Triple
TripleCache.put ( Triple t ) :  Triple
TripleCache.TripleCache ( )

cdk-1.4.0.jar, TripleIterator.class
package com.hp.hpl.jena.graph
TripleIterator.nextTriple ( ) [abstract] :  Triple

cdk-1.4.0.jar, TripleMatch.class
package com.hp.hpl.jena.graph
TripleMatch.asTriple ( ) [abstract] :  Triple
TripleMatch.getMatchObject ( ) [abstract] :  Node
TripleMatch.getMatchPredicate ( ) [abstract] :  Node
TripleMatch.getMatchSubject ( ) [abstract] :  Node

cdk-1.4.0.jar, TripleMatchFilter.class
package com.hp.hpl.jena.graph
TripleMatchFilter.accept ( Object x0 ) :  boolean
TripleMatchFilter.accept ( Triple t ) :  boolean
TripleMatchFilter.TripleMatchFilter ( Triple tMatch )

cdk-1.4.0.jar, TripleMatchIterator.class
package com.hp.hpl.jena.graph
TripleMatchIterator.TripleMatchIterator ( Triple m, Iterator iter )

cdk-1.4.0.jar, TriplePattern.class
package com.hp.hpl.jena.reasoner
TriplePattern.asTriple ( ) :  Triple
TriplePattern.asTripleMatch ( ) :  TripleMatch
TriplePattern.compatibleWith ( TriplePattern pattern ) :  boolean
TriplePattern.equals ( Object o ) :  boolean
TriplePattern.getObject ( ) :  Node
TriplePattern.getPredicate ( ) :  Node
TriplePattern.getSubject ( ) :  Node
TriplePattern.hashCode ( ) :  int
TriplePattern.isGround ( ) :  boolean
TriplePattern.isLegal ( ) :  boolean
TriplePattern.sameAs ( Object o ) :  boolean
TriplePattern.simplePrintString ( Node n ) [static] :  String
TriplePattern.simplePrintString ( Triple t ) [static] :  String
TriplePattern.subsumes ( TriplePattern arg ) :  boolean
TriplePattern.toString ( ) :  String
TriplePattern.TriplePattern ( Node subject, Node predicate, Node object )
TriplePattern.TriplePattern ( Triple match )
TriplePattern.TriplePattern ( TripleMatch match )
TriplePattern.variantOf ( TriplePattern pattern ) :  boolean

cdk-1.4.0.jar, TripleSorter.class
package com.hp.hpl.jena.graph.query
TripleSorter.sort ( Triple[ ] p1 ) [abstract] :  Triple[ ]

cdk-1.4.0.jar, TupleItem.class
package com.hp.hpl.jena.util.tuple
TupleItem.asQuotedString ( ) :  String
TupleItem.get ( ) :  String
TupleItem.getDT ( ) :  String
TupleItem.getType ( ) :  int
TupleItem.isAnon ( ) :  boolean
TupleItem.isString ( ) :  boolean
TupleItem.isUnknown ( ) :  boolean
TupleItem.isUnquoted ( ) :  boolean
TupleItem.isURI ( ) :  boolean
TupleItem.toString ( ) :  String

cdk-1.4.0.jar, TupleSet.class
package com.hp.hpl.jena.util.tuple
TupleSet.hasNext ( ) :  boolean
TupleSet.next ( ) :  List
TupleSet.next ( ) :  Object
TupleSet.remove ( ) :  void
TupleSet.TupleSet ( Reader r )

cdk-1.4.0.jar, turtle.class
package jena
turtle.main ( String[ ] args ) [static] :  void
turtle.parse ( String baseURI, InputStream in ) [static] :  void
turtle.parse ( String baseURI, String filename ) [static] :  void
turtle.parseDebug ( String baseURI, Reader reader ) [static] :  void
turtle.turtle ( )

cdk-1.4.0.jar, TurtleEventDump.class
package com.hp.hpl.jena.n3.turtle
TurtleEventDump.endFormula ( int line, int col ) :  void
TurtleEventDump.prefix ( int line, int col, String prefix, String iri ) :  void
TurtleEventDump.startFormula ( int line, int col ) :  void
TurtleEventDump.triple ( int line, int col, Triple triple ) :  void
TurtleEventDump.TurtleEventDump ( )

cdk-1.4.0.jar, TurtleEventHandler.class
package com.hp.hpl.jena.n3.turtle
TurtleEventHandler.endFormula ( int p1, int p2 ) [abstract] :  void
TurtleEventHandler.prefix ( int p1, int p2, String p3, String p4 ) [abstract] :  void
TurtleEventHandler.startFormula ( int p1, int p2 ) [abstract] :  void
TurtleEventHandler.triple ( int p1, int p2, Triple p3 ) [abstract] :  void

cdk-1.4.0.jar, TurtleEventInserter.class
package com.hp.hpl.jena.n3.turtle
TurtleEventInserter.endFormula ( int line, int col ) :  void
TurtleEventInserter.prefix ( int line, int col, String prefix, String iri ) :  void
TurtleEventInserter.startFormula ( int line, int col ) :  void
TurtleEventInserter.triple ( int line, int col, Triple triple ) :  void
TurtleEventInserter.TurtleEventInserter ( Graph graph )

cdk-1.4.0.jar, TurtleEventNull.class
package com.hp.hpl.jena.n3.turtle
TurtleEventNull.endFormula ( int line, int col ) :  void
TurtleEventNull.prefix ( int line, int col, String prefix, String iri ) :  void
TurtleEventNull.startFormula ( int line, int col ) :  void
TurtleEventNull.triple ( int line, int col, Triple triple ) :  void
TurtleEventNull.TurtleEventNull ( )

cdk-1.4.0.jar, TurtleParseException.class
package com.hp.hpl.jena.n3.turtle
TurtleParseException.TurtleParseException ( )
TurtleParseException.TurtleParseException ( String msg )
TurtleParseException.TurtleParseException ( String msg, Throwable cause )
TurtleParseException.TurtleParseException ( Throwable cause )

cdk-1.4.0.jar, TurtleParser.class
package com.hp.hpl.jena.n3.turtle.parser
TurtleParser.AnyDirective ( ) :  Token
TurtleParser.BlankNode ( ) :  Node
TurtleParser.BlankNodePropertyList ( ) :  Node
TurtleParser.BooleanLiteral ( ) :  Node
TurtleParser.Collection ( ) :  Node
TurtleParser.Directive ( ) :  void
TurtleParser.disable_tracing ( ) :  void
TurtleParser.enable_tracing ( ) :  void
TurtleParser.Formula ( ) :  Node
TurtleParser.generateParseException ( ) :  ParseException
TurtleParser.getNextToken ( ) :  Token
TurtleParser.getToken ( int index ) :  Token
TurtleParser.GraphNode ( ) :  Node
TurtleParser.GraphTerm ( ) :  Node
TurtleParser.IRI_REF ( ) :  String
TurtleParser.IRIref ( ) :  String
TurtleParser.Langtag ( ) :  String
TurtleParser.NumericLiteral ( ) :  Node
TurtleParser.Object ( Node s, Node p ) :  void
TurtleParser.ObjectList ( Node s, Node p ) :  void
TurtleParser.parse ( ) :  void
TurtleParser.PrefixedName ( ) :  String
TurtleParser.PropertyList ( Node s ) :  void
TurtleParser.PropertyListNotEmpty ( Node s ) :  void
TurtleParser.RDFLiteral ( ) :  Node
TurtleParser.ReInit ( InputStream stream ) :  void
TurtleParser.ReInit ( InputStream stream, String encoding ) :  void
TurtleParser.ReInit ( Reader stream ) :  void
TurtleParser.ReInit ( TurtleParserTokenManager tm ) :  void
TurtleParser.Statement ( ) :  void
TurtleParser.String ( ) :  String
TurtleParser.Term ( ) :  Node
TurtleParser.TriplesNode ( ) :  Node
TurtleParser.TriplesSameSubject ( ) :  void
TurtleParser.TurtleParser ( InputStream stream )
TurtleParser.TurtleParser ( InputStream stream, String encoding )
TurtleParser.TurtleParser ( Reader stream )
TurtleParser.TurtleParser ( TurtleParserTokenManager tm )
TurtleParser.Var ( ) :  Node
TurtleParser.Verb ( ) :  Node

cdk-1.4.0.jar, TurtleParserTokenManager.class
package com.hp.hpl.jena.n3.turtle.parser
TurtleParserTokenManager.getNextToken ( ) :  Token
TurtleParserTokenManager.jjFillToken ( ) :  Token
TurtleParserTokenManager.ReInit ( JavaCharStream stream ) :  void
TurtleParserTokenManager.ReInit ( JavaCharStream stream, int lexState ) :  void
TurtleParserTokenManager.setDebugStream ( PrintStream ds ) :  void
TurtleParserTokenManager.SwitchTo ( int lexState ) :  void
TurtleParserTokenManager.TurtleParserTokenManager ( JavaCharStream stream )
TurtleParserTokenManager.TurtleParserTokenManager ( JavaCharStream stream, int lexState )

cdk-1.4.0.jar, TurtleReader.class
package com.hp.hpl.jena.n3.turtle
TurtleReader.readWorker ( Model model, Reader reader, String base ) :  void
TurtleReader.TurtleReader ( )

cdk-1.4.0.jar, Type.class
package org.openscience.cdk.renderer.elements.path
Type.valueOf ( String name ) [static] :  Type
Type.values ( ) [static] :  Type[ ]

cdk-1.4.0.jar, TypedStream.class
package com.hp.hpl.jena.util
TypedStream.getCharset ( ) :  String
TypedStream.getInput ( ) :  InputStream
TypedStream.getMimeType ( ) :  String
TypedStream.TypedStream ( InputStream in )
TypedStream.TypedStream ( InputStream in, String header )
TypedStream.TypedStream ( InputStream in, String t, String c )

cdk-1.4.0.jar, TypedValue.class
package com.hp.hpl.jena.datatypes
BaseDatatype.TypedValue.BaseDatatype.TypedValue ( String lexicalValue, String datatypeURI )
BaseDatatype.TypedValue.equals ( Object other ) :  boolean
BaseDatatype.TypedValue.hashCode ( ) :  int

cdk-1.4.0.jar, TypeHandler.class
package org.apache.commons.cli
TypeHandler.createClass ( String str ) [static] :  Class
TypeHandler.createDate ( String str ) [static] :  Date
TypeHandler.createFile ( String str ) [static] :  File
TypeHandler.createFiles ( String str ) [static] :  File[ ]
TypeHandler.createNumber ( String str ) [static] :  Number
TypeHandler.createObject ( String str ) [static] :  Object
TypeHandler.createURL ( String str ) [static] :  URL
TypeHandler.createValue ( String str, Class clazz ) [static] :  Object
TypeHandler.createValue ( String str, Object obj ) [static] :  Object
TypeHandler.TypeHandler ( )

cdk-1.4.0.jar, TypeMapper.class
package com.hp.hpl.jena.datatypes
TypeMapper.getInstance ( ) [static] :  TypeMapper
TypeMapper.getSafeTypeByName ( String uri ) :  RDFDatatype
TypeMapper.getTypeByClass ( Class clazz ) :  RDFDatatype
TypeMapper.getTypeByName ( String uri ) :  RDFDatatype
TypeMapper.getTypeByValue ( Object value ) :  RDFDatatype
TypeMapper.listTypes ( ) :  Iterator
TypeMapper.main ( String[ ] args ) [static] :  void
TypeMapper.registerDatatype ( RDFDatatype type ) :  void
TypeMapper.TypeMapper ( )

cdk-1.4.0.jar, UCharacter.class
package com.ibm.icu.lang
UCharacter.charCount ( int cp ) [static] :  int *DEPRECATED*
UCharacter.codePointAt ( char[ ] text, int index ) [static] :  int *DEPRECATED*
UCharacter.codePointAt ( char[ ] text, int index, int limit ) [static] :  int *DEPRECATED*
UCharacter.codePointAt ( CharSequence seq, int index ) [static] :  int *DEPRECATED*
UCharacter.codePointBefore ( char[ ] text, int index ) [static] :  int *DEPRECATED*
UCharacter.codePointBefore ( char[ ] text, int index, int limit ) [static] :  int *DEPRECATED*
UCharacter.codePointBefore ( CharSequence seq, int index ) [static] :  int *DEPRECATED*
UCharacter.codePointCount ( char[ ] text, int start, int limit ) [static] :  int *DEPRECATED*
UCharacter.codePointCount ( CharSequence text, int start, int limit ) [static] :  int *DEPRECATED*
UCharacter.digit ( int ch ) [static] :  int
UCharacter.digit ( int ch, int radix ) [static] :  int
UCharacter.foldCase ( int ch, boolean defaultmapping ) [static] :  int
UCharacter.foldCase ( int ch, int options ) [static] :  int
UCharacter.foldCase ( String str, boolean defaultmapping ) [static] :  String
UCharacter.foldCase ( String str, int options ) [static] :  String
UCharacter.forDigit ( int digit, int radix ) [static] :  char *DEPRECATED*
UCharacter.getAge ( int ch ) [static] :  VersionInfo
UCharacter.getCharFromExtendedName ( String name ) [static] :  int
UCharacter.getCharFromName ( String name ) [static] :  int
UCharacter.getCharFromName1_0 ( String name ) [static] :  int
UCharacter.getCodePoint ( char char16 ) [static] :  int
UCharacter.getCodePoint ( char lead, char trail ) [static] :  int
UCharacter.getCombiningClass ( int ch ) [static] :  int
UCharacter.getDirection ( int ch ) [static] :  int
UCharacter.getDirectionality ( int cp ) [static] :  byte *DEPRECATED*
UCharacter.getExtendedName ( int ch ) [static] :  String
UCharacter.getExtendedNameIterator ( ) [static] :  ValueIterator
UCharacter.getHanNumericValue ( int ch ) [static] :  int
UCharacter.getIntPropertyMaxValue ( int type ) [static] :  int
UCharacter.getIntPropertyMinValue ( int type ) [static] :  int
UCharacter.getIntPropertyValue ( int ch, int type ) [static] :  int
UCharacter.getISOComment ( int ch ) [static] :  String
UCharacter.getMirror ( int ch ) [static] :  int
UCharacter.getName ( int ch ) [static] :  String
UCharacter.getName ( String s, String separator ) [static] :  String
UCharacter.getName1_0 ( int ch ) [static] :  String
UCharacter.getName1_0Iterator ( ) [static] :  ValueIterator
UCharacter.getNameIterator ( ) [static] :  ValueIterator
UCharacter.getNumericValue ( int ch ) [static] :  int
UCharacter.getPropertyEnum ( String propertyAlias ) [static] :  int
UCharacter.getPropertyName ( int property, int nameChoice ) [static] :  String
UCharacter.getPropertyValueEnum ( int property, String valueAlias ) [static] :  int
UCharacter.getPropertyValueName ( int property, int value, int nameChoice ) [static] :  String
UCharacter.getStringPropertyValue ( int propertyEnum, int codepoint, int nameChoice ) [static] :  String *DEPRECATED*
UCharacter.getType ( int ch ) [static] :  int
UCharacter.getTypeIterator ( ) [static] :  RangeValueIterator
UCharacter.getUnicodeNumericValue ( int ch ) [static] :  double
UCharacter.getUnicodeVersion ( ) [static] :  VersionInfo
UCharacter.hasBinaryProperty ( int ch, int property ) [static] :  boolean
UCharacter.isBaseForm ( int ch ) [static] :  boolean
UCharacter.isBMP ( int ch ) [static] :  boolean
UCharacter.isDefined ( int ch ) [static] :  boolean
UCharacter.isDigit ( int ch ) [static] :  boolean
UCharacter.isHighSurrogate ( char ch ) [static] :  boolean *DEPRECATED*
UCharacter.isIdentifierIgnorable ( int ch ) [static] :  boolean
UCharacter.isISOControl ( int ch ) [static] :  boolean
UCharacter.isJavaIdentifierPart ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isJavaIdentifierStart ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isJavaLetter ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isJavaLetterOrDigit ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isLegal ( int ch ) [static] :  boolean
UCharacter.isLegal ( String str ) [static] :  boolean
UCharacter.isLetter ( int ch ) [static] :  boolean
UCharacter.isLetterOrDigit ( int ch ) [static] :  boolean
UCharacter.isLowerCase ( int ch ) [static] :  boolean
UCharacter.isLowSurrogate ( char ch ) [static] :  boolean *DEPRECATED*
UCharacter.isMirrored ( int ch ) [static] :  boolean
UCharacter.isPrintable ( int ch ) [static] :  boolean
UCharacter.isSpace ( int ch ) [static] :  boolean *DEPRECATED*
UCharacter.isSpaceChar ( int ch ) [static] :  boolean
UCharacter.isSupplementary ( int ch ) [static] :  boolean
UCharacter.isSupplementaryCodePoint ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isSurrogatePair ( char high, char low ) [static] :  boolean *DEPRECATED*
UCharacter.isTitleCase ( int ch ) [static] :  boolean
UCharacter.isUAlphabetic ( int ch ) [static] :  boolean
UCharacter.isULowercase ( int ch ) [static] :  boolean
UCharacter.isUnicodeIdentifierPart ( int ch ) [static] :  boolean
UCharacter.isUnicodeIdentifierStart ( int ch ) [static] :  boolean
UCharacter.isUpperCase ( int ch ) [static] :  boolean
UCharacter.isUUppercase ( int ch ) [static] :  boolean
UCharacter.isUWhiteSpace ( int ch ) [static] :  boolean
UCharacter.isValidCodePoint ( int cp ) [static] :  boolean *DEPRECATED*
UCharacter.isWhitespace ( int ch ) [static] :  boolean
UCharacter.offsetByCodePoints ( char[ ] text, int start, int count, int index, int codePointOffset ) [static] :  int *DEPRECATED*
UCharacter.offsetByCodePoints ( CharSequence text, int index, int codePointOffset ) [static] :  int *DEPRECATED*
UCharacter.toChars ( int cp ) [static] :  char[ ] *DEPRECATED*
UCharacter.toChars ( int cp, char[ ] dst, int dstIndex ) [static] :  int *DEPRECATED*
UCharacter.toCodePoint ( char high, char low ) [static] :  int *DEPRECATED*
UCharacter.toLowerCase ( int ch ) [static] :  int
UCharacter.toLowerCase ( Locale locale, String str ) [static] :  String
UCharacter.toLowerCase ( String str ) [static] :  String
UCharacter.toLowerCase ( ULocale locale, String str ) [static] :  String *DEPRECATED*
UCharacter.toString ( int ch ) [static] :  String
UCharacter.toTitleCase ( int ch ) [static] :  int
UCharacter.toTitleCase ( Locale locale, String str, BreakIterator breakiter ) [static] :  String
UCharacter.toTitleCase ( String str, BreakIterator breakiter ) [static] :  String
UCharacter.toTitleCase ( ULocale locale, String str, BreakIterator titleIter ) [static] :  String *DEPRECATED*
UCharacter.toUpperCase ( int ch ) [static] :  int
UCharacter.toUpperCase ( Locale locale, String str ) [static] :  String
UCharacter.toUpperCase ( String str ) [static] :  String
UCharacter.toUpperCase ( ULocale locale, String str ) [static] :  String *DEPRECATED*

cdk-1.4.0.jar, UCharacterCategory.class
package com.ibm.icu.lang
UCharacterCategory.toString ( int category ) [static] :  String

cdk-1.4.0.jar, UCharacterDirection.class
package com.ibm.icu.lang
UCharacterDirection.toString ( int dir ) [static] :  String

cdk-1.4.0.jar, UCharacterIterator.class
package com.ibm.icu.text
UCharacterIterator.clone ( ) :  Object
UCharacterIterator.current ( ) [abstract] :  int
UCharacterIterator.currentCodePoint ( ) :  int
UCharacterIterator.getCharacterIterator ( ) :  CharacterIterator
UCharacterIterator.getIndex ( ) [abstract] :  int
UCharacterIterator.getInstance ( char[ ] source ) [static] :  UCharacterIterator
UCharacterIterator.getInstance ( char[ ] source, int start, int limit ) [static] :  UCharacterIterator
UCharacterIterator.getInstance ( CharacterIterator source ) [static] :  UCharacterIterator
UCharacterIterator.getInstance ( Replaceable source ) [static] :  UCharacterIterator
UCharacterIterator.getInstance ( String source ) [static] :  UCharacterIterator
UCharacterIterator.getInstance ( StringBuffer source ) [static] :  UCharacterIterator
UCharacterIterator.getLength ( ) [abstract] :  int
UCharacterIterator.getText ( ) :  String
UCharacterIterator.getText ( char[ ] fillIn ) :  int
UCharacterIterator.getText ( char[ ] p1, int p2 ) [abstract] :  int
UCharacterIterator.moveCodePointIndex ( int delta ) :  int
UCharacterIterator.moveIndex ( int delta ) :  int
UCharacterIterator.next ( ) [abstract] :  int
UCharacterIterator.nextCodePoint ( ) :  int
UCharacterIterator.previous ( ) [abstract] :  int
UCharacterIterator.previousCodePoint ( ) :  int
UCharacterIterator.setIndex ( int p1 ) [abstract] :  void
UCharacterIterator.setToLimit ( ) :  void
UCharacterIterator.setToStart ( ) :  void
UCharacterIterator.UCharacterIterator ( )

cdk-1.4.0.jar, UFormat.class
package com.ibm.icu.text
UFormat.getLocale ( ULocale.Type type ) :  ULocale *DEPRECATED*
UFormat.UFormat ( ) *DEPRECATED*

cdk-1.4.0.jar, UForwardCharacterIterator.class
package com.ibm.icu.text
UForwardCharacterIterator.next ( ) [abstract] :  int
UForwardCharacterIterator.nextCodePoint ( ) [abstract] :  int

cdk-1.4.0.jar, ULocale.class
package com.ibm.icu.util
ULocale.acceptLanguage ( String acceptLanguageList, boolean[ ] fallback ) [static] :  ULocale *DEPRECATED*
ULocale.acceptLanguage ( String acceptLanguageList, ULocale[ ] availableLocales, boolean[ ] fallback ) [static] :  ULocale *DEPRECATED*
ULocale.acceptLanguage ( ULocale[ ] acceptLanguageList, boolean[ ] fallback ) [static] :  ULocale *DEPRECATED*
ULocale.acceptLanguage ( ULocale[ ] acceptLanguageList, ULocale[ ] availableLocales, boolean[ ] fallback ) [static] :  ULocale *DEPRECATED*
ULocale.canonicalize ( String localeID ) [static] :  String *DEPRECATED*
ULocale.clone ( ) :  Object *DEPRECATED*
ULocale.createCanonical ( String nonCanonicalID ) [static] :  ULocale *DEPRECATED*
ULocale.equals ( Object obj ) :  boolean *DEPRECATED*
ULocale.forLocale ( Locale loc ) [static] :  ULocale *DEPRECATED*
ULocale.getAvailableLocales ( ) [static] :  ULocale[ ] *DEPRECATED*
ULocale.getBaseName ( ) :  String *DEPRECATED*
ULocale.getBaseName ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getCountry ( ) :  String *DEPRECATED*
ULocale.getCountry ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getDefault ( ) [static] :  ULocale
ULocale.getDisplayCountry ( ) :  String *DEPRECATED*
ULocale.getDisplayCountry ( String localeID, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayCountry ( String localeID, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayCountry ( ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getDisplayKeyword ( String keyword ) [static] :  String *DEPRECATED*
ULocale.getDisplayKeyword ( String keyword, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayKeyword ( String keyword, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayKeywordValue ( String keyword ) :  String *DEPRECATED*
ULocale.getDisplayKeywordValue ( String keyword, ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getDisplayKeywordValue ( String localeID, String keyword, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayKeywordValue ( String localeID, String keyword, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayLanguage ( ) :  String *DEPRECATED*
ULocale.getDisplayLanguage ( String localeID, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayLanguage ( String localeID, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayLanguage ( ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getDisplayName ( ) :  String *DEPRECATED*
ULocale.getDisplayName ( String localeID, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayName ( String localeID, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayName ( ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getDisplayScript ( ) :  String *DEPRECATED*
ULocale.getDisplayScript ( String localeID, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayScript ( String localeID, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayScript ( ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getDisplayVariant ( ) :  String *DEPRECATED*
ULocale.getDisplayVariant ( String localeID, String displayLocaleID ) [static] :  String *DEPRECATED*
ULocale.getDisplayVariant ( String localeID, ULocale displayLocale ) [static] :  String *DEPRECATED*
ULocale.getDisplayVariant ( ULocale displayLocale ) :  String *DEPRECATED*
ULocale.getFallback ( ) :  ULocale *DEPRECATED*
ULocale.getFallback ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getISO3Country ( ) :  String *DEPRECATED*
ULocale.getISO3Country ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getISO3Language ( ) :  String *DEPRECATED*
ULocale.getISO3Language ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getISOCountries ( ) [static] :  String[ ] *DEPRECATED*
ULocale.getISOLanguages ( ) [static] :  String[ ] *DEPRECATED*
ULocale.getKeywords ( ) :  Iterator *DEPRECATED*
ULocale.getKeywords ( String localeID ) [static] :  Iterator *DEPRECATED*
ULocale.getKeywordValue ( String keywordName ) :  String *DEPRECATED*
ULocale.getKeywordValue ( String localeID, String keywordName ) [static] :  String *DEPRECATED*
ULocale.getLanguage ( ) :  String *DEPRECATED*
ULocale.getLanguage ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getName ( ) :  String *DEPRECATED*
ULocale.getName ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getScript ( ) :  String *DEPRECATED*
ULocale.getScript ( String localeID ) [static] :  String *DEPRECATED*
ULocale.getVariant ( ) :  String *DEPRECATED*
ULocale.getVariant ( String localeID ) [static] :  String *DEPRECATED*
ULocale.hashCode ( ) :  int *DEPRECATED*
ULocale.setDefault ( ULocale newLocale ) [static] :  void *DEPRECATED*
ULocale.setKeywordValue ( String keyword, String value ) :  ULocale *DEPRECATED*
ULocale.setKeywordValue ( String localeID, String keyword, String value ) [static] :  String *DEPRECATED*
ULocale.toLocale ( ) :  Locale
ULocale.toString ( ) :  String *DEPRECATED*
ULocale.ULocale ( String a, String b ) *DEPRECATED*
ULocale.ULocale ( String a, String b, String c ) *DEPRECATED*
ULocale.ULocale ( String localeID )

cdk-1.4.0.jar, Unbound.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
Unbound.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
Unbound.getName ( ) :  String
Unbound.Unbound ( )

cdk-1.4.0.jar, UnboundVariableException.class
package com.hp.hpl.jena.graph.query
Query.UnboundVariableException.Query.UnboundVariableException ( Node n )

cdk-1.4.0.jar, UnicodeBlock.class
package com.ibm.icu.lang
UCharacter.UnicodeBlock.forName ( String blockName ) [static] :  UCharacter.UnicodeBlock *DEPRECATED*
UCharacter.UnicodeBlock.getID ( ) :  int
UCharacter.UnicodeBlock.getInstance ( int id ) [static] :  UCharacter.UnicodeBlock
UCharacter.UnicodeBlock.of ( int ch ) [static] :  UCharacter.UnicodeBlock

cdk-1.4.0.jar, UnicodeCompressor.class
package com.ibm.icu.text
UnicodeCompressor.compress ( char[ ] buffer, int start, int limit ) [static] :  byte[ ]
UnicodeCompressor.compress ( char[ ] charBuffer, int charBufferStart, int charBufferLimit, int[ ] charsRead, byte[ ] byteBuffer, int byteBufferStart, int byteBufferLimit ) :  int
UnicodeCompressor.compress ( String buffer ) [static] :  byte[ ]
UnicodeCompressor.reset ( ) :  void
UnicodeCompressor.UnicodeCompressor ( )

cdk-1.4.0.jar, UnicodeDecompressor.class
package com.ibm.icu.text
UnicodeDecompressor.decompress ( byte[ ] buffer ) [static] :  String
UnicodeDecompressor.decompress ( byte[ ] buffer, int start, int limit ) [static] :  char[ ]
UnicodeDecompressor.decompress ( byte[ ] byteBuffer, int byteBufferStart, int byteBufferLimit, int[ ] bytesRead, char[ ] charBuffer, int charBufferStart, int charBufferLimit ) :  int
UnicodeDecompressor.reset ( ) :  void
UnicodeDecompressor.UnicodeDecompressor ( )

cdk-1.4.0.jar, UnicodeFilter.class
package com.ibm.icu.text
UnicodeFilter.contains ( int p1 ) [abstract] :  boolean
UnicodeFilter.matches ( Replaceable text, int[ ] offset, int limit, boolean incremental ) :  int
UnicodeFilter.UnicodeFilter ( )

cdk-1.4.0.jar, UnicodeMatcher.class
package com.ibm.icu.text
UnicodeMatcher.addMatchSetTo ( UnicodeSet p1 ) [abstract] :  void
UnicodeMatcher.matches ( Replaceable p1, int[ ] p2, int p3, boolean p4 ) [abstract] :  int
UnicodeMatcher.matchesIndexValue ( int p1 ) [abstract] :  boolean
UnicodeMatcher.toPattern ( boolean p1 ) [abstract] :  String

cdk-1.4.0.jar, UnicodeSet.class
package com.ibm.icu.text
UnicodeSet._generatePattern ( StringBuffer result, boolean escapeUnprintable ) :  StringBuffer
UnicodeSet.add ( int c ) :  UnicodeSet
UnicodeSet.add ( int start, int end ) :  UnicodeSet
UnicodeSet.add ( String s ) :  UnicodeSet
UnicodeSet.addAll ( Collection source ) :  void
UnicodeSet.addAll ( String s ) :  UnicodeSet
UnicodeSet.addAll ( UnicodeSet c ) :  UnicodeSet
UnicodeSet.addAllTo ( Collection target ) :  void
UnicodeSet.addMatchSetTo ( UnicodeSet toUnionTo ) :  void
UnicodeSet.applyIntPropertyValue ( int prop, int value ) :  UnicodeSet
UnicodeSet.applyPattern ( String pattern ) :  UnicodeSet
UnicodeSet.applyPattern ( String pattern, boolean ignoreWhitespace ) :  UnicodeSet
UnicodeSet.applyPattern ( String pattern, int options ) :  UnicodeSet
UnicodeSet.applyPropertyAlias ( String propertyAlias, String valueAlias ) :  UnicodeSet
UnicodeSet.applyPropertyAlias ( String propertyAlias, String valueAlias, SymbolTable symbols ) :  UnicodeSet *DEPRECATED*
UnicodeSet.charAt ( int index ) :  int
UnicodeSet.clear ( ) :  UnicodeSet
UnicodeSet.clone ( ) :  Object
UnicodeSet.closeOver ( int attribute ) :  UnicodeSet
UnicodeSet.compact ( ) :  UnicodeSet
UnicodeSet.complement ( ) :  UnicodeSet
UnicodeSet.complement ( int c ) :  UnicodeSet
UnicodeSet.complement ( int start, int end ) :  UnicodeSet
UnicodeSet.complement ( String s ) :  UnicodeSet
UnicodeSet.complementAll ( String s ) :  UnicodeSet
UnicodeSet.complementAll ( UnicodeSet c ) :  UnicodeSet
UnicodeSet.contains ( int c ) :  boolean
UnicodeSet.contains ( int start, int end ) :  boolean
UnicodeSet.contains ( String s ) :  boolean
UnicodeSet.containsAll ( String s ) :  boolean
UnicodeSet.containsAll ( UnicodeSet c ) :  boolean
UnicodeSet.containsNone ( int start, int end ) :  boolean
UnicodeSet.containsNone ( String s ) :  boolean
UnicodeSet.containsNone ( UnicodeSet c ) :  boolean
UnicodeSet.containsSome ( int start, int end ) :  boolean
UnicodeSet.containsSome ( String s ) :  boolean
UnicodeSet.containsSome ( UnicodeSet s ) :  boolean
UnicodeSet.equals ( Object o ) :  boolean
UnicodeSet.from ( String s ) [static] :  UnicodeSet
UnicodeSet.fromAll ( String s ) [static] :  UnicodeSet
UnicodeSet.getRangeCount ( ) :  int
UnicodeSet.getRangeEnd ( int index ) :  int
UnicodeSet.getRangeStart ( int index ) :  int
UnicodeSet.hashCode ( ) :  int
UnicodeSet.indexOf ( int c ) :  int
UnicodeSet.isEmpty ( ) :  boolean
UnicodeSet.matches ( Replaceable text, int[ ] offset, int limit, boolean incremental ) :  int
UnicodeSet.matchesIndexValue ( int v ) :  boolean
UnicodeSet.remove ( int c ) :  UnicodeSet
UnicodeSet.remove ( int start, int end ) :  UnicodeSet
UnicodeSet.remove ( String s ) :  UnicodeSet
UnicodeSet.removeAll ( String s ) :  UnicodeSet
UnicodeSet.removeAll ( UnicodeSet c ) :  UnicodeSet
UnicodeSet.resemblesPattern ( String pattern, int pos ) [static] :  boolean
UnicodeSet.retain ( int c ) :  UnicodeSet
UnicodeSet.retain ( int start, int end ) :  UnicodeSet
UnicodeSet.retain ( String s ) :  UnicodeSet
UnicodeSet.retainAll ( String s ) :  UnicodeSet
UnicodeSet.retainAll ( UnicodeSet c ) :  UnicodeSet
UnicodeSet.set ( int start, int end ) :  UnicodeSet
UnicodeSet.set ( UnicodeSet other ) :  UnicodeSet
UnicodeSet.size ( ) :  int
UnicodeSet.toPattern ( boolean escapeUnprintable ) :  String
UnicodeSet.toString ( ) :  String
UnicodeSet.UnicodeSet ( )
UnicodeSet.UnicodeSet ( int start, int end )
UnicodeSet.UnicodeSet ( String pattern )
UnicodeSet.UnicodeSet ( String pattern, boolean ignoreWhitespace )
UnicodeSet.UnicodeSet ( String pattern, int options )
UnicodeSet.UnicodeSet ( String pattern, ParsePosition pos, SymbolTable symbols )
UnicodeSet.UnicodeSet ( String pattern, ParsePosition pos, SymbolTable symbols, int options ) *DEPRECATED*
UnicodeSet.UnicodeSet ( UnicodeSet other )

cdk-1.4.0.jar, UnicodeSetIterator.class
package com.ibm.icu.text
UnicodeSetIterator.getString ( ) :  String
UnicodeSetIterator.loadRange ( int range ) :  void
UnicodeSetIterator.next ( ) :  boolean
UnicodeSetIterator.nextRange ( ) :  boolean
UnicodeSetIterator.reset ( ) :  void
UnicodeSetIterator.reset ( UnicodeSet set ) :  void
UnicodeSetIterator.UnicodeSetIterator ( )
UnicodeSetIterator.UnicodeSetIterator ( UnicodeSet set )

cdk-1.4.0.jar, Union.class
package com.hp.hpl.jena.graph.compose
Union.graphBaseContains ( Triple t ) :  boolean
Union.graphBaseFind ( TripleMatch t ) :  ExtendedIterator
Union.performAdd ( Triple t ) :  void
Union.performDelete ( Triple t ) :  void
Union.Union ( Graph L, Graph R )

cdk-1.4.0.jar, UnionModelAssembler.class
package com.hp.hpl.jena.assembler.assemblers
UnionModelAssembler.openEmptyModel ( Assembler a, Resource root, Mode mode ) :  Model
UnionModelAssembler.UnionModelAssembler ( )

cdk-1.4.0.jar, UniqueExtendedIterator.class
package com.hp.hpl.jena.util.iterator
UniqueExtendedIterator.create ( Iterator it ) [static] :  ExtendedIterator
UniqueExtendedIterator.hasNext ( ) :  boolean
UniqueExtendedIterator.next ( ) :  Object
UniqueExtendedIterator.nextIfNew ( ) :  Object
UniqueExtendedIterator.UniqueExtendedIterator ( Iterator underlying )

cdk-1.4.0.jar, UniversalIsomorphismTester.class
package org.openscience.cdk.isomorphism
UniversalIsomorphismTester.setTimeout ( long timeout ) [static] :  void

cdk-1.4.0.jar, UniversalTimeScale.class
package com.ibm.icu.util
UniversalTimeScale.bigDecimalFrom ( BigDecimal otherTime, int timeScale ) [static] :  BigDecimal *DEPRECATED*
UniversalTimeScale.bigDecimalFrom ( double otherTime, int timeScale ) [static] :  BigDecimal *DEPRECATED*
UniversalTimeScale.bigDecimalFrom ( long otherTime, int timeScale ) [static] :  BigDecimal *DEPRECATED*
UniversalTimeScale.from ( long otherTime, int timeScale ) [static] :  long *DEPRECATED*
UniversalTimeScale.getTimeScaleValue ( int scale, int value ) [static] :  long *DEPRECATED*
UniversalTimeScale.toBigDecimal ( BigDecimal universalTime, int timeScale ) [static] :  BigDecimal *DEPRECATED*
UniversalTimeScale.toBigDecimal ( long universalTime, int timeScale ) [static] :  BigDecimal *DEPRECATED*
UniversalTimeScale.toBigDecimalTrunc ( BigDecimal universalTime, int timeScale ) [static] :  BigDecimal
UniversalTimeScale.toLong ( long universalTime, int timeScale ) [static] :  long *DEPRECATED*

cdk-1.4.0.jar, UnknownEncodingException.class
package com.hp.hpl.jena.assembler.exceptions
UnknownEncodingException.getEncoding ( ) :  String
UnknownEncodingException.UnknownEncodingException ( Resource root, String encoding )

cdk-1.4.0.jar, UnknownPropertyException.class
package com.hp.hpl.jena.shared
UnknownPropertyException.UnknownPropertyException ( String property )

cdk-1.4.0.jar, UnknownReasonerException.class
package com.hp.hpl.jena.assembler.exceptions
UnknownReasonerException.getURL ( ) :  Resource
UnknownReasonerException.UnknownReasonerException ( Resource root, Resource url )

cdk-1.4.0.jar, UnknownStyleException.class
package com.hp.hpl.jena.assembler.exceptions
UnknownStyleException.getStyle ( ) :  Resource
UnknownStyleException.UnknownStyleException ( Resource root, Resource style )

cdk-1.4.0.jar, UnrecognizedOptionException.class
package org.apache.commons.cli
UnrecognizedOptionException.UnrecognizedOptionException ( String message )

cdk-1.4.0.jar, UnsupportedPolymorphismException.class
package com.hp.hpl.jena.enhanced
UnsupportedPolymorphismException.getBadClass ( ) :  Class
UnsupportedPolymorphismException.getBadGraph ( ) :  EnhGraph
UnsupportedPolymorphismException.getBadNode ( ) :  Object
UnsupportedPolymorphismException.UnsupportedPolymorphismException ( EnhNode node, Class type )

cdk-1.4.0.jar, UpdateDeniedException.class
package com.hp.hpl.jena.shared
UpdateDeniedException.getTriple ( ) :  Triple
UpdateDeniedException.UpdateDeniedException ( String message )
UpdateDeniedException.UpdateDeniedException ( String message, Triple triple )

cdk-1.4.0.jar, UResourceBundle.class
package com.ibm.icu.util
UResourceBundle.getBaseName ( ) [abstract] :  String *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName, Locale locale ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName, String localeName ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName, String localeName, ClassLoader root ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName, String localeName, ClassLoader root, boolean disableFallback ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( String baseName, ULocale locale ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getBundleInstance ( ULocale locale ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.getLocale ( ) :  Locale *DEPRECATED*
UResourceBundle.getLocaleID ( ) [abstract] :  String *DEPRECATED*
UResourceBundle.getParent ( ) [abstract] :  UResourceBundle *DEPRECATED*
UResourceBundle.getULocale ( ) [abstract] :  ULocale *DEPRECATED*
UResourceBundle.instantiateBundle ( String baseName, String localeName, ClassLoader root, boolean disableFallback ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.instantiateICUResource ( String baseName, String localeID, ClassLoader root ) [static] :  UResourceBundle *DEPRECATED*
UResourceBundle.setLoadingStatus ( int p1 ) [abstract] :  void
UResourceBundle.UResourceBundle ( ) *DEPRECATED*

cdk-1.4.0.jar, UResourceTypeMismatchException.class
package com.ibm.icu.util
UResourceTypeMismatchException.UResourceTypeMismatchException ( String msg ) *DEPRECATED*

cdk-1.4.0.jar, UriConcat.class
package com.hp.hpl.jena.reasoner.rulesys.builtins
UriConcat.bodyCall ( Node[ ] args, int length, RuleContext context ) :  boolean
UriConcat.getName ( ) :  String
UriConcat.UriConcat ( )

cdk-1.4.0.jar, URIref.class
package com.hp.hpl.jena.util
URIref.decode ( String uri ) [static] :  String
URIref.encode ( String unicode ) [static] :  String
URIref.main ( String[ ] args ) [static] :  void
URIref.URIref ( )

cdk-1.4.0.jar, UrlSource.class
package net.sf.jnati.deploy.source
UrlSource.close ( ) :  void
UrlSource.containsFile ( String path ) :  boolean
UrlSource.getPath ( ) :  File
UrlSource.isLocal ( ) :  boolean
UrlSource.openFile ( String path ) :  InputStream
UrlSource.UrlSource ( URL url, Artefact artefact, String artefactPath )

cdk-1.4.0.jar, UScript.class
package com.ibm.icu.lang
UScript.getCode ( Locale locale ) [static] :  int[ ]
UScript.getCode ( String nameOrAbbrOrLocale ) [static] :  int[ ]
UScript.getCode ( ULocale locale ) [static] :  int[ ] *DEPRECATED*
UScript.getCodeFromName ( String nameOrAbbr ) [static] :  int
UScript.getName ( int scriptCode ) [static] :  String
UScript.getScript ( int codepoint ) [static] :  int
UScript.getShortName ( int scriptCode ) [static] :  String

cdk-1.4.0.jar, UScriptRun.class
package com.ibm.icu.lang
UScriptRun.getScriptCode ( ) :  int
UScriptRun.getScriptLimit ( ) :  int
UScriptRun.getScriptStart ( ) :  int
UScriptRun.next ( ) :  boolean
UScriptRun.reset ( ) :  void
UScriptRun.reset ( char[ ] chars ) :  void
UScriptRun.reset ( char[ ] chars, int start, int count ) :  void
UScriptRun.reset ( int start, int count ) :  void
UScriptRun.reset ( String text ) :  void
UScriptRun.reset ( String text, int start, int count ) :  void
UScriptRun.UScriptRun ( )
UScriptRun.UScriptRun ( char[ ] chars )
UScriptRun.UScriptRun ( char[ ] chars, int start, int count )
UScriptRun.UScriptRun ( String text )
UScriptRun.UScriptRun ( String text, int start, int count )

cdk-1.4.0.jar, UseAntiAliasing.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.UseAntiAliasing.BasicSceneGenerator.UseAntiAliasing ( )
BasicSceneGenerator.UseAntiAliasing.getDefault ( ) :  Boolean
BasicSceneGenerator.UseAntiAliasing.getDefault ( ) :  Object

cdk-1.4.0.jar, UsedFontStyle.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.UsedFontStyle.BasicSceneGenerator.UsedFontStyle ( )
BasicSceneGenerator.UsedFontStyle.getDefault ( ) :  IFontManager.FontStyle
BasicSceneGenerator.UsedFontStyle.getDefault ( ) :  Object

cdk-1.4.0.jar, UTF16.class
package com.ibm.icu.text
UTF16.append ( char[ ] target, int limit, int char32 ) [static] :  int
UTF16.append ( StringBuffer target, int char32 ) [static] :  StringBuffer
UTF16.appendCodePoint ( StringBuffer target, int cp ) [static] :  StringBuffer *DEPRECATED*
UTF16.bounds ( char[ ] source, int start, int limit, int offset16 ) [static] :  int
UTF16.bounds ( String source, int offset16 ) [static] :  int
UTF16.bounds ( StringBuffer source, int offset16 ) [static] :  int
UTF16.charAt ( char[ ] source, int start, int limit, int offset16 ) [static] :  int
UTF16.charAt ( Replaceable source, int offset16 ) [static] :  int
UTF16.charAt ( String source, int offset16 ) [static] :  int
UTF16.charAt ( StringBuffer source, int offset16 ) [static] :  int
UTF16.countCodePoint ( char[ ] source, int start, int limit ) [static] :  int
UTF16.countCodePoint ( String source ) [static] :  int
UTF16.countCodePoint ( StringBuffer source ) [static] :  int
UTF16.delete ( char[ ] target, int limit, int offset16 ) [static] :  int
UTF16.delete ( StringBuffer target, int offset16 ) [static] :  StringBuffer
UTF16.findCodePointOffset ( char[ ] source, int start, int limit, int offset16 ) [static] :  int
UTF16.findCodePointOffset ( String source, int offset16 ) [static] :  int
UTF16.findCodePointOffset ( StringBuffer source, int offset16 ) [static] :  int
UTF16.findOffsetFromCodePoint ( char[ ] source, int start, int limit, int offset32 ) [static] :  int
UTF16.findOffsetFromCodePoint ( String source, int offset32 ) [static] :  int
UTF16.findOffsetFromCodePoint ( StringBuffer source, int offset32 ) [static] :  int
UTF16.getCharCount ( int char32 ) [static] :  int
UTF16.getLeadSurrogate ( int char32 ) [static] :  char
UTF16.getTrailSurrogate ( int char32 ) [static] :  char
UTF16.hasMoreCodePointsThan ( char[ ] source, int start, int limit, int number ) [static] :  boolean
UTF16.hasMoreCodePointsThan ( String source, int number ) [static] :  boolean
UTF16.hasMoreCodePointsThan ( StringBuffer source, int number ) [static] :  boolean
UTF16.indexOf ( String source, int char32 ) [static] :  int
UTF16.indexOf ( String source, int char32, int fromIndex ) [static] :  int
UTF16.indexOf ( String source, String str ) [static] :  int
UTF16.indexOf ( String source, String str, int fromIndex ) [static] :  int
UTF16.insert ( char[ ] target, int limit, int offset16, int char32 ) [static] :  int
UTF16.insert ( StringBuffer target, int offset16, int char32 ) [static] :  StringBuffer
UTF16.isLeadSurrogate ( char char16 ) [static] :  boolean
UTF16.isSurrogate ( char char16 ) [static] :  boolean
UTF16.isTrailSurrogate ( char char16 ) [static] :  boolean
UTF16.lastIndexOf ( String source, int char32 ) [static] :  int
UTF16.lastIndexOf ( String source, int char32, int fromIndex ) [static] :  int
UTF16.lastIndexOf ( String source, String str ) [static] :  int
UTF16.lastIndexOf ( String source, String str, int fromIndex ) [static] :  int
UTF16.moveCodePointOffset ( char[ ] source, int start, int limit, int offset16, int shift32 ) [static] :  int
UTF16.moveCodePointOffset ( String source, int offset16, int shift32 ) [static] :  int
UTF16.moveCodePointOffset ( StringBuffer source, int offset16, int shift32 ) [static] :  int
UTF16.newString ( int[ ] codePoints, int offset, int count ) [static] :  String *DEPRECATED*
UTF16.replace ( String source, int oldChar32, int newChar32 ) [static] :  String
UTF16.replace ( String source, String oldStr, String newStr ) [static] :  String
UTF16.reverse ( StringBuffer source ) [static] :  StringBuffer
UTF16.setCharAt ( char[ ] target, int limit, int offset16, int char32 ) [static] :  int
UTF16.setCharAt ( StringBuffer target, int offset16, int char32 ) [static] :  void
UTF16.valueOf ( char[ ] source, int start, int limit, int offset16 ) [static] :  String
UTF16.valueOf ( int char32 ) [static] :  String
UTF16.valueOf ( String source, int offset16 ) [static] :  String
UTF16.valueOf ( StringBuffer source, int offset16 ) [static] :  String

cdk-1.4.0.jar, Util.class
package com.hp.hpl.jena.graph
Reifier.Util.couldBeStatement ( Node node ) [static] :  boolean
Reifier.Util.isReificationPredicate ( Node node ) [static] :  boolean
Reifier.Util.isReificationType ( Node P, Node O ) [static] :  boolean
Reifier.Util.Reifier.Util ( )
package com.hp.hpl.jena.graph.query
Expression.Util.addVariablesOf ( Set s, Expression e ) [static] :  Set
Expression.Util.containsAllVariablesOf ( Set variables, Expression e ) [static] :  boolean
Expression.Util.equals ( Expression L, Expression R ) [static] :  boolean
Expression.Util.Expression.Util ( )
Expression.Util.sameApply ( Expression L, Expression R ) [static] :  boolean
Expression.Util.sameArgs ( Expression L, Expression R ) [static] :  boolean
Expression.Util.variablesOf ( Expression e ) [static] :  Set
Util.union ( Set x, Set y ) [static] :  Set
Util.Util ( )
Util.variablesOf ( Triple t ) [static] :  Set
package com.hp.hpl.jena.rdf.model
Statement.Util.Statement.Util ( )
package com.hp.hpl.jena.reasoner.rulesys
Util.checkBinaryPredicate ( Property predicate, Resource configuration ) [static] :  Boolean
Util.compareInstants ( Node n1, Node n2 ) [static] :  int
Util.compareNumbers ( Node n1, Node n2 ) [static] :  int
Util.convertBooleanPredicateArg ( Property parameter, Object value ) [static] :  boolean
Util.convertIntegerPredicateArg ( Property parameter, Object value ) [static] :  int
Util.convertList ( Node root, RuleContext context ) [static] :  List
Util.getIntegerPredicate ( Property predicate, Resource configuration ) [static] :  Integer
Util.getIntValue ( Node n ) [static] :  int
Util.getPropValue ( Node root, Node prop, Finder context ) [static] :  Node
Util.getPropValue ( Node root, Node prop, Graph context ) [static] :  Node
Util.getPropValue ( Node root, Node prop, RuleContext context ) [static] :  Node
Util.isInstant ( Node n ) [static] :  boolean
Util.isNumeric ( Node n ) [static] :  boolean
Util.loadRuleParserFromResourceFile ( String filename ) [static] :  Rule.Parser
Util.loadURLFile ( String urlStr ) [static] :  String
Util.makeDoubleNode ( double value ) [static] :  Node
Util.makeIntNode ( int value ) [static] :  Node
Util.makeList ( Node[ ] nodes, Graph graph ) [static] :  Node
Util.makeLongNode ( long value ) [static] :  Node
Util.updateParameter ( Resource config, Property parameter, Object value ) [static] :  void
Util.Util ( )
package org.slf4j.helpers
Util.reportFailure ( String msg ) [static] :  void
Util.reportFailure ( String msg, Throwable t ) [static] :  void
Util.Util ( )

cdk-1.4.0.jar, UUID_nil.class
package com.hp.hpl.jena.shared.uuid
UUID_nil.equals ( Object other ) :  boolean
UUID_nil.getLeastSignificantBits ( ) :  long
UUID_nil.getMostSignificantBits ( ) :  long
UUID_nil.getNil ( ) [static] :  UUID_nil
UUID_nil.getNilString ( ) [static] :  String
UUID_nil.getVariant ( ) :  int
UUID_nil.getVersion ( ) :  int
UUID_nil.toString ( ) :  String

cdk-1.4.0.jar, UUID_V1.class
package com.hp.hpl.jena.shared.uuid
UUID_V1.equals ( Object other ) :  boolean
UUID_V1.getClockSequence ( ) :  long
UUID_V1.getLeastSignificantBits ( ) :  long
UUID_V1.getMostSignificantBits ( ) :  long
UUID_V1.getNode ( ) :  long
UUID_V1.getTimestamp ( ) :  long
UUID_V1.getVariant ( ) :  int
UUID_V1.getVersion ( ) :  int
UUID_V1.hashCode ( ) :  int
UUID_V1.toString ( ) :  String

cdk-1.4.0.jar, UUID_V1_Gen.class
package com.hp.hpl.jena.shared.uuid
UUID_V1_Gen.generate ( ) :  JenaUUID
UUID_V1_Gen.generate ( int version, int variant, long timestamp, long clockSeq, long node ) [static] :  UUID_V1
UUID_V1_Gen.generateV1 ( ) :  UUID_V1
UUID_V1_Gen.parse ( String s ) :  JenaUUID
UUID_V1_Gen.reset ( ) :  void
UUID_V1_Gen.unparse ( UUID_V1 uuid ) [static] :  String
UUID_V1_Gen.UUID_V1_Gen ( )

cdk-1.4.0.jar, UUID_V4.class
package com.hp.hpl.jena.shared.uuid
UUID_V4.equals ( Object other ) :  boolean
UUID_V4.getLeastSignificantBits ( ) :  long
UUID_V4.getMostSignificantBits ( ) :  long
UUID_V4.getVariant ( ) :  int
UUID_V4.getVersion ( ) :  int
UUID_V4.hashCode ( ) :  int
UUID_V4.init ( ) [static] :  void
UUID_V4.reset ( ) [static] :  void
UUID_V4.toString ( ) :  String
UUID_V4.uninit ( ) [static] :  void

cdk-1.4.0.jar, UUID_V4_Gen.class
package com.hp.hpl.jena.shared.uuid
UUID_V4_Gen.generate ( ) :  JenaUUID
UUID_V4_Gen.generateV4 ( ) :  UUID_V4
UUID_V4_Gen.parse ( String s ) :  JenaUUID
UUID_V4_Gen.parseV4 ( String s ) :  UUID_V4
UUID_V4_Gen.reset ( ) :  void
UUID_V4_Gen.unparse ( UUID_V4 uuid ) [static] :  String
UUID_V4_Gen.UUID_V4_Gen ( )

cdk-1.4.0.jar, UUIDFactory.class
package com.hp.hpl.jena.shared.uuid
UUIDFactory.generate ( ) [abstract] :  JenaUUID
UUIDFactory.parse ( String p1 ) [abstract] :  JenaUUID
UUIDFactory.reset ( ) [abstract] :  void

cdk-1.4.0.jar, VABCDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
VABCDescriptor.calculate ( IAtomContainer atomContainer ) :  DescriptorValue
VABCDescriptor.getDescriptorNames ( ) :  String[ ]
VABCDescriptor.getDescriptorResultType ( ) :  IDescriptorResult
VABCDescriptor.getParameterNames ( ) :  String[ ]
VABCDescriptor.getParameters ( ) :  Object[ ]
VABCDescriptor.getParameterType ( String name ) :  Object
VABCDescriptor.getSpecification ( ) :  DescriptorSpecification
VABCDescriptor.setParameters ( Object[ ] params ) :  void
VABCDescriptor.VABCDescriptor ( )

cdk-1.4.0.jar, VABCVolume.class
package org.openscience.cdk.geometry.volume
VABCVolume.calculate ( IMolecule molecule ) [static] :  double
VABCVolume.VABCVolume ( )

cdk-1.4.0.jar, ValidityReport.class
package com.hp.hpl.jena.reasoner
ValidityReport.getReports ( ) [abstract] :  Iterator
ValidityReport.isClean ( ) [abstract] :  boolean
ValidityReport.isValid ( ) [abstract] :  boolean

cdk-1.4.0.jar, Valof.class
package com.hp.hpl.jena.graph.query
Expression.Valof.Expression.Valof ( VariableIndexes map )
Expression.Valof.get ( String name ) :  Object
Expression.Valof.setDomain ( IndexValues d ) :  Expression.Valof

cdk-1.4.0.jar, Valuator.class
package com.hp.hpl.jena.graph.query
Valuator.evalBool ( IndexValues p1 ) [abstract] :  boolean
Valuator.evalObject ( IndexValues p1 ) [abstract] :  Object

cdk-1.4.0.jar, ValuatorSet.class
package com.hp.hpl.jena.graph.query
ValuatorSet.add ( Valuator e ) :  ValuatorSet
ValuatorSet.evalBool ( IndexValues vv ) :  boolean
ValuatorSet.isNonTrivial ( ) :  boolean
ValuatorSet.ValuatorSet ( )

cdk-1.4.0.jar, ValueIterator.class
package com.ibm.icu.util
ValueIterator.next ( ValueIterator.Element p1 ) [abstract] :  boolean
ValueIterator.reset ( ) [abstract] :  void
ValueIterator.setRange ( int p1, int p2 ) [abstract] :  void

cdk-1.4.0.jar, Variable.class
package com.hp.hpl.jena.graph.query
Expression.Variable.Expression.Variable ( )
Expression.Variable.getName ( ) [abstract] :  String
Expression.Variable.isVariable ( ) :  boolean

cdk-1.4.0.jar, VariableIndexes.class
package com.hp.hpl.jena.graph.query
VariableIndexes.indexOf ( String p1 ) [abstract] :  int

cdk-1.4.0.jar, VariableName.class
package com.hp.hpl.jena.graph
Node_Variable.VariableName.equals ( Object other ) :  boolean
Node_Variable.VariableName.hashCode ( ) :  int
Node_Variable.VariableName.Node_Variable.VariableName ( String name )
Node_Variable.VariableName.toString ( ) :  String

cdk-1.4.0.jar, VariableValues.class
package com.hp.hpl.jena.graph.query
VariableValues.get ( String p1 ) [abstract] :  Object

cdk-1.4.0.jar, VCARD.class
package com.hp.hpl.jena.vocabulary
VCARD.getURI ( ) [static] :  String
VCARD.VCARD ( )

cdk-1.4.0.jar, Vector.class
package org.openscience.cdk.math
Vector.add ( Vector b ) :  Vector
Vector.cross ( Vector b ) :  Vector
Vector.dot ( Vector b ) :  double
Vector.duplicate ( ) :  Vector
Vector.getSize ( ) :  int
Vector.length ( ) :  double
Vector.mul ( double b ) :  Vector
Vector.negate ( ) :  Vector
Vector.normalize ( ) :  Vector
Vector.sub ( Vector b ) :  Vector
Vector.toString ( ) :  String
Vector.Vector ( double[ ] array )
Vector.Vector ( int size )
Vector.Vector ( Tuple3d t )

cdk-1.4.0.jar, version.class
package jena
version.main ( String[ ] args ) [static] :  void
version.version ( )

cdk-1.4.0.jar, VersionInfo.class
package com.ibm.icu.util
VersionInfo.compareTo ( VersionInfo other ) :  int
VersionInfo.equals ( Object other ) :  boolean
VersionInfo.getInstance ( int major ) [static] :  VersionInfo
VersionInfo.getInstance ( int major, int minor ) [static] :  VersionInfo
VersionInfo.getInstance ( int major, int minor, int milli ) [static] :  VersionInfo
VersionInfo.getInstance ( int major, int minor, int milli, int micro ) [static] :  VersionInfo
VersionInfo.getInstance ( String version ) [static] :  VersionInfo
VersionInfo.getMajor ( ) :  int
VersionInfo.getMicro ( ) :  int
VersionInfo.getMilli ( ) :  int
VersionInfo.getMinor ( ) :  int
VersionInfo.javaVersion ( ) [static] :  VersionInfo *DEPRECATED*
VersionInfo.toString ( ) :  String

cdk-1.4.0.jar, VFAtomMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
VFAtomMatcher.matches ( TargetProperties p1, IAtom p2 ) [abstract] :  boolean

cdk-1.4.0.jar, VFBondMatcher.class
package org.openscience.cdk.smsd.algorithm.matchers
VFBondMatcher.matches ( TargetProperties p1, IBond p2 ) [abstract] :  boolean

cdk-1.4.0.jar, VFlibMCSHandler.class
package org.openscience.cdk.smsd.algorithm.vflib
VFlibMCSHandler.getAllAtomMapping ( ) :  List
VFlibMCSHandler.getAllMapping ( ) :  List
VFlibMCSHandler.getFirstAtomMapping ( ) :  Map
VFlibMCSHandler.getFirstMapping ( ) :  Map
VFlibMCSHandler.isBondMatchFlag ( ) :  boolean
VFlibMCSHandler.searchMCS ( boolean bondTypeMatch ) :  void
VFlibMCSHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
VFlibMCSHandler.set ( MolHandler reactant, MolHandler product ) :  void
VFlibMCSHandler.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
VFlibMCSHandler.VFlibMCSHandler ( )

cdk-1.4.0.jar, VFlibSubStructureHandler.class
package org.openscience.cdk.smsd.algorithm.vflib
VFlibSubStructureHandler.getAllAtomMapping ( ) :  List
VFlibSubStructureHandler.getAllMapping ( ) :  List
VFlibSubStructureHandler.getFirstAtomMapping ( ) :  Map
VFlibSubStructureHandler.getFirstMapping ( ) :  Map
VFlibSubStructureHandler.isBondMatchFlag ( ) :  boolean
VFlibSubStructureHandler.isSubgraph ( boolean shouldMatchBonds ) :  boolean
VFlibSubStructureHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
VFlibSubStructureHandler.set ( MolHandler reactant, MolHandler product ) :  void
VFlibSubStructureHandler.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
VFlibSubStructureHandler.VFlibSubStructureHandler ( )

cdk-1.4.0.jar, VFlibTurboHandler.class
package org.openscience.cdk.smsd.algorithm.vflib
VFlibTurboHandler.getAllAtomMapping ( ) :  List
VFlibTurboHandler.getAllMapping ( ) :  List
VFlibTurboHandler.getFirstAtomMapping ( ) :  Map
VFlibTurboHandler.getFirstMapping ( ) :  Map
VFlibTurboHandler.isBondMatchFlag ( ) :  boolean
VFlibTurboHandler.isSubgraph ( boolean shouldMatchBonds ) :  boolean
VFlibTurboHandler.set ( IQueryAtomContainer source, IAtomContainer target ) :  void
VFlibTurboHandler.set ( MolHandler reactant, MolHandler product ) :  void
VFlibTurboHandler.setBondMatchFlag ( boolean shouldMatchBonds ) :  void
VFlibTurboHandler.VFlibTurboHandler ( )

cdk-1.4.0.jar, VFMapper.class
package org.openscience.cdk.smsd.algorithm.vflib.map
VFMapper.countMaps ( IAtomContainer target ) :  int
VFMapper.countMaps ( TargetProperties targetMolecule ) :  int
VFMapper.getFirstMap ( IAtomContainer target ) :  Map
VFMapper.getFirstMap ( TargetProperties targetMolecule ) :  Map
VFMapper.getMaps ( IAtomContainer target ) :  List
VFMapper.getMaps ( TargetProperties targetMolecule ) :  List
VFMapper.getTimeManager ( ) [static] :  TimeManager
VFMapper.getTimeout ( ) [static] :  double
VFMapper.hasMap ( IAtomContainer targetMolecule ) :  boolean
VFMapper.hasMap ( TargetProperties targetMolecule ) :  boolean
VFMapper.isTimeOut ( ) [static] :  boolean
VFMapper.setTimeManager ( TimeManager aTimeManager ) [static] :  void
VFMapper.VFMapper ( IAtomContainer queryMolecule, boolean bondMatcher )
VFMapper.VFMapper ( IQuery query )

cdk-1.4.0.jar, VFMCSMapper.class
package org.openscience.cdk.smsd.algorithm.vflib.map
VFMCSMapper.countMaps ( IAtomContainer target ) :  int
VFMCSMapper.countMaps ( TargetProperties targetMolecule ) :  int
VFMCSMapper.getFirstMap ( IAtomContainer target ) :  Map
VFMCSMapper.getFirstMap ( TargetProperties targetMolecule ) :  Map
VFMCSMapper.getMaps ( IAtomContainer target ) :  List
VFMCSMapper.getMaps ( TargetProperties targetMolecule ) :  List
VFMCSMapper.getTimeManager ( ) [static] :  TimeManager
VFMCSMapper.getTimeout ( ) [static] :  double
VFMCSMapper.hasMap ( IAtomContainer targetMolecule ) :  boolean
VFMCSMapper.hasMap ( TargetProperties targetMolecule ) :  boolean
VFMCSMapper.isTimeOut ( ) [static] :  boolean
VFMCSMapper.setTimeManager ( TimeManager aTimeManager ) [static] :  void
VFMCSMapper.VFMCSMapper ( IAtomContainer queryMolecule, boolean bondMatcher )
VFMCSMapper.VFMCSMapper ( IQuery query )

cdk-1.4.0.jar, VFQueryBuilder.class
package org.openscience.cdk.smsd.algorithm.vflib.builder
VFQueryBuilder.addNode ( VFAtomMatcher matcher, IAtom atom ) :  INode
VFQueryBuilder.connect ( INode source, INode target, VFBondMatcher matcher ) :  IEdge
VFQueryBuilder.countEdges ( ) :  int
VFQueryBuilder.countNodes ( ) :  int
VFQueryBuilder.edges ( ) :  Iterable
VFQueryBuilder.getAtom ( INode node ) :  IAtom
VFQueryBuilder.getEdge ( INode source, INode target ) :  IEdge
VFQueryBuilder.getEdge ( int index ) :  IEdge
VFQueryBuilder.getNode ( IAtom atom ) :  INode
VFQueryBuilder.getNode ( int index ) :  INode
VFQueryBuilder.nodes ( ) :  Iterable
VFQueryBuilder.VFQueryBuilder ( )

cdk-1.4.0.jar, VFState.class
package org.openscience.cdk.smsd.algorithm.vflib.map
VFState.backTrack ( ) :  void
VFState.getMap ( ) :  Map
VFState.hasNextCandidate ( ) :  boolean
VFState.isDead ( ) :  boolean
VFState.isGoal ( ) :  boolean
VFState.isMatchFeasible ( Match match ) :  boolean
VFState.nextCandidate ( ) :  Match
VFState.nextState ( Match match ) :  IState
VFState.VFState ( IQuery query, TargetProperties target )

cdk-1.4.0.jar, Violation.class
package com.hp.hpl.jena.iri
Violation.codeName ( ) [abstract] :  String
Violation.component ( ) [abstract] :  String
Violation.getComponent ( ) [abstract] :  int
Violation.getIRI ( ) [abstract] :  IRI
Violation.getLongMessage ( ) [abstract] :  String
Violation.getShortMessage ( ) [abstract] :  String
Violation.getSpecificationURL ( ) [abstract] :  String
Violation.getViolationCode ( ) [abstract] :  int
Violation.isError ( ) [abstract] :  boolean
Violation.Violation ( )

cdk-1.4.0.jar, VirtualGraphBuilder.class
package signature
VirtualGraphBuilder.makeEdge ( int vertexIndex1, int vertexIndex2, String vertexSymbol1, String vertexSymbol2, String edgeLabel ) :  void
VirtualGraphBuilder.makeGraph ( ) :  void
VirtualGraphBuilder.makeVertex ( String label ) :  void
VirtualGraphBuilder.toEdgeString ( ) :  String
VirtualGraphBuilder.VirtualGraphBuilder ( )

cdk-1.4.0.jar, VisitableColoredTree.class
package signature
VisitableColoredTree.accept ( ColoredTreeVisitor p1 ) [abstract] :  void

cdk-1.4.0.jar, VisitableDAG.class
package signature
VisitableDAG.accept ( DAGVisitor p1 ) [abstract] :  void

cdk-1.4.0.jar, VisitedAtoms.class
package org.openscience.cdk.geometry.cip
VisitedAtoms.isVisited ( IAtom atom ) :  boolean
VisitedAtoms.visited ( IAtom atom ) :  void
VisitedAtoms.visited ( VisitedAtoms visitedAtoms ) :  void
VisitedAtoms.VisitedAtoms ( )

cdk-1.4.0.jar, WantDescription.class
package com.hp.hpl.jena.rdf.arp.states
WantDescription.abort ( ) :  void
WantDescription.aPredAndObj ( ANode p, ANode o ) :  void
WantDescription.endElement ( ) :  void
WantDescription.makeSubjectReificationWith ( ANode r ) :  void
WantDescription.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
WantDescription.WantDescription ( FrameI s, AbsXMLContext x )
WantDescription.WantDescription ( FrameI s, AttributeLexer x )
WantDescription.WantDescription ( XMLHandler handler, AbsXMLContext x )

cdk-1.4.0.jar, WantEmpty.class
package com.hp.hpl.jena.rdf.arp.states
WantEmpty.characters ( char[ ] ch, int start, int length ) :  void
WantEmpty.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
WantEmpty.WantEmpty ( FrameI s, AbsXMLContext x )

cdk-1.4.0.jar, WantLiteralValueOrDescription.class
package com.hp.hpl.jena.rdf.arp.states
WantLiteralValueOrDescription.characters ( char[ ] ch, int start, int length ) :  void
WantLiteralValueOrDescription.comment ( char[ ] x0, int x1, int x2 ) :  void
WantLiteralValueOrDescription.endElement ( ) :  void
WantLiteralValueOrDescription.processingInstruction ( String x0, String x1 ) :  void
WantLiteralValueOrDescription.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
WantLiteralValueOrDescription.WantLiteralValueOrDescription ( WantsObjectFrameI s, AbsXMLContext x )

cdk-1.4.0.jar, WantPropertyElement.class
package com.hp.hpl.jena.rdf.arp.states
WantPropertyElement.abort ( ) :  void
WantPropertyElement.aPredAndObj ( ANode p, ANode o ) :  void
WantPropertyElement.endElement ( ) :  void
WantPropertyElement.makeSubjectReificationWith ( ANode r ) :  void
WantPropertyElement.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
WantPropertyElement.theObject ( ANode o ) :  void
WantPropertyElement.WantPropertyElement ( HasSubjectFrameI s, AbsXMLContext x )

cdk-1.4.0.jar, WantTopLevelDescription.class
package com.hp.hpl.jena.rdf.arp.states
WantTopLevelDescription.abort ( ) :  void
WantTopLevelDescription.endElement ( ) :  void
WantTopLevelDescription.WantTopLevelDescription ( FrameI s, AttributeLexer x )
WantTopLevelDescription.WantTopLevelDescription ( XMLHandler handler, AbsXMLContext x )

cdk-1.4.0.jar, WantTypedLiteral.class
package com.hp.hpl.jena.rdf.arp.states
WantTypedLiteral.afterChild ( ) :  void
WantTypedLiteral.characters ( char[ ] x0, int x1, int x2 ) :  void
WantTypedLiteral.comment ( char[ ] x0, int x1, int x2 ) :  void
WantTypedLiteral.endElement ( ) :  void
WantTypedLiteral.processingInstruction ( String x0, String x1 ) :  void
WantTypedLiteral.startElement ( String uri, String localName, String rawName, Attributes atts ) :  FrameI
WantTypedLiteral.WantTypedLiteral ( WantsObjectFrameI p, String datatypeURI, AbsXMLContext ap )

cdk-1.4.0.jar, WedgeLineElement.class
package org.openscience.cdk.renderer.elements
WedgeLineElement.accept ( IRenderingVisitor v ) :  void
WedgeLineElement.WedgeLineElement ( double x1, double y1, double x2, double y2, double width, boolean dashed, WedgeLineElement.Direction direction, Color color )
WedgeLineElement.WedgeLineElement ( LineElement element, boolean dashed, WedgeLineElement.Direction direction, Color color )

cdk-1.4.0.jar, WedgeWidth.class
package org.openscience.cdk.renderer.generators
BasicBondGenerator.WedgeWidth.BasicBondGenerator.WedgeWidth ( )
BasicBondGenerator.WedgeWidth.getDefault ( ) :  Double
BasicBondGenerator.WedgeWidth.getDefault ( ) :  Object

cdk-1.4.0.jar, Work.class
package com.hp.hpl.jena.graph.query
PatternStageBase.Work.PatternStageBase.Work ( PatternStageBase source, Pipe sink, Pipe e, StageElement p4 )
PatternStageBase.Work.run ( ) :  void

cdk-1.4.0.jar, WrappedException.class
package com.hp.hpl.jena.shared
WrappedException.WrappedException ( String message, Throwable cause )
WrappedException.WrappedException ( Throwable cause )

cdk-1.4.0.jar, WrappedHashMap.class
package com.hp.hpl.jena.mem
WrappedHashMap.clear ( ) :  void
WrappedHashMap.get ( Object key ) :  TripleBunch
WrappedHashMap.keyIterator ( ) :  ExtendedIterator
WrappedHashMap.put ( Object key, TripleBunch value ) :  void
WrappedHashMap.remove ( Object key ) :  void
WrappedHashMap.size ( ) :  long
WrappedHashMap.WrappedHashMap ( )

cdk-1.4.0.jar, WrappedIOException.class
package com.hp.hpl.jena.shared
WrappedIOException.WrappedIOException ( IOException cause )
WrappedIOException.WrappedIOException ( String message, IOException cause )

cdk-1.4.0.jar, WrappedIterator.class
package com.hp.hpl.jena.util.iterator
WrappedIterator.close ( ) :  void
WrappedIterator.close ( Iterator it ) [static] :  void
WrappedIterator.create ( Iterator it ) [static] :  ExtendedIterator
WrappedIterator.createNoRemove ( Iterator it ) [static] :  WrappedIterator
WrappedIterator.forTestingOnly_getBase ( ) :  Iterator
WrappedIterator.hasNext ( ) :  boolean
WrappedIterator.next ( ) :  Object
WrappedIterator.remove ( ) :  void
WrappedIterator.WrappedIterator ( Iterator base )
WrappedIterator.WrappedIterator ( Iterator base, boolean removeDenied )

cdk-1.4.0.jar, WriterTest.class
package signature.chemistry
WriterTest.minimalTest ( ) :  void
WriterTest.WriterTest ( )

cdk-1.4.0.jar, XSD.class
package com.hp.hpl.jena.vocabulary
XSD.getURI ( ) [static] :  String
XSD.XSD ( )

cdk-1.4.0.jar, XSDbase64Binary.class
package com.hp.hpl.jena.datatypes.xsd
XSDbase64Binary.getHashCode ( LiteralLabel lit ) :  int
XSDbase64Binary.isEqual ( LiteralLabel value1, LiteralLabel value2 ) :  boolean
XSDbase64Binary.isValidValue ( Object valueForm ) :  boolean
XSDbase64Binary.unparse ( Object value ) :  String
XSDbase64Binary.XSDbase64Binary ( String typeName )

cdk-1.4.0.jar, XSDDatatype.class
package com.hp.hpl.jena.datatypes.xsd
XSDDatatype.convertValidatedDataValue ( ValidatedInfo validatedInfo ) :  Object
XSDDatatype.extendedTypeDefinition ( ) :  Object
XSDDatatype.getHashCode ( byte[ ] bytes ) :  int
XSDDatatype.getJavaClass ( ) :  Class
XSDDatatype.isBaseTypeCompatible ( LiteralLabel lit ) :  boolean
XSDDatatype.isEqual ( LiteralLabel value1, LiteralLabel value2 ) :  boolean
XSDDatatype.isValidLiteral ( LiteralLabel lit ) :  boolean
XSDDatatype.loadUserDefined ( String uri, Reader reader, String encoding, TypeMapper tm ) [static] :  List
XSDDatatype.loadUserDefined ( String uri, String encoding, TypeMapper tm ) [static] :  List
XSDDatatype.loadXSDSimpleTypes ( TypeMapper tm ) [static] :  void
XSDDatatype.main ( String[ ] args ) [static] :  void
XSDDatatype.parse ( String lexicalForm ) :  Object
XSDDatatype.parseValidated ( String lexical ) :  Object
XSDDatatype.suitableInteger ( long number ) [static] :  Number
XSDDatatype.suitableInteger ( String lexical ) :  Number
XSDDatatype.trimPlus ( String str ) [static] :  String
XSDDatatype.unparse ( Object value ) :  String
XSDDatatype.XSDDatatype ( String typeName )
XSDDatatype.XSDDatatype ( String typeName, Class javaClass )
XSDDatatype.XSDDatatype ( XSSimpleType xstype, String namespace )

cdk-1.4.0.jar, XSDDateTime.class
package com.hp.hpl.jena.datatypes.xsd
XSDDateTime.asCalendar ( ) :  Calendar
XSDDateTime.getDays ( ) :  int
XSDDateTime.getFullSeconds ( ) :  int
XSDDateTime.getHours ( ) :  int
XSDDateTime.getMinutes ( ) :  int
XSDDateTime.getMonths ( ) :  int
XSDDateTime.getNarrowedDatatype ( ) :  XSDDatatype
XSDDateTime.getSeconds ( ) :  double
XSDDateTime.getTimePart ( ) :  double
XSDDateTime.getYears ( ) :  int
XSDDateTime.narrowType ( XSDDatatype dt ) :  void
XSDDateTime.timeLexicalForm ( ) :  String
XSDDateTime.toString ( ) :  String
XSDDateTime.XSDDateTime ( Calendar date )
XSDDateTime.XSDDateTime ( Object value, int mask )

cdk-1.4.0.jar, XSDDuration.class
package com.hp.hpl.jena.datatypes.xsd
XSDDuration.compareDates ( int[ ] date1, int[ ] date2, boolean strict ) :  short
XSDDuration.getBigSeconds ( ) :  BigDecimal
XSDDuration.getDays ( ) :  int
XSDDuration.getFullSeconds ( ) :  int
XSDDuration.getHours ( ) :  int
XSDDuration.getMinutes ( ) :  int
XSDDuration.getMonths ( ) :  int
XSDDuration.getSeconds ( ) :  double
XSDDuration.getTimePart ( ) :  double
XSDDuration.getYears ( ) :  int
XSDDuration.toString ( ) :  String
XSDDuration.XSDDuration ( Object value )

cdk-1.4.0.jar, XSDhexBinary.class
package com.hp.hpl.jena.datatypes.xsd
XSDhexBinary.getHashCode ( LiteralLabel lit ) :  int
XSDhexBinary.isEqual ( LiteralLabel value1, LiteralLabel value2 ) :  boolean
XSDhexBinary.isValidValue ( Object valueForm ) :  boolean
XSDhexBinary.unparse ( Object value ) :  String
XSDhexBinary.XSDhexBinary ( String typeName )

cdk-1.4.0.jar, ZeroOrMore.class
package com.hp.hpl.jena.graph.query.regexptrees
ZeroOrMore.equals ( Object x ) :  boolean
ZeroOrMore.hashCode ( ) :  int
ZeroOrMore.toString ( ) :  String
ZeroOrMore.ZeroOrMore ( RegexpTree operand )

cdk-1.4.0.jar, ZoomFactor.class
package org.openscience.cdk.renderer.generators
BasicSceneGenerator.ZoomFactor.BasicSceneGenerator.ZoomFactor ( )
BasicSceneGenerator.ZoomFactor.getDefault ( ) :  Double
BasicSceneGenerator.ZoomFactor.getDefault ( ) :  Object

to the top

Removed Methods (4833)

cdk-1.2.10.jar, AbstractUserClass.class
package org.omegahat.Environment.Language.UserClasses
AbstractUserClass.AbstractUserClass ( )
AbstractUserClass.AbstractUserClass ( int p1 )
AbstractUserClass.AbstractUserClass ( String p1 )
AbstractUserClass.AbstractUserClass ( String p1, Environment.Language.UserClasses.AbstractUserClass p2 )
AbstractUserClass.AbstractUserClass ( String p1, Environment.Language.UserClasses.AbstractUserClass[ ] p2 )
AbstractUserClass.AbstractUserClass ( String p1, Vector p2 )
AbstractUserClass.addChangeListener ( Environment.Language.UserClasses.UserClassChangeListener p1 ) :  Vector
AbstractUserClass.addConstructor ( Environment.Language.Function p1 ) :  Environment.Language.Method
AbstractUserClass.addConstructor ( Environment.Language.Method p1 ) :  Environment.Language.Method
AbstractUserClass.addMethod ( Environment.Language.Function p1 ) :  Environment.Language.Method
AbstractUserClass.addMethod ( String p1, Environment.Language.Function p2 ) :  Environment.Language.Method
AbstractUserClass.classRepresentationChanged ( Environment.Language.UserClasses.UserClassChangeEvent p1, boolean p2 ) :  boolean
AbstractUserClass.constructors ( ) :  Environment.Language.Method
AbstractUserClass.constructors ( Environment.Language.Method p1 ) :  Environment.Language.Method
AbstractUserClass.getDeclaredFields ( ) :  Vector
AbstractUserClass.getDynamicField ( String p1 ) :  Object
AbstractUserClass.getField ( String p1 ) :  Environment.Language.UserClasses.OmegaField
AbstractUserClass.getFields ( ) :  Vector
AbstractUserClass.getFields ( boolean p1 ) :  Vector
AbstractUserClass.getMethod ( String p1 ) :  Environment.Language.Method
AbstractUserClass.getSuperclass ( ) :  Vector
AbstractUserClass.invoke ( String p1, Environment.Parser.Parse.List p2, Environment.Interpreter.Evaluator p3 ) :  Object
AbstractUserClass.invoke ( String p1, Object[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Object
AbstractUserClass.listeners ( ) :  Vector
AbstractUserClass.listeners ( Vector p1 ) :  Vector
AbstractUserClass.mergeMethods ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
AbstractUserClass.methods ( ) :  Environment.Databases.Database
AbstractUserClass.methods ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
AbstractUserClass.name ( ) :  String
AbstractUserClass.name ( String p1 ) :  String
AbstractUserClass.processSuperClass ( Environment.Language.UserClasses.UserClass p1, boolean p2 ) :  Environment.Language.UserClasses.UserClass
AbstractUserClass.removeChangeListener ( Environment.Language.UserClasses.UserClassChangeListener p1 ) :  boolean
AbstractUserClass.setDynamicField ( String p1, Object p2 ) :  Object
AbstractUserClass.setField ( Environment.Language.UserClasses.OmegaField p1 ) :  Environment.Language.UserClasses.OmegaField
AbstractUserClass.setField ( String p1 ) :  Environment.Language.UserClasses.OmegaField
AbstractUserClass.setField ( String p1, Class p2 ) :  Environment.Language.UserClasses.OmegaField
AbstractUserClass.setField ( String p1, String p2 ) :  Environment.Language.UserClasses.OmegaField
AbstractUserClass.staticFields ( ) :  Environment.Databases.Database
AbstractUserClass.staticFields ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
AbstractUserClass.staticFields ( int p1 ) :  Environment.Databases.Database
AbstractUserClass.superClass ( ) :  Vector
AbstractUserClass.superClass ( Environment.Language.UserClasses.AbstractUserClass p1 ) :  Vector
AbstractUserClass.superClass ( Vector p1 ) :  Vector
AbstractUserClass.superClass ( Vector p1, boolean p2 ) :  Vector

cdk-1.2.10.jar, Activable.class
package org.omegahat.Environment.Databases
Activable.getState ( ) [abstract] :  int
Activable.setState ( int p1 ) [abstract] :  int

cdk-1.2.10.jar, Addable.class
package org.omegahat.Environment.DataStructures
Addable.addValue ( Object p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, AngleBending.class
package org.openscience.cdk.modeling.forcefield
AngleBending.AngleBending ( )
AngleBending.functionMMFF94SumEA ( GVector coord3d ) :  double
AngleBending.get2ndOrderErrorApproximateGradientMMFF94SumEA ( ) :  GVector
AngleBending.get2ndOrderErrorApproximateHessianMMFF94SumEA ( ) :  GMatrix
AngleBending.get5thOrderErrorApproximateGradientMMFF94SumEA ( ) :  GVector
AngleBending.getAngleBending2ndOrderErrorApproximateGradient ( ) :  double[ ][ ]
AngleBending.getAngleBending2ndOrderErrorApproximateHessian ( ) :  double[ ][ ][ ]
AngleBending.getAngleBendingFirstDerivative ( ) :  double[ ][ ]
AngleBending.getAngleBendingSecondDerivative ( ) :  double[ ][ ][ ]
AngleBending.getDeltav ( ) :  double[ ]
AngleBending.getGradientMMFF94SumEA ( ) :  GVector
AngleBending.getHessianMMFF94SumEA ( ) :  GMatrix
AngleBending.set2ndOrderErrorApproximateGradientMMFF94SumEA ( GVector coord3d ) :  void
AngleBending.set2ndOrderErrorApproximateHessianMMFF94SumEA ( GVector coord3d ) :  void
AngleBending.set5thOrderErrorApproximateGradientMMFF94SumEA ( GVector coord3d ) :  void
AngleBending.setAngleBending2ndOrderErrorApproximateGradient ( GVector coord3d ) :  void
AngleBending.setAngleBending2ndOrderErrorApproximateHessian ( GVector coord3d ) :  void
AngleBending.setAngleBendingFirstDerivative ( GVector coord3d ) :  void
AngleBending.setAngleBendingFlag ( boolean flag ) :  void
AngleBending.setAngleBendingSecondDerivative ( GVector coord3d ) :  void
AngleBending.setDeltav ( GVector coord3d ) :  void
AngleBending.setGradientMMFF94SumEA ( GVector coord3d ) :  void
AngleBending.setHessianMMFF94SumEA ( GVector coord3d ) :  void
AngleBending.setMMFF94AngleBendingParameters ( IAtomContainer molecule, Map parameterSet, boolean angleBendingFlag ) :  void

cdk-1.2.10.jar, AnonymousReference.class
package org.omegahat.Interfaces.NativeInterface
AnonymousReference.AnonymousReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
AnonymousReference.AnonymousReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2, Environment.Databases.Database p3, String p4 )

cdk-1.2.10.jar, ArchiveClassList.class
package org.omegahat.Environment.Tools.ClassList
ArchiveClassList.add ( Object p1 ) :  Object
ArchiveClassList.add ( ZipEntry p1 ) :  Object
ArchiveClassList.ArchiveClassList ( )
ArchiveClassList.ArchiveClassList ( File p1 )
ArchiveClassList.readExternal ( ObjectInput p1 ) :  void
ArchiveClassList.writeExternal ( ObjectOutput p1 ) :  void
ArchiveClassList.zipFile ( ) :  ZipFile
ArchiveClassList.zipFile ( File p1 ) :  ZipFile
ArchiveClassList.zipFile ( ZipFile p1 ) :  ZipFile

cdk-1.2.10.jar, ArchiveEntry.class
package org.omegahat.Environment.IO
ArchiveEntry.ArchiveEntry ( File p1, String p2 )
ArchiveEntry.entry ( ) :  ZipEntry
ArchiveEntry.entry ( boolean p1 ) :  ZipEntry
ArchiveEntry.entry ( ZipEntry p1 ) :  ZipEntry
ArchiveEntry.entryName ( ) :  String
ArchiveEntry.entryName ( String p1 ) :  String
ArchiveEntry.inputStream ( ) :  InputStream

cdk-1.2.10.jar, ArgList.class
package org.omegahat.Environment.Parser.Parse
ArgList.ArgList ( )
ArgList.ArgList ( AST p1 )
ArgList.ArgList ( AST p1, boolean p2 )
ArgList.ArgList ( Environment.Parser.Parse.List p1 )
ArgList.ArgList ( Environment.Parser.Parse.List p1, boolean p2 )
ArgList.ArgList ( Object p1 )
ArgList.ArgList ( Object[ ] p1 )
ArgList.hasNames ( ) :  boolean
ArgList.toString ( ) :  String

cdk-1.2.10.jar, ArrayAccess.class
package org.omegahat.Environment.Parser.Parse
ArrayAccess.add ( Object p1 ) :  void
ArrayAccess.array ( Environment.Interpreter.Evaluator p1 ) :  Object
ArrayAccess.ArrayAccess ( Object p1, Object p2 )
ArrayAccess.ArrayAccess ( Object p1, Object p2, boolean p3 )
ArrayAccess.assign ( Environment.Parser.Parse.ExpressionInt p1, Environment.Interpreter.Evaluator p2 ) :  Object
ArrayAccess.assign ( Object p1, Environment.Interpreter.Evaluator p2 ) :  Object
ArrayAccess.classInit ( ) [static] :  Class
ArrayAccess.doubleBrackets ( ) :  boolean
ArrayAccess.doubleBrackets ( boolean p1 ) :  boolean
ArrayAccess.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ArrayAccess.get ( Object p1, Environment.Parser.Parse.List p2, Environment.Interpreter.Evaluator p3 ) :  Object
ArrayAccess.get ( Object p1, Environment.Parser.Parse.List p2, int p3, Environment.Interpreter.Evaluator p4 ) :  Object
ArrayAccess.get ( Object p1, Environment.Parser.Parse.List p2, int p3, int p4, Environment.Interpreter.Evaluator p5 ) :  Object
ArrayAccess.getFromArray ( Object p1, Environment.Parser.Parse.List p2, int p3, int p4 ) :  Object
ArrayAccess.indeces ( Environment.Interpreter.Evaluator p1 ) :  Environment.Parser.Parse.List
ArrayAccess.name ( ) :  Environment.Parser.Parse.Name
ArrayAccess.name ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
ArrayAccess.put ( Object p1, Environment.Parser.Parse.List p2, int p3, Object p4 ) :  void
ArrayAccess.render ( boolean p1 ) :  String
ArrayAccess.show ( Object p1 ) :  void
ArrayAccess.subset ( Hashtable p1, Environment.Parser.Parse.List p2, int p3, int p4 ) :  Object
ArrayAccess.subset ( Vector p1, Environment.Parser.Parse.List p2, int p3, int p4 ) :  Object
ArrayAccess.subsetGeneric ( Object p1, Environment.Parser.Parse.List p2, int p3, int p4, Environment.Interpreter.Evaluator p5 ) :  Object
ArrayAccess.subsetGeneric ( Object p1, int p2 ) :  Object
ArrayAccess.subsetGeneric ( Object p1, Object p2 ) :  Object
ArrayAccess.subsetGeneric ( Object p1, String p2 ) :  Object
ArrayAccess.toString ( ) :  String

cdk-1.2.10.jar, ArrayAccessAssignExpression.class
package org.omegahat.Environment.Parser.Parse
ArrayAccessAssignExpression.ArrayAccessAssignExpression ( Environment.Parser.Parse.ArrayAccess p1, Object p2, int p3 )
ArrayAccessAssignExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object

cdk-1.2.10.jar, ArrayAccessInfix.class
package org.omegahat.Environment.Parser.Parse
ArrayAccessInfix.ArrayAccessInfix ( Environment.Parser.Parse.ArrayAccess p1, int p2 )
ArrayAccessInfix.ArrayAccessInfix ( Environment.Parser.Parse.ArrayAccess p1, int p2, boolean p3 )
ArrayAccessInfix.get ( Object p1, Environment.Parser.Parse.List p2, int p3, int p4, Environment.Interpreter.Evaluator p5 ) :  Object
ArrayAccessInfix.isPrefix ( ) :  boolean
ArrayAccessInfix.isPrefix ( boolean p1 ) :  boolean
ArrayAccessInfix.operate ( Object p1, Object p2 ) :  Object
ArrayAccessInfix.operator ( ) :  int
ArrayAccessInfix.operator ( int p1 ) :  int
ArrayAccessInfix.toString ( ) :  String

cdk-1.2.10.jar, ArrayConstructorExpression.class
package org.omegahat.Environment.Parser.Parse
ArrayConstructorExpression.ArrayConstructorExpression ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.ArrayDimensionExpression p2 )
ArrayConstructorExpression.ArrayConstructorExpression ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.ArrayDimensionExpression p2, Object p3 )
ArrayConstructorExpression.ArrayConstructorExpression ( String p1, Environment.Parser.Parse.ArrayDimensionExpression p2 )
ArrayConstructorExpression.ArrayConstructorExpression ( String p1, Environment.Parser.Parse.ArrayDimensionExpression p2, Object p3 )
ArrayConstructorExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ArrayConstructorExpression.initializer ( ) :  Environment.Parser.Parse.List
ArrayConstructorExpression.initializer ( Object p1 ) :  Environment.Parser.Parse.List
ArrayConstructorExpression.toArray ( Object p1, Class p2, int p3, int[ ] p4, Environment.Interpreter.Evaluator p5 ) :  Object
ArrayConstructorExpression.toString ( ) :  String

cdk-1.2.10.jar, ArrayDimensionExpression.class
package org.omegahat.Environment.Parser.Parse
ArrayDimensionExpression.add ( Environment.Parser.Parse.ArrayDimensionExpression p1 ) :  void
ArrayDimensionExpression.add ( Object p1 ) :  void
ArrayDimensionExpression.ArrayDimensionExpression ( )
ArrayDimensionExpression.ArrayDimensionExpression ( Environment.Parser.Parse.List p1 )
ArrayDimensionExpression.ArrayDimensionExpression ( Object p1 )
ArrayDimensionExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ArrayDimensionExpression.toString ( ) :  String

cdk-1.2.10.jar, ArrayType.class
package org.omegahat.Environment.Parser.Parse
ArrayType.addDimension ( ) :  void
ArrayType.addDimension ( int p1 ) :  void
ArrayType.ArrayType ( )
ArrayType.ArrayType ( Environment.Parser.Parse.Name p1 )
ArrayType.ArrayType ( Environment.Parser.Parse.Name p1, int p2 )
ArrayType.ArrayType ( String p1 )
ArrayType.ArrayType ( String p1, int p2 )
ArrayType.clone ( ) :  Object
ArrayType.copyDims ( Environment.Parser.Parse.ArrayType p1 ) :  void
ArrayType.dims ( ) :  Environment.Parser.Parse.List
ArrayType.dims ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
ArrayType.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ArrayType.toString ( ) :  String
ArrayType.toString ( boolean p1 ) :  String

cdk-1.2.10.jar, Artefact.class
package net.sf.jnati.deploy.artefact
Artefact.getArtefactLocation ( ) :  ArtefactLocation
Artefact.getConfiguration ( ) :  Configuration
Artefact.setConfiguration ( Configuration config ) :  void

cdk-1.2.10.jar, ArtefactLocation.class
package net.sf.jnati
ArtefactLocation.ArtefactLocation ( String id, String version, String osarch, File root )
ArtefactLocation.getId ( ) :  String
ArtefactLocation.getOsArch ( ) :  String
ArtefactLocation.getPath ( ) :  File
ArtefactLocation.getVersion ( ) :  String

cdk-1.2.10.jar, AsciiCP.class
package jas
AsciiCP.AsciiCP ( String s )
AsciiCP.toString ( ) :  String

cdk-1.2.10.jar, AssignableSubset.class
package org.omegahat.Environment.DataStructures
AssignableSubset.assignSubset ( Object p1, Object p2 ) [abstract] :  Object

cdk-1.2.10.jar, AssignExpression.class
package org.omegahat.Environment.Parser.Parse
AssignExpression.arrayAssignment ( ) :  boolean
AssignExpression.arrayOperation ( Object p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  Object
AssignExpression.AssignExpression ( Object p1, Object p2 )
AssignExpression.AssignExpression ( Object p1, Object p2, int p3 )
AssignExpression.AssignExpression ( Object p1, Object p2, Integer p3 )
AssignExpression.computeNumeric ( double[ ] p1 ) :  double
AssignExpression.database ( ) :  Environment.Databases.Database
AssignExpression.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
AssignExpression.databaseId ( ) :  int
AssignExpression.databaseId ( int p1 ) :  int
AssignExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
AssignExpression.getDatabase ( String p1, Environment.Interpreter.Evaluator p2 ) :  Environment.Databases.Database
AssignExpression.getName ( Environment.Interpreter.Evaluator p1 ) :  String
AssignExpression.isMathOperation ( ) :  boolean
AssignExpression.numericComputation ( Object[ ] p1 ) :  Object
AssignExpression.operate ( Object p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  Object
AssignExpression.setField ( Environment.Parser.Parse.FieldAccess p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  Object

cdk-1.2.10.jar, ASTFrame.class
package org.omegahat.Environment.Debugger.ParserViewer
ASTFrame.ASTFrame ( String p1, AST p2 )
ASTFrame.main ( String[ ] p1 ) [static] :  void

cdk-1.2.10.jar, Atom.class
package org.openscience.cdk
Atom.getHydrogenCount ( ) :  Integer
Atom.setHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.2.10.jar, AtomContainer.class
package org.openscience.cdk
AtomContainer.addAtomParity ( IAtomParity parity ) :  void
AtomContainer.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
AtomContainer.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, AtomContainerAtomPermutor.class
package org.openscience.cdk.graph
AtomContainerAtomPermutor.AtomContainerAtomPermutor ( AtomContainer ac )

cdk-1.2.10.jar, AtomContainerBondPermutor.class
package org.openscience.cdk.graph
AtomContainerBondPermutor.AtomContainerBondPermutor ( AtomContainer ac )

cdk-1.2.10.jar, AtomContainerPermutor.class
package org.openscience.cdk.graph
AtomContainerPermutor.setAtomContainer ( AtomContainer ac ) :  void

cdk-1.2.10.jar, AttachableSearchPath.class
package org.omegahat.Environment.Databases
AttachableSearchPath.attach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
AttachableSearchPath.AttachableSearchPath ( )
AttachableSearchPath.AttachableSearchPath ( Environment.Databases.Database p1 )
AttachableSearchPath.AttachableSearchPath ( int p1 )
AttachableSearchPath.AttachableSearchPath ( String p1 )
AttachableSearchPath.AttachableSearchPath ( Vector p1 )
AttachableSearchPath.detach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
AttachableSearchPath.getName ( ) :  String
AttachableSearchPath.getState ( ) :  int
AttachableSearchPath.setName ( String p1 ) :  String
AttachableSearchPath.setState ( int p1 ) :  int

cdk-1.2.10.jar, AttachedDatabase.class
package org.omegahat.Environment.Databases
AttachedDatabase.AttachedDatabase ( Environment.Databases.Database p1, int p2 )
AttachedDatabase.AttachedDatabase ( Environment.Databases.Database p1, int p2, Environment.Databases.SearchPath p3 )
AttachedDatabase.database ( ) :  Environment.Databases.Database
AttachedDatabase.index ( ) :  int
AttachedDatabase.searchPath ( ) :  Environment.Databases.SearchPath
AttachedDatabase.searchPath ( Environment.Databases.SearchPath p1 ) :  Environment.Databases.SearchPath

cdk-1.2.10.jar, BasicConvertibleClassifier.class
package org.omegahat.Interfaces.NativeInterface
BasicConvertibleClassifier.BasicConvertibleClassifier ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, BasicDatabaseRenderer.class
package org.omegahat.Environment.GUI
BasicDatabaseRenderer.BasicDatabaseRenderer ( )
BasicDatabaseRenderer.BasicDatabaseRenderer ( Environment.Databases.Database p1 )
BasicDatabaseRenderer.database ( ) :  Environment.Databases.Database
BasicDatabaseRenderer.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
BasicDatabaseRenderer.getListCellRendererComponent ( JList p1, Object p2, int p3, boolean p4, boolean p5 ) :  Component
BasicDatabaseRenderer.icon ( String p1, Object p2 ) :  Icon

cdk-1.2.10.jar, BasicErrorHandler.class
package org.omegahat.Environment.Debugger
BasicErrorHandler.BasicErrorHandler ( )
BasicErrorHandler.BasicErrorHandler ( Environment.Interpreter.Evaluator p1 )
BasicErrorHandler.BasicErrorHandler ( Throwable p1, String p2, Environment.Interpreter.Evaluator p3 )
BasicErrorHandler.error ( Throwable p1, String p2 ) :  Object
BasicErrorHandler.error ( Throwable p1, String p2, Environment.Parser.Parse.ExpressionInt p3 ) [abstract] :  Object
BasicErrorHandler.evaluator ( ) :  Environment.Interpreter.Evaluator
BasicErrorHandler.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator

cdk-1.2.10.jar, BasicEvaluator.class
package org.omegahat.Environment.Interpreter
BasicEvaluator.addEvaluationListener ( Environment.Interpreter.EvaluationListener p1 ) :  int
BasicEvaluator.addFunctionTable ( Object p1 ) :  int
BasicEvaluator.addFunctionTable ( Object p1, String p2 ) :  int
BasicEvaluator.addMethod ( Environment.Language.Method p1, Environment.Parser.Parse.Name p2 ) :  boolean
BasicEvaluator.addSourceInput ( Object p1 ) :  Object
BasicEvaluator.addToHistory ( Object p1, Object p2, String p3 ) :  Environment.Interpreter.Task
BasicEvaluator.allowUnrestrictedAccess ( ) :  boolean
BasicEvaluator.allowUnrestrictedAccess ( boolean p1 ) :  boolean
BasicEvaluator.asObject ( Environment.Parser.Parse.Name p1 ) :  Object
BasicEvaluator.asObject ( Environment.Parser.Parse.Name p1, int p2 ) :  Object
BasicEvaluator.asObject ( Environment.Parser.Parse.Name p1, int p2, boolean p3 ) :  Object
BasicEvaluator.asObjectName ( Environment.Parser.Parse.Name p1 ) :  String
BasicEvaluator.asPrimitiveClass ( String p1 ) :  Class
BasicEvaluator.assign ( String p1, Object p2 ) :  boolean
BasicEvaluator.assign ( String p1, Object p2, Environment.Databases.Database p3 ) :  boolean
BasicEvaluator.assign ( String p1, Object p2, int p3 ) :  boolean
BasicEvaluator.asWriter ( OutputStream p1 ) :  PrintWriter
BasicEvaluator.attach ( Environment.Databases.Database p1 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( Environment.Databases.Database p1, int p2 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( File p1 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( File p1, int p2 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( String p1 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( String p1, int p2 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.attach ( URL p1 ) :  Environment.Databases.AttachedDatabase
BasicEvaluator.BasicEvaluator ( )
BasicEvaluator.BasicEvaluator ( Environment.Interpreter.Evaluator p1 )
BasicEvaluator.BasicEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
BasicEvaluator.BasicEvaluator ( Environment.Interpreter.Options p1 )
BasicEvaluator.classInit ( ) [static] :  Hashtable
BasicEvaluator.classLists ( ) :  Environment.Tools.ClassList.ClassLocatorInt
BasicEvaluator.classLists ( Environment.Tools.ClassList.ClassLocatorInt p1 ) :  Environment.Tools.ClassList.ClassLocatorInt
BasicEvaluator.classPath ( ) :  Vector
BasicEvaluator.classPath ( String p1 ) :  Vector
BasicEvaluator.commandLine ( ) :  String[ ]
BasicEvaluator.convertPrimitive ( Object p1, Class p2 ) :  Object
BasicEvaluator.copy ( Object p1 ) :  Object
BasicEvaluator.copy ( Object p1, boolean p2 ) :  Object
BasicEvaluator.copyByConstructor ( Object p1, boolean p2 ) :  Object
BasicEvaluator.copyBySerialization ( Object p1 ) :  Object
BasicEvaluator.createClassLists ( ) :  Environment.Tools.ClassList.ClassLocatorInt
BasicEvaluator.currentExpression ( ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.currentExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.data ( ) :  Object
BasicEvaluator.data ( Object p1 ) :  Object
BasicEvaluator.database ( ) :  Environment.Databases.Database
BasicEvaluator.database ( int p1 ) :  Environment.Databases.Database
BasicEvaluator.database ( String p1 ) :  Environment.Databases.Database
BasicEvaluator.Debug ( ) :  boolean
BasicEvaluator.Debug ( Boolean p1 ) :  boolean
BasicEvaluator.Debug ( boolean p1 ) :  boolean
BasicEvaluator.Debug ( Object p1 ) :  boolean
BasicEvaluator.Debug ( String p1 ) :  boolean
BasicEvaluator.debugger ( ) :  Environment.Debugger.Debugger
BasicEvaluator.debugger ( Environment.Debugger.Debugger p1 ) :  Environment.Debugger.Debugger
BasicEvaluator.defaultDatabase ( ) :  Environment.Databases.Database
BasicEvaluator.defaultDatabase ( boolean p1 ) :  Environment.Databases.Database
BasicEvaluator.defaultDatabase ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
BasicEvaluator.defaultErrorHandler ( ) :  Environment.Debugger.ErrorHandler
BasicEvaluator.detach ( Environment.Databases.Database p1 ) :  int
BasicEvaluator.detach ( int p1 ) :  int
BasicEvaluator.displayTask ( Environment.Interpreter.Task p1 ) :  boolean
BasicEvaluator.displayTask ( Object p1, Object p2, String p3 ) :  boolean
BasicEvaluator.displayWarnings ( ) :  int
BasicEvaluator.displayWarnings ( int p1 ) :  int
BasicEvaluator.dynamicClassLoader ( ) :  Environment.System.DynamicClassLoader
BasicEvaluator.dynamicClassLoader ( Environment.System.DynamicClassLoader p1 ) :  Environment.System.DynamicClassLoader
BasicEvaluator.endSource ( ) :  void
BasicEvaluator.endSource ( String p1 ) :  void
BasicEvaluator.endSource ( String p1, boolean p2 ) :  void
BasicEvaluator.endTaskEvaluation ( Environment.Parser.Parse.ExpressionInt p1 ) :  void
BasicEvaluator.error ( String p1 ) :  Exception
BasicEvaluator.error ( Throwable p1, String p2 ) :  Exception
BasicEvaluator.errorHandler ( ) :  Environment.Debugger.ErrorHandler
BasicEvaluator.errorHandler ( Environment.Debugger.ErrorHandler p1 ) :  Environment.Debugger.ErrorHandler
BasicEvaluator.evaluate ( Environment.Interpreter.Task p1 ) :  Object
BasicEvaluator.evaluate ( Environment.Parser.Parse.ExpressionInt p1 ) :  Object
BasicEvaluator.evaluate ( Object p1, String p2 ) :  Object
BasicEvaluator.evaluate ( String p1 ) :  Object
BasicEvaluator.evaluationError ( Throwable p1 ) :  boolean
BasicEvaluator.evaluationListeners ( ) :  Vector
BasicEvaluator.evaluationListeners ( boolean p1 ) :  Vector
BasicEvaluator.evaluationListeners ( Vector p1 ) :  Vector
BasicEvaluator.exists ( String p1 ) :  boolean
BasicEvaluator.exit ( ) :  void
BasicEvaluator.exit ( int p1 ) :  void
BasicEvaluator.expandClassName ( String p1 ) :  String
BasicEvaluator.expandedClassPathElement ( String p1, Object p2 ) :  String
BasicEvaluator.find ( String p1, boolean p2 ) :  Environment.Databases.Database[ ]
BasicEvaluator.findAsField ( Environment.Parser.Parse.Name p1, int p2, boolean p3 ) :  Object
BasicEvaluator.findClass ( Environment.Parser.Parse.Name p1 ) :  Class
BasicEvaluator.findClass ( String p1 ) :  Class
BasicEvaluator.findClass ( String p1, boolean p2 ) :  Class
BasicEvaluator.findClass ( String p1, int p2 ) :  Class
BasicEvaluator.findFunction ( String p1 ) :  Environment.Language.Function
BasicEvaluator.findFunctionOrMethod ( String p1 ) :  Environment.Language.Evaluable
BasicEvaluator.functionTableList ( ) :  Environment.Utils.OrderedTable
BasicEvaluator.get ( Environment.Databases.NameTypeSearchFilter p1 ) :  Object
BasicEvaluator.get ( Environment.Parser.Parse.Name p1 ) :  Object
BasicEvaluator.get ( String p1 ) :  Object
BasicEvaluator.get ( String p1, boolean p2 ) :  Object
BasicEvaluator.get ( String p1, boolean p2, boolean p3 ) :  Object
BasicEvaluator.get ( String p1, Class p2 ) :  Object
BasicEvaluator.get ( String p1, Class p2, boolean p3 ) :  Object
BasicEvaluator.get ( String p1, String p2 ) :  Object
BasicEvaluator.get ( String p1, String p2, boolean p3 ) :  Object
BasicEvaluator.getBaseURL ( String p1 ) :  Object
BasicEvaluator.getEvaluationEvent ( ) :  Environment.Interpreter.EvaluationEvent
BasicEvaluator.getEvaluationListeners ( ) :  Vector
BasicEvaluator.getField ( String p1, Object p2, boolean p3 ) :  Object
BasicEvaluator.getSubEvaluationListeners ( ) :  Vector
BasicEvaluator.help ( ) :  Object
BasicEvaluator.Import ( Environment.Parser.Parse.Name p1 ) :  Environment.Tools.ClassList.ClassList
BasicEvaluator.Import ( File p1 ) :  Environment.Tools.ClassList.ClassList
BasicEvaluator.Import ( URL p1 ) :  Environment.Tools.ClassList.ClassList
BasicEvaluator.init ( ) :  void
BasicEvaluator.initialize ( Environment.Interpreter.Evaluator p1 ) :  boolean
BasicEvaluator.initTaskEvaluation ( Environment.Parser.Parse.ExpressionInt p1 ) :  void
BasicEvaluator.internalFunctionTables ( Environment.Utils.OrderedTable p1 ) :  Environment.Utils.OrderedTable
BasicEvaluator.isPrimitive ( Class p1 ) [static] :  boolean
BasicEvaluator.isPrimitive ( Object p1 ) [static] :  boolean
BasicEvaluator.javaVersion ( ) :  int
BasicEvaluator.lexer ( ) :  Tokenizer
BasicEvaluator.lexer ( Reader p1 ) :  Tokenizer
BasicEvaluator.lexer ( Tokenizer p1 ) :  Tokenizer
BasicEvaluator.localClasses ( ) :  Environment.Tools.ClassList.LocalClassLocator
BasicEvaluator.localClasses ( Environment.Tools.ClassList.LocalClassLocator p1 ) :  Environment.Tools.ClassList.LocalClassLocator
BasicEvaluator.manager ( ) :  Environment.Interpreter.EvaluatorManager
BasicEvaluator.manager ( Environment.Interpreter.EvaluatorManager p1 ) :  Environment.Interpreter.EvaluatorManager
BasicEvaluator.newDatabase ( ) :  Environment.Databases.Database
BasicEvaluator.newDatabase ( String p1 ) :  Environment.Databases.Database
BasicEvaluator.notifyListeners ( Environment.Parser.Parse.ExpressionInt p1 ) :  int
BasicEvaluator.notifyListeners ( Environment.Parser.Parse.ExpressionInt p1, boolean p2 ) :  int
BasicEvaluator.objects ( ) :  String[ ]
BasicEvaluator.objects ( Environment.Databases.Database p1 ) :  String[ ]
BasicEvaluator.objects ( int p1 ) :  String[ ]
BasicEvaluator.options ( ) :  Environment.Interpreter.Options
BasicEvaluator.options ( Environment.Interpreter.Options p1 ) :  Environment.Interpreter.Options
BasicEvaluator.output ( ) :  Environment.IO.ObjectDisplayFilter
BasicEvaluator.output ( boolean p1 ) :  Environment.IO.ObjectDisplayFilter
BasicEvaluator.output ( Environment.IO.ObjectDisplayFilter p1 ) :  Environment.IO.ObjectDisplayFilter
BasicEvaluator.parse ( Environment.Parser.AntlrParser.omegaJavaGrammar p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.parse ( Reader p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.parse ( String p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.parse ( Tokenizer p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.parser ( Tokenizer p1 ) :  Environment.Parser.AntlrParser.omegaJavaGrammar
BasicEvaluator.primitiveClass ( Object p1 ) [static] :  Class
BasicEvaluator.q ( ) :  boolean
BasicEvaluator.q ( boolean p1 ) :  boolean
BasicEvaluator.remove ( String p1 ) :  boolean
BasicEvaluator.remove ( String p1, Environment.Databases.Database p2 ) :  boolean
BasicEvaluator.remove ( String p1, int p2 ) :  boolean
BasicEvaluator.removeFunctionTable ( Object p1 ) :  boolean
BasicEvaluator.run ( ) :  void
BasicEvaluator.same ( Object p1, Object p2 ) :  boolean
BasicEvaluator.searchForClass ( String p1 ) :  Class
BasicEvaluator.searchPath ( ) :  Environment.Databases.SearchPath
BasicEvaluator.searchPath ( Environment.Databases.SearchPath p1 ) :  Environment.Databases.SearchPath
BasicEvaluator.searchPath ( Environment.Databases.SearchPath p1, boolean p2 ) :  Environment.Databases.SearchPath
BasicEvaluator.searchPath ( Vector p1 ) :  Environment.Databases.SearchPath
BasicEvaluator.setEvaluationEvent ( Environment.Interpreter.EvaluationEvent p1 ) :  Environment.Interpreter.EvaluationEvent
BasicEvaluator.setEvaluationListeners ( Vector p1 ) :  Vector
BasicEvaluator.setField ( String p1, Object p2, Object p3 ) :  Object
BasicEvaluator.setSubEvaluationListeners ( Vector p1 ) :  Vector
BasicEvaluator.show ( ) :  Object
BasicEvaluator.show ( Object p1 ) :  Object
BasicEvaluator.show ( Object p1, boolean p2 ) :  Object
BasicEvaluator.source ( Environment.IO.ArchiveEntry p1 ) :  Object
BasicEvaluator.source ( Environment.IO.InputFileInt p1 ) :  Object
BasicEvaluator.source ( File p1 ) :  Object
BasicEvaluator.source ( Object p1 ) :  Object
BasicEvaluator.source ( Reader p1 ) :  Object
BasicEvaluator.source ( Reader p1, Object p2 ) :  Object
BasicEvaluator.source ( String p1 ) :  Object
BasicEvaluator.source ( String p1, boolean p2 ) :  Object
BasicEvaluator.source ( URL p1 ) :  Object
BasicEvaluator.sourceStack ( ) :  Stack
BasicEvaluator.stderr ( ) :  PrintWriter
BasicEvaluator.stderr ( OutputStream p1 ) :  PrintWriter
BasicEvaluator.stdout ( ) :  PrintWriter
BasicEvaluator.stdout ( OutputStream p1 ) :  PrintWriter
BasicEvaluator.taskHistory ( ) :  Vector
BasicEvaluator.taskHistory ( Vector p1 ) :  Vector
BasicEvaluator.toplevelExpression ( ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.toplevelExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicEvaluator.useLazyEvaluation ( ) :  boolean
BasicEvaluator.warning ( String p1 ) :  void
BasicEvaluator.warning ( String p1, boolean p2 ) :  void
BasicEvaluator.warning ( Throwable p1, String p2 ) :  void
BasicEvaluator.warnings ( ) :  Vector
BasicEvaluator.warnings ( Vector p1 ) :  Vector
BasicEvaluator.where ( String p1 ) :  Environment.Databases.Database[ ]
BasicEvaluator.which ( Environment.Parser.Parse.Name p1 ) :  Environment.Databases.Database
BasicEvaluator.which ( String p1 ) :  Environment.Databases.Database

cdk-1.2.10.jar, BasicExpression.class
package org.omegahat.Environment.Parser.Parse
BasicExpression.addChild ( Environment.Parser.Parse.TreeNodeInt p1 ) :  Environment.Parser.Parse.TreeNodeInt
BasicExpression.addComment ( Environment.Parser.Parse.Comment p1, int p2 ) :  int
BasicExpression.apply ( Environment.Language.Function p1 ) :  Object
BasicExpression.apply ( Environment.Language.Function p1, Environment.Interpreter.Evaluator p2 ) :  Object
BasicExpression.apply ( Environment.Language.Function p1, Environment.Interpreter.Evaluator p2, Vector p3 ) :  Object
BasicExpression.BasicExpression ( )
BasicExpression.BasicExpression ( Environment.Parser.Parse.TreeNodeInt p1 )
BasicExpression.children ( ) :  Vector
BasicExpression.children ( Vector p1 ) :  Vector
BasicExpression.comment ( int p1 ) :  Environment.Parser.Parse.Comment
BasicExpression.comment ( int p1, Environment.Parser.Parse.Comment p2 ) :  Environment.Parser.Parse.Comment
BasicExpression.depth ( ) :  int
BasicExpression.error ( String p1, Environment.Interpreter.Evaluator p2 ) :  Exception
BasicExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
BasicExpression.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
BasicExpression.evalInit ( Environment.Interpreter.Evaluator p1 ) :  void
BasicExpression.evaluationFrame ( String p1, Environment.Interpreter.Evaluator p2 ) :  Environment.Databases.Database
BasicExpression.evaluator ( ) :  Environment.Interpreter.Evaluator
BasicExpression.getReferencedVariables ( ) :  AbstractCollection
BasicExpression.getReferencedVariables ( boolean p1 ) :  AbstractCollection
BasicExpression.getReferencedVariables ( boolean p1, AbstractCollection p2 ) :  AbstractCollection
BasicExpression.isActive ( ) :  boolean
BasicExpression.isActive ( boolean p1 ) :  boolean
BasicExpression.parent ( ) :  Environment.Parser.Parse.TreeNodeInt
BasicExpression.parent ( Environment.Parser.Parse.TreeNodeInt p1 ) :  Environment.Parser.Parse.TreeNodeInt
BasicExpression.postComment ( ) :  Environment.Parser.Parse.Comment
BasicExpression.postComment ( Environment.Parser.Parse.Comment p1 ) :  Environment.Parser.Parse.Comment
BasicExpression.preComment ( ) :  Environment.Parser.Parse.Comment
BasicExpression.preComment ( Environment.Parser.Parse.Comment p1 ) :  Environment.Parser.Parse.Comment
BasicExpression.render ( boolean p1 ) :  String
BasicExpression.replaceChild ( Environment.Parser.Parse.TreeNodeInt p1, Environment.Parser.Parse.TreeNodeInt p2 ) :  int
BasicExpression.resolve ( Environment.Interpreter.Evaluator p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicExpression.run ( ) :  void
BasicExpression.setParent ( Enumeration p1 ) :  boolean
BasicExpression.setParent ( Environment.Parser.Parse.List p1 ) :  boolean
BasicExpression.setParent ( Environment.Parser.Parse.TreeNodeInt p1 ) :  boolean
BasicExpression.setParent ( Vector p1 ) :  boolean
BasicExpression.showComments ( int p1 ) :  String
BasicExpression.showComments ( int p1, int p2 ) :  String
BasicExpression.subset ( Object p1, boolean p2 ) :  Object
BasicExpression.substitute ( Hashtable p1 ) :  Environment.Parser.Parse.ExpressionInt
BasicExpression.substitute ( Hashtable p1, boolean p2 ) :  Environment.Parser.Parse.ExpressionInt
BasicExpression.toString ( ) :  String

cdk-1.2.10.jar, BasicHelpSystem.class
package org.omegahat.Environment.System.Functions
BasicHelpSystem.BasicHelpSystem ( )
BasicHelpSystem.BasicHelpSystem ( HelpSet p1 )
BasicHelpSystem.BasicHelpSystem ( String p1 )
BasicHelpSystem.help ( ) :  Object
BasicHelpSystem.help ( HelpSet p1, String p2 ) :  Object
BasicHelpSystem.help ( HelpSet p1, String p2, boolean p3 ) :  Object
BasicHelpSystem.help ( String p1 ) :  Object
BasicHelpSystem.helpSet ( ) :  HelpSet
BasicHelpSystem.helpSet ( HelpSet p1 ) :  HelpSet
BasicHelpSystem.helpSet ( String p1 ) :  HelpSet
BasicHelpSystem.helpSet ( String p1, boolean p2 ) :  HelpSet
BasicHelpSystem.helpSet ( URL p1 ) :  HelpSet
BasicHelpSystem.helpViewer ( ) :  JHelp
BasicHelpSystem.helpViewer ( JHelp p1 ) :  JHelp
BasicHelpSystem.main ( String[ ] p1 ) [static] :  void

cdk-1.2.10.jar, BasicObjectDisplay.class
package org.omegahat.Environment.IO
BasicObjectDisplay.BasicObjectDisplay ( )
BasicObjectDisplay.BasicObjectDisplay ( PrintWriter p1 )
BasicObjectDisplay.defaultDisplay ( Object p1 ) :  boolean
BasicObjectDisplay.defaultDisplay ( Object p1, long p2 ) :  boolean
BasicObjectDisplay.display ( Enumeration p1 ) :  boolean
BasicObjectDisplay.display ( Object p1 ) :  boolean
BasicObjectDisplay.display ( Object p1, long p2 ) :  boolean
BasicObjectDisplay.displayArray ( Object p1 ) :  boolean
BasicObjectDisplay.stdout ( ) :  PrintWriter
BasicObjectDisplay.stdout ( PrintWriter p1 ) :  PrintWriter
BasicObjectDisplay.toString ( Object p1 ) :  String
BasicObjectDisplay.toWriter ( Object p1 ) :  Writer
BasicObjectDisplay.writer ( ) :  Writer

cdk-1.2.10.jar, BasicServerPool.class
package org.omegahat.Environment.TaskManagement
BasicServerPool.BasicServerPool ( )
BasicServerPool.BasicServerPool ( int p1 )
BasicServerPool.BasicServerPool ( Vector p1 )

cdk-1.2.10.jar, BasicTaskDisplay.class
package org.omegahat.Environment.IO
BasicTaskDisplay.BasicTaskDisplay ( )
BasicTaskDisplay.BasicTaskDisplay ( PrintWriter p1 )
BasicTaskDisplay.BasicTaskDisplay ( PrintWriter p1, int p2, int p3 )
BasicTaskDisplay.display ( Environment.Interpreter.Task p1 ) :  boolean
BasicTaskDisplay.taskObject ( Environment.Interpreter.Task p1 ) :  Object

cdk-1.2.10.jar, BasicValidator.class
package org.openscience.cdk.validate
BasicValidator.validateAtom ( Atom subject ) :  ValidationReport
BasicValidator.validateBond ( Bond subject ) :  ValidationReport
BasicValidator.validateMolecule ( Molecule subject ) :  ValidationReport
BasicValidator.validateReaction ( Reaction subject ) :  ValidationReport

cdk-1.2.10.jar, BinaryExpression.class
package org.omegahat.Environment.Parser.Parse
BinaryExpression.BinaryExpression ( )
BinaryExpression.BinaryExpression ( Object p1 )
BinaryExpression.BinaryExpression ( Object p1, Object p2 )
BinaryExpression.element ( int p1 ) :  Object
BinaryExpression.element ( Object p1, int p2 ) :  Object
BinaryExpression.elements ( ) :  Object[ ]
BinaryExpression.elements ( Object[ ] p1 ) :  Object[ ]
BinaryExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
BinaryExpression.getFirstChild ( ) :  AST
BinaryExpression.replaceChild ( Environment.Parser.Parse.TreeNodeInt p1, Environment.Parser.Parse.TreeNodeInt p2 ) :  int
BinaryExpression.separator ( ) :  String
BinaryExpression.subset ( Object p1, boolean p2 ) :  Object
BinaryExpression.toString ( ) :  String

cdk-1.2.10.jar, Bond.class
package org.openscience.cdk
Bond.Bond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo )
Bond.getStereo ( ) :  int
Bond.setStereo ( int stereo ) :  void

cdk-1.2.10.jar, BondStretching.class
package org.openscience.cdk.modeling.forcefield
BondStretching.BondStretching ( )
BondStretching.calculateDeltar ( GVector coord3d ) :  void
BondStretching.functionMMFF94SumEB ( GVector coord3d ) :  double
BondStretching.get2ndOrderErrorApproximateHessianMMFF94SumEB ( ) :  GMatrix
BondStretching.getBondLengthsFirstDerivative ( ) :  double[ ][ ]
BondStretching.getBondLengthsSecondDerivative ( ) :  double[ ][ ][ ]
BondStretching.getForHessianMMFF94SumEB ( ) :  double[ ]
BondStretching.getGradientMMFF94SumEB ( ) :  GVector
BondStretching.getHessianMMFF94SumEB ( ) :  GMatrix
BondStretching.set2ndOrderErrorApproximateHessianMMFF94SumEB ( GVector coord3d ) :  void
BondStretching.setBondLengthsFirstDerivative ( GVector coord3d, double[ ] deltar, int[ ][ ] bondAtomPosition ) :  void
BondStretching.setBondLengthsSecondDerivative ( GVector coord3d, double[ ] deltar, int[ ][ ] bondAtomPosition ) :  void
BondStretching.setGradientMMFF94SumEB ( GVector coord3d ) :  void
BondStretching.setHessianMMFF94SumEB ( GVector coord3d ) :  void
BondStretching.setMMFF94BondStretchingParameters ( IAtomContainer molecule, Map parameterSet ) :  void

cdk-1.2.10.jar, BugReportData.class
package org.omegahat.Environment.Debugger
BugReportData.BugReportData ( )
BugReportData.compute ( ) [static] :  void
BugReportData.computeCompiler ( ) [static] :  String
BugReportData.computeJDKVersion ( ) [static] :  String
BugReportData.computeJVM ( ) [static] :  String
BugReportData.computeOmegaVersion ( ) [static] :  String
BugReportData.computeOS ( ) [static] :  String
BugReportData.main ( String[ ] p1 ) [static] :  void
BugReportData.show ( ) [static] :  Hashtable
BugReportData.show ( Properties p1 ) [static] :  Hashtable
BugReportData.showSystem ( ) [static] :  void
BugReportData.showSystem ( Properties p1 ) [static] :  void

cdk-1.2.10.jar, CastExpression.class
package org.omegahat.Environment.Parser.Parse
CastExpression.castClass ( ) :  Class
CastExpression.castClass ( Class p1 ) :  Class
CastExpression.castClass ( Environment.Interpreter.Evaluator p1 ) :  Class
CastExpression.CastExpression ( boolean p1, Object p2 )
CastExpression.CastExpression ( Environment.Parser.Parse.Name p1, Object p2 )
CastExpression.convertToClass ( Class p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  Object
CastExpression.error ( Class p1, Object p2 ) :  void
CastExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
CastExpression.expression ( ) :  Object
CastExpression.expression ( Object p1 ) :  Object
CastExpression.isSuper ( ) :  boolean
CastExpression.isSuper ( boolean p1 ) :  boolean
CastExpression.toBoolean ( Object p1 ) :  Object
CastExpression.toDouble ( Object p1 ) :  Object
CastExpression.toFloat ( Object p1 ) :  Object
CastExpression.toInt ( Object p1 ) :  Object
CastExpression.toLong ( Object p1 ) :  Object
CastExpression.toShort ( Object p1 ) :  Object
CastExpression.toString ( ) :  String
CastExpression.value ( ) :  Object

cdk-1.2.10.jar, CastFunctionCall.class
package org.omegahat.Environment.Interpreter
CastFunctionCall.callMethod ( String p1, Object p2, Object[ ] p3, Environment.Interpreter.Evaluator p4 ) :  Object
CastFunctionCall.CastFunctionCall ( Method p1, Object p2, Object[ ] p3, Environment.Interpreter.Evaluator p4, boolean p5 )
CastFunctionCall.CastFunctionCall ( Method p1, Object p2, Object[ ] p3, Environment.Interpreter.Evaluator p4, boolean p5, String p6 )
CastFunctionCall.makeClass ( Method p1 ) :  void
CastFunctionCall.makeMethod ( Method p1 ) :  boolean
CastFunctionCall.value ( ) :  Object
CastFunctionCall.value ( Object p1 ) :  Object

cdk-1.2.10.jar, Catch.class
package org.omegahat.Environment.Parser.Parse
Catch.body ( ) :  Environment.Parser.Parse.StatementList
Catch.body ( Environment.Parser.Parse.StatementList p1 ) :  Environment.Parser.Parse.StatementList
Catch.Catch ( Environment.Parser.Parse.MethodParameter p1, Environment.Parser.Parse.StatementList p2 )
Catch.Catch ( Environment.Parser.Parse.StatementList p1, boolean p2 )
Catch.Class ( Environment.Interpreter.Evaluator p1 ) :  Class
Catch.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
Catch.eval ( Throwable p1, Environment.Interpreter.Evaluator p2 ) :  Object
Catch.getFirstChild ( ) :  AST
Catch.thrownClass ( ) :  Environment.Parser.Parse.MethodParameter
Catch.thrownClass ( Environment.Parser.Parse.MethodParameter p1 ) :  Environment.Parser.Parse.MethodParameter
Catch.toString ( ) :  String

cdk-1.2.10.jar, CatchEntry.class
package jas
CatchEntry.CatchEntry ( Label start, Label end, Label handler, CP cat )

cdk-1.2.10.jar, Catchtable.class
package jas
Catchtable.addEntry ( CatchEntry entry ) :  void
Catchtable.addEntry ( Label start, Label end, Label handler, CP cat ) :  void
Catchtable.Catchtable ( )

cdk-1.2.10.jar, character.class
package org.omegahat.Environment.DataStructures
character.character ( )
character.character ( int p1 )
character.character ( String p1 )
character.character ( String[ ] p1 )
character.Data ( ) :  String[ ]
character.data ( int p1 ) :  Object
character.data ( String p1 ) :  Object
character.data ( String[ ] p1 ) :  Object
character.getElement ( int p1 ) :  String
character.setData ( String[ ] p1 ) :  int
package org.omegahat.Environment.ObjectDataStructures
character.character ( )
character.character ( int p1 )
character.character ( String p1 )
character.character ( String[ ] p1 )
character.convertElement ( Object p1 ) :  Object
character.Data ( ) :  String[ ]
character.data ( String p1 ) :  Object
character.data ( String[ ] p1 ) :  Object
character.getElement ( int p1 ) :  String
character.setData ( String[ ] p1 ) :  int
character.targetClass ( ) :  Class

cdk-1.2.10.jar, ChiIndexUtils.class
package org.openscience.cdk.qsar.descriptors.molecular
ChiIndexUtils.ChiIndexUtils ( )

cdk-1.2.10.jar, ClassCP.class
package jas
ClassCP.ClassCP ( String name )

cdk-1.2.10.jar, ClassDefinition.class
package org.omegahat.Environment.Parser.Parse
ClassDefinition.addMethod ( String p1, Environment.Parser.Parse.FunctionExpression p2, Environment.Interpreter.Evaluator p3 ) :  Environment.Language.Method
ClassDefinition.body ( ) :  Environment.Parser.Parse.List
ClassDefinition.body ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
ClassDefinition.ClassDefinition ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.Name p2, Environment.Parser.Parse.List p3, Environment.Parser.Parse.List p4 )
ClassDefinition.constructors ( ) :  Environment.Language.Method
ClassDefinition.constructors ( Environment.Language.Method p1 ) :  Environment.Language.Method
ClassDefinition.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ClassDefinition.fields ( ) :  Environment.Parser.Parse.List
ClassDefinition.fields ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
ClassDefinition.interfaces ( ) :  Environment.Parser.Parse.List
ClassDefinition.interfaces ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
ClassDefinition.methods ( ) :  Environment.Language.UserClasses.MethodsCollection
ClassDefinition.methods ( Environment.Language.UserClasses.MethodsCollection p1 ) :  Environment.Language.UserClasses.MethodsCollection
ClassDefinition.name ( ) :  Environment.Parser.Parse.Name
ClassDefinition.name ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
ClassDefinition.superClass ( ) :  Environment.Parser.Parse.Name
ClassDefinition.superClass ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name

cdk-1.2.10.jar, ClassEnv.class
package jas
ClassEnv.addCPItem ( CP cp ) :  void
ClassEnv.addField ( Var v ) :  void
ClassEnv.addGenericAttr ( GenericAttr g ) :  void
ClassEnv.addInterface ( CP ifc ) :  void
ClassEnv.addInterface ( CP[ ] ilist ) :  void
ClassEnv.addMethod ( Method m ) :  void
ClassEnv.addMethod ( short acc, String name, String sig, CodeAttr code, ExceptAttr ex ) :  void
ClassEnv.ClassEnv ( )
ClassEnv.setClass ( CP name ) :  void
ClassEnv.setClassAccess ( short access ) :  void
ClassEnv.setSource ( SourceAttr source ) :  void
ClassEnv.setSource ( String source ) :  void
ClassEnv.setSuperClass ( CP name ) :  void
ClassEnv.write ( DataOutputStream out ) :  void

cdk-1.2.10.jar, ClassFileFilter.class
package org.omegahat.Environment.Tools.ClassList
ClassFileFilter.ClassFileFilter ( )

cdk-1.2.10.jar, ClassList.class
package org.omegahat.Environment.Parser.Parse
ClassList.ClassList ( Object p1 )
package org.omegahat.Environment.Tools.ClassList
ClassList.add ( Object p1, Object p2 ) :  Object
ClassList.ClassList ( )
ClassList.ClassList ( File p1 )
ClassList.find ( String p1 ) :  Object
ClassList.findClass ( String p1 ) :  Class
ClassList.loadClass ( String p1 ) :  Class
ClassList.lookup ( ) :  int
ClassList.lookupZip ( ZipFile p1 ) :  int
ClassList.packageName ( ) :  String
ClassList.packageName ( Object p1 ) :  String
ClassList.setPackageName ( String p1 ) :  void
ClassList.toClassName ( String p1 ) :  String

cdk-1.2.10.jar, ClassLocator.class
package org.omegahat.Environment.Tools.ClassList
ClassLocator.add ( Environment.Tools.ClassList.ClassList p1 ) :  Object
ClassLocator.add ( File p1 ) :  Object
ClassLocator.add ( File[ ] p1 ) :  Object
ClassLocator.add ( Object p1 ) :  Object
ClassLocator.add ( String p1 ) :  Object
ClassLocator.add ( String[ ] p1 ) :  Object
ClassLocator.add ( URL p1 ) :  Object
ClassLocator.add ( URL[ ] p1 ) :  Object
ClassLocator.append ( String[ ] p1 ) :  int
ClassLocator.append ( Vector p1 ) :  int
ClassLocator.canReadSerializedLists ( File p1 ) :  boolean
ClassLocator.classList ( File p1 ) :  Environment.Tools.ClassList.ClassList
ClassLocator.classList ( File p1, String p2 ) :  Environment.Tools.ClassList.ClassList
ClassLocator.classList ( URL p1 ) :  Environment.Tools.ClassList.ClassList
ClassLocator.classList ( URL p1, String p2 ) :  Environment.Tools.ClassList.ClassList
ClassLocator.ClassLocator ( )
ClassLocator.ClassLocator ( Environment.Tools.ClassList.ClassList p1 )
ClassLocator.ClassLocator ( File p1 )
ClassLocator.ClassLocator ( String[ ] p1 )
ClassLocator.ClassLocator ( URL p1 )
ClassLocator.ClassLocator ( Vector p1 )
ClassLocator.findClass ( String p1 ) :  Class
ClassLocator.findClasses ( String p1, Vector p2 ) :  Vector
ClassLocator.serializedName ( File p1 ) :  String

cdk-1.2.10.jar, ClassLocatorInt.class
package org.omegahat.Environment.Tools.ClassList
ClassLocatorInt.add ( String p1 ) [abstract] :  Object
ClassLocatorInt.containsKey ( Object p1 ) [abstract] :  boolean
ClassLocatorInt.elements ( ) [abstract] :  Enumeration
ClassLocatorInt.findClass ( String p1 ) [abstract] :  Class
ClassLocatorInt.findClasses ( String p1, Vector p2 ) [abstract] :  Vector
ClassLocatorInt.get ( Object p1 ) [abstract] :  Object
ClassLocatorInt.orderedKeys ( ) [abstract] :  Vector
ClassLocatorInt.size ( ) [abstract] :  int

cdk-1.2.10.jar, ClassName.class
package org.omegahat.Environment.Parser.Parse
ClassName.ClassName ( )
ClassName.ClassName ( Environment.Parser.Parse.FieldAccess p1 )
ClassName.ClassName ( Environment.Parser.Parse.Name p1 )
ClassName.ClassName ( int p1 )
ClassName.ClassName ( String p1 )
ClassName.eval ( Environment.Interpreter.Evaluator p1 ) :  Object

cdk-1.2.10.jar, ClassNameListCellRenderer.class
package org.omegahat.Environment.GUI
ClassNameListCellRenderer.ClassNameListCellRenderer ( )
ClassNameListCellRenderer.getListCellRendererComponent ( JList p1, Object p2, int p3, boolean p4, boolean p5 ) :  Component

cdk-1.2.10.jar, ClassNode.class
package org.omegahat.Environment.Tools.ClassHierarchy
ClassNode.addChild ( Environment.Tools.ClassHierarchy.ClassNode p1 ) :  boolean
ClassNode.agent ( ) :  Environment.Tools.ClassHierarchy.ClassNodeAgent
ClassNode.agent ( Environment.Tools.ClassHierarchy.ClassNodeAgent p1 ) :  Environment.Tools.ClassHierarchy.ClassNodeAgent
ClassNode.children ( ) :  Vector
ClassNode.classInit ( ) [static] :  Class
ClassNode.ClassNode ( )
ClassNode.ClassNode ( Class p1, Environment.Tools.ClassHierarchy.ClassNodeAgent p2 )
ClassNode.compute ( ) :  boolean
ClassNode.findInterfaces ( ) :  int
ClassNode.findParents ( ) :  int
ClassNode.listChildren ( PrintStream p1 ) :  int
ClassNode.listElements ( PrintStream p1, Vector p2 ) :  int
ClassNode.listParents ( PrintStream p1 ) :  int
ClassNode.parents ( ) :  Vector
ClassNode.thisClass ( ) :  Class
ClassNode.thisClass ( Class p1 ) :  Class

cdk-1.2.10.jar, ClassNodeAgent.class
package org.omegahat.Environment.Tools.ClassHierarchy
ClassNodeAgent.addClass ( Class p1 ) [abstract] :  Environment.Tools.ClassHierarchy.ClassNode
ClassNodeAgent.addClass ( Class p1, Environment.Tools.ClassHierarchy.ClassNode p2 ) [abstract] :  Environment.Tools.ClassHierarchy.ClassNode

cdk-1.2.10.jar, ClassPathViewer.class
package org.omegahat.Environment.GUI
ClassPathViewer.addSelectionListener ( ListSelectionListener p1 ) :  void
ClassPathViewer.assignPerformed ( Environment.Utils.OrderedListEvent p1 ) :  void
ClassPathViewer.ClassPathViewer ( Environment.Interpreter.Evaluator p1 )
ClassPathViewer.ClassPathViewer ( Environment.Interpreter.Evaluator p1, boolean p2 )
ClassPathViewer.getName ( Object p1 ) :  String
ClassPathViewer.make ( ) :  boolean
ClassPathViewer.makeElement ( Object p1 ) :  Component
ClassPathViewer.merge ( Environment.Tools.ClassList.ClassLocator p1 ) :  int
ClassPathViewer.removePerformed ( Environment.Utils.OrderedListEvent p1 ) :  void

cdk-1.2.10.jar, ClassPathViewerFrame.class
package org.omegahat.Environment.GUI
ClassPathViewerFrame.ClassPathViewerFrame ( )
ClassPathViewerFrame.ClassPathViewerFrame ( Environment.GUI.ClassPathViewer p1 )
ClassPathViewerFrame.ClassPathViewerFrame ( Environment.Interpreter.Evaluator p1 )
ClassPathViewerFrame.ClassPathViewerFrame ( Environment.Interpreter.Evaluator p1, boolean p2 )

cdk-1.2.10.jar, ClassReference.class
package org.omegahat.Environment.Parser.Parse
ClassReference.ClassReference ( )
ClassReference.ClassReference ( Environment.Parser.Parse.FieldAccess p1 )
ClassReference.ClassReference ( Environment.Parser.Parse.Name p1 )
ClassReference.ClassReference ( String p1 )
ClassReference.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ClassReference.processFieldAccess ( Environment.Parser.Parse.FieldAccess p1 ) :  boolean

cdk-1.2.10.jar, ClassTreeRenderer.class
package org.omegahat.Environment.GUITools
ClassTreeRenderer.ClassTreeRenderer ( )
ClassTreeRenderer.getTreeCellRendererComponent ( JTree p1, Object p2, boolean p3, boolean p4, boolean p5, int p6, boolean p7 ) :  Component

cdk-1.2.10.jar, ClassTreeViewer.class
package org.omegahat.Environment.GUI
ClassTreeViewer.ClassTreeViewer ( )
ClassTreeViewer.ClassTreeViewer ( Environment.Tools.ClassList.ClassList p1 )
ClassTreeViewer.getTreeCellRendererComponent ( JTree p1, Object p2, boolean p3, boolean p4, boolean p5, int p6, boolean p7 ) :  Component

cdk-1.2.10.jar, ClassViewer.class
package org.omegahat.Environment.GUI
ClassViewer.add ( Object p1 ) :  String
ClassViewer.ClassViewer ( Environment.Interpreter.BasicEvaluator p1, Environment.Tools.ClassList.ClassList p2 )
ClassViewer.ClassViewer ( Environment.Interpreter.BasicEvaluator p1, Object p2 )
ClassViewer.listView ( ) :  JList
ClassViewer.update ( Environment.Tools.ClassList.ClassList p1 ) :  int

cdk-1.2.10.jar, ClassViewerTreeModel.class
package org.omegahat.Environment.GUI
ClassViewerTreeModel.addTreeModelListener ( TreeModelListener p1 ) :  void
ClassViewerTreeModel.ClassViewerTreeModel ( )
ClassViewerTreeModel.ClassViewerTreeModel ( Environment.Tools.ClassList.ClassList p1 )
ClassViewerTreeModel.getChild ( Object p1, int p2 ) :  Object
ClassViewerTreeModel.getChildCount ( Object p1 ) :  int
ClassViewerTreeModel.getClassList ( ) :  Environment.Tools.ClassList.ClassList
ClassViewerTreeModel.getIndexOfChild ( Object p1, Object p2 ) :  int
ClassViewerTreeModel.getRoot ( ) :  Object
ClassViewerTreeModel.isLeaf ( Object p1 ) :  boolean
ClassViewerTreeModel.removeTreeModelListener ( TreeModelListener p1 ) :  void
ClassViewerTreeModel.setClassList ( Environment.Tools.ClassList.ClassList p1 ) :  Environment.Tools.ClassList.ClassList
ClassViewerTreeModel.valueForPathChanged ( TreePath p1, Object p2 ) :  void

cdk-1.2.10.jar, Closure.class
package org.omegahat.Environment.Language
Closure.Closure ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Interpreter.Evaluator p6 )
Closure.eval ( Environment.Databases.Database p1, boolean p2, Environment.Interpreter.Evaluator p3 ) :  Object
Closure.findStatics ( Environment.Parser.Parse.ExpressionInt p1 ) :  int
Closure.initializeStatics ( Environment.Interpreter.Evaluator p1 ) :  int
Closure.isInitialized ( ) :  boolean
Closure.isInitialized ( boolean p1 ) :  boolean
Closure.isStaticVariable ( Environment.Parser.Parse.LocalVariable p1 ) :  boolean
Closure.staticDeclarations ( ) :  Environment.Parser.Parse.List
Closure.staticDeclarations ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
Closure.staticVariables ( ) :  Environment.Databases.Database
Closure.staticVariables ( Environment.Databases.Database p1 ) :  Environment.Databases.Database

cdk-1.2.10.jar, ClosureDatabase.class
package org.omegahat.Environment.Databases
ClosureDatabase.ClosureDatabase ( )
ClosureDatabase.ClosureDatabase ( int p1 )
ClosureDatabase.ClosureDatabase ( String p1 )

cdk-1.2.10.jar, CNNClassificationModel.class
package org.openscience.cdk.qsar.model.R
CNNClassificationModel.build ( ) :  void
CNNClassificationModel.CNNClassificationModel ( )
CNNClassificationModel.CNNClassificationModel ( double[ ][ ] x, String[ ] y, int size )
CNNClassificationModel.CNNClassificationModel ( double[ ][ ] x, String[ ][ ] y, int size )
CNNClassificationModel.getFitFitted ( ) :  double[ ][ ]
CNNClassificationModel.getFitHessian ( ) :  double[ ][ ]
CNNClassificationModel.getFitResiduals ( ) :  double[ ][ ]
CNNClassificationModel.getFitValue ( ) :  double
CNNClassificationModel.getFitWeights ( ) :  double[ ]
CNNClassificationModel.getPredictPredictedClass ( ) :  String[ ]
CNNClassificationModel.getPredictPredictedRaw ( ) :  double[ ][ ]
CNNClassificationModel.loadModel ( String fileName ) :  void
CNNClassificationModel.loadModel ( String serializedModel, String modelName ) :  void
CNNClassificationModel.predict ( ) :  void
CNNClassificationModel.setParameters ( String key, Object obj ) :  void

cdk-1.2.10.jar, CNNClassificationModelFit.class
package org.openscience.cdk.qsar.model.R
CNNClassificationModelFit.CNNClassificationModelFit ( int noutput, int nobs, double[ ] weights, double[ ] fitted, double[ ] residual, double value )
CNNClassificationModelFit.CNNClassificationModelFit ( int noutput, int nobs, double[ ] weights, double[ ] fitted, double[ ] residual, double value, double[ ] hessian )
CNNClassificationModelFit.getFitted ( ) :  double[ ][ ]
CNNClassificationModelFit.getHessian ( ) :  double[ ][ ]
CNNClassificationModelFit.getResiduals ( ) :  double[ ][ ]
CNNClassificationModelFit.getValue ( ) :  double
CNNClassificationModelFit.getWeights ( ) :  double[ ]
CNNClassificationModelFit.setFitted ( double[ ][ ] fitted ) :  void
CNNClassificationModelFit.setHessian ( double[ ][ ] theHessian ) :  void
CNNClassificationModelFit.setResiduals ( double[ ][ ] residuals ) :  void
CNNClassificationModelFit.setValue ( double value ) :  void
CNNClassificationModelFit.setWeights ( double[ ] weights ) :  void

cdk-1.2.10.jar, CNNClassificationModelPredict.class
package org.openscience.cdk.qsar.model.R
CNNClassificationModelPredict.CNNClassificationModelPredict ( int noutput, double values )
CNNClassificationModelPredict.CNNClassificationModelPredict ( int noutput, double[ ] values )
CNNClassificationModelPredict.CNNClassificationModelPredict ( String values )
CNNClassificationModelPredict.CNNClassificationModelPredict ( String[ ] values )
CNNClassificationModelPredict.getPredictedClass ( ) :  String[ ]
CNNClassificationModelPredict.getPredictedRaw ( ) :  double[ ][ ]
CNNClassificationModelPredict.setPredictedRaw ( double[ ][ ] predicted ) :  void

cdk-1.2.10.jar, CNNRegressionModel.class
package org.openscience.cdk.qsar.model.R
CNNRegressionModel.build ( ) :  void
CNNRegressionModel.CNNRegressionModel ( )
CNNRegressionModel.CNNRegressionModel ( double[ ][ ] x, double[ ] y, int size )
CNNRegressionModel.CNNRegressionModel ( double[ ][ ] x, double[ ][ ] y, int size )
CNNRegressionModel.getFitFitted ( ) :  double[ ][ ]
CNNRegressionModel.getFitHessian ( ) :  double[ ][ ]
CNNRegressionModel.getFitResiduals ( ) :  double[ ][ ]
CNNRegressionModel.getFitValue ( ) :  double
CNNRegressionModel.getFitWeights ( ) :  double[ ]
CNNRegressionModel.getPredictPredicted ( ) :  double[ ][ ]
CNNRegressionModel.loadModel ( String fileName ) :  void
CNNRegressionModel.loadModel ( String serializedModel, String modelName ) :  void
CNNRegressionModel.predict ( ) :  void
CNNRegressionModel.setParameters ( String key, Object obj ) :  void
CNNRegressionModel.summary ( ) :  R.CNNRegressionModelSummary
package org.openscience.cdk.qsar.model.R2
CNNRegressionModel.build ( ) :  void
CNNRegressionModel.CNNRegressionModel ( )
CNNRegressionModel.CNNRegressionModel ( double[ ][ ] x, double[ ] y, int size )
CNNRegressionModel.CNNRegressionModel ( double[ ][ ] x, double[ ][ ] y, int size )
CNNRegressionModel.getCensored ( ) :  JRI.RBool
CNNRegressionModel.getConn ( ) :  double[ ]
CNNRegressionModel.getDecay ( ) :  double
CNNRegressionModel.getEntropy ( ) :  JRI.RBool
CNNRegressionModel.getFittedValues ( ) :  double[ ][ ]
CNNRegressionModel.getN ( ) :  double[ ]
CNNRegressionModel.getNconn ( ) :  double[ ]
CNNRegressionModel.getNsunits ( ) :  double
CNNRegressionModel.getNunits ( ) :  double
CNNRegressionModel.getPredictions ( ) :  double[ ][ ]
CNNRegressionModel.getResiduals ( ) :  double[ ][ ]
CNNRegressionModel.getSoftmax ( ) :  JRI.RBool
CNNRegressionModel.getValue ( ) :  double
CNNRegressionModel.getWts ( ) :  double[ ]
CNNRegressionModel.loadModel ( String fileName ) :  void
CNNRegressionModel.loadModel ( String serializedModel, String modelName ) :  void
CNNRegressionModel.predict ( ) :  void
CNNRegressionModel.setParameters ( String key, Object obj ) :  void
CNNRegressionModel.summary ( ) :  JRI.RList

cdk-1.2.10.jar, CNNRegressionModelFit.class
package org.openscience.cdk.qsar.model.R
CNNRegressionModelFit.CNNRegressionModelFit ( int noutput, int nobs, double[ ] weights, double[ ] fitted, double[ ] residual, double value )
CNNRegressionModelFit.CNNRegressionModelFit ( int noutput, int nobs, double[ ] weights, double[ ] fitted, double[ ] residual, double value, double[ ] hessian )
CNNRegressionModelFit.getFitted ( ) :  double[ ][ ]
CNNRegressionModelFit.getHessian ( ) :  double[ ][ ]
CNNRegressionModelFit.getResiduals ( ) :  double[ ][ ]
CNNRegressionModelFit.getValue ( ) :  double
CNNRegressionModelFit.getWeights ( ) :  double[ ]
CNNRegressionModelFit.setFitted ( double[ ][ ] fitted ) :  void
CNNRegressionModelFit.setHessian ( double[ ][ ] theHessian ) :  void
CNNRegressionModelFit.setResiduals ( double[ ][ ] residuals ) :  void
CNNRegressionModelFit.setValue ( double value ) :  void
CNNRegressionModelFit.setWeights ( double[ ] weights ) :  void

cdk-1.2.10.jar, CNNRegressionModelPredict.class
package org.openscience.cdk.qsar.model.R
CNNRegressionModelPredict.CNNRegressionModelPredict ( int noutput, double values )
CNNRegressionModelPredict.CNNRegressionModelPredict ( int noutput, double[ ] values )
CNNRegressionModelPredict.getPredicted ( ) :  double[ ][ ]
CNNRegressionModelPredict.setPredicted ( double[ ][ ] predicted ) :  void

cdk-1.2.10.jar, CNNRegressionModelSummary.class
package org.openscience.cdk.qsar.model.R
CNNRegressionModelSummary.CNNRegressionModelSummary ( double[ ] n, boolean entropy, boolean softmax, boolean censored, double value, double[ ] residuals )
CNNRegressionModelSummary.CNNRegressionModelSummary ( int[ ] n, boolean entropy, boolean softmax, boolean censored, double value, double[ ] residuals )
CNNRegressionModelSummary.getCensored ( ) :  boolean
CNNRegressionModelSummary.getEntropy ( ) :  boolean
CNNRegressionModelSummary.getNumNeurons ( ) :  int[ ]
CNNRegressionModelSummary.getResiduals ( ) :  double[ ]
CNNRegressionModelSummary.getSoftmax ( ) :  boolean
CNNRegressionModelSummary.getValue ( ) :  double

cdk-1.2.10.jar, CodeAttr.class
package jas
CodeAttr.addGenericAttr ( GenericAttr g ) :  void
CodeAttr.addInsn ( Insn insn ) :  void
CodeAttr.CodeAttr ( )
CodeAttr.setCatchtable ( Catchtable ctb ) :  void
CodeAttr.setLineTable ( LineTableAttr ltab ) :  void
CodeAttr.setLocalVarTable ( LocalVarTableAttr lvar ) :  void
CodeAttr.setStackSize ( short stack_size ) :  void
CodeAttr.setVarSize ( short num_vars ) :  void
CodeAttr.toString ( ) :  String

cdk-1.2.10.jar, Comment.class
package org.omegahat.Environment.Parser.Parse
Comment.Comment ( )
Comment.Comment ( String p1 )
Comment.nextComment ( ) :  Environment.Parser.Parse.Comment
Comment.nextComment ( Environment.Parser.Parse.Comment p1 ) :  Environment.Parser.Parse.Comment
Comment.showComments ( ) :  String
Comment.text ( ) :  String
Comment.text ( String p1 ) :  String

cdk-1.2.10.jar, ConditionalExpressionStatement.class
package org.omegahat.Environment.Parser.Parse
ConditionalExpressionStatement.body ( ) :  Object
ConditionalExpressionStatement.body ( Object p1 ) :  Object
ConditionalExpressionStatement.condition ( ) :  Object
ConditionalExpressionStatement.condition ( Object p1 ) :  Object
ConditionalExpressionStatement.ConditionalExpressionStatement ( )
ConditionalExpressionStatement.ConditionalExpressionStatement ( Object p1, Object p2 )
ConditionalExpressionStatement.conditionIsTrue ( Environment.Interpreter.Evaluator p1 ) :  boolean
ConditionalExpressionStatement.evaluateBody ( Environment.Interpreter.Evaluator p1 ) :  Object
ConditionalExpressionStatement.prefix ( ) :  String
ConditionalExpressionStatement.suffix ( ) :  String
ConditionalExpressionStatement.toString ( ) :  String

cdk-1.2.10.jar, ConfigManager.class
package net.sf.jnati.deploy.artefact
ConfigManager.getConfig ( String id, String version ) [static] :  Configuration
ConfigManager.getDefaultConfig ( ) [static] :  Configuration

cdk-1.2.10.jar, Configuration.class
package sea36.util.config
Configuration.Configuration ( )
Configuration.Configuration ( Configuration parentConfig, Map params )
Configuration.Configuration ( Map params )
Configuration.getProperty ( String key ) :  String
Configuration.loadConfiguration ( InputStream in ) :  void
Configuration.loadDefaults ( InputStream in ) :  void
Configuration.setConfiguration ( Map config ) :  void
Configuration.setDefaults ( Map defaults ) :  void

cdk-1.2.10.jar, ConjugateGradientMethod.class
package org.openscience.cdk.modeling.forcefield
ConjugateGradientMethod.ConjugateGradientMethod ( )
ConjugateGradientMethod.initialize ( GVector gradient ) :  void
ConjugateGradientMethod.setDirection ( GVector gradient, GVector previousGradient ) :  void
ConjugateGradientMethod.setFletcherReeves_uk ( GVector gkminus1, GVector gk ) :  void
ConjugateGradientMethod.setPolankRibierePlus_uk ( GVector gkminus1, GVector gk ) :  void

cdk-1.2.10.jar, ConstantExpression.class
package org.omegahat.Environment.Parser.Parse
ConstantExpression.ConstantExpression ( )
ConstantExpression.ConstantExpression ( Object p1 )
ConstantExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ConstantExpression.toString ( ) :  String
ConstantExpression.value ( ) :  Object
ConstantExpression.value ( Object p1 ) :  Object

cdk-1.2.10.jar, ConstantSymbol.class
package org.omegahat.Environment.Parser.Parse
ConstantSymbol.ConstantSymbol ( int p1 )
ConstantSymbol.ConstantSymbol ( String p1 )
ConstantSymbol.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ConstantSymbol.toString ( ) :  String
ConstantSymbol.type ( ) :  int
ConstantSymbol.type ( int p1 ) :  int
ConstantSymbol.type ( String p1 ) :  int

cdk-1.2.10.jar, ConstAttr.class
package jas
ConstAttr.ConstAttr ( CP val )

cdk-1.2.10.jar, ConstructorDefinitionExpression.class
package org.omegahat.Environment.Parser.Parse
ConstructorDefinitionExpression.ConstructorDefinitionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 )
ConstructorDefinitionExpression.toString ( ) :  String

cdk-1.2.10.jar, ConstructorExpression.class
package org.omegahat.Environment.Parser.Parse
ConstructorExpression.ConstructorExpression ( )
ConstructorExpression.ConstructorExpression ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2 )
ConstructorExpression.ConstructorExpression ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2, boolean p3 )
ConstructorExpression.ConstructorExpression ( Environment.Parser.Parse.Name p1, Object[ ] p2, boolean p3 )
ConstructorExpression.ConstructorExpression ( Object p1, Environment.Parser.Parse.List p2 )
ConstructorExpression.ConstructorExpression ( Object p1, Object p2, Environment.Parser.Parse.List p3 )
ConstructorExpression.ConstructorExpression ( String p1, Environment.Parser.Parse.List p2 )
ConstructorExpression.ConstructorExpression ( String p1, Environment.Parser.Parse.List p2, boolean p3 )
ConstructorExpression.ConstructorExpression ( String p1, Object[ ] p2 )
ConstructorExpression.ConstructorExpression ( String p1, Object[ ] p2, boolean p3 )
ConstructorExpression.eval ( Class p1, Environment.Interpreter.Evaluator p2 ) :  Object
ConstructorExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ConstructorExpression.matchConstructor ( Constructor p1, Class[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Class[ ]
ConstructorExpression.searchConstructors ( Class p1, Object[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Constructor

cdk-1.2.10.jar, ControlFlowException.class
package org.omegahat.Environment.Parser.Parse
ControlFlowException.ControlFlowException ( )
ControlFlowException.ControlFlowException ( int p1, Object p2 )
ControlFlowException.type ( ) :  int
ControlFlowException.type ( int p1 ) :  int
ControlFlowException.value ( ) :  Object
ControlFlowException.value ( Object p1 ) :  Object

cdk-1.2.10.jar, ConvertibleClassifier.class
package org.omegahat.Interfaces.NativeInterface
ConvertibleClassifier.add ( Object p1 ) :  boolean
ConvertibleClassifier.ConvertibleClassifier ( )
ConvertibleClassifier.ConvertibleClassifier ( Environment.Interpreter.Evaluator p1 )
ConvertibleClassifier.ConvertibleClassifier ( int p1 )
ConvertibleClassifier.getConvertibleClasses ( ) :  String[ ]
ConvertibleClassifier.getEvaluator ( ) :  Environment.Interpreter.Evaluator
ConvertibleClassifier.isConvertible ( Object p1 ) :  boolean
ConvertibleClassifier.isConvertible ( Object p1, Class p2 ) :  boolean
ConvertibleClassifier.longCheck ( Class p1, Object p2 ) :  boolean
ConvertibleClassifier.setConvertible ( Class p1, boolean p2 ) :  void
ConvertibleClassifier.setConvertible ( Class p1, int p2, boolean p3 ) :  void
ConvertibleClassifier.setEvaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator

cdk-1.2.10.jar, ConvertibleClassifierInt.class
package org.omegahat.Interfaces.NativeInterface
ConvertibleClassifierInt.getConvertibleClasses ( ) [abstract] :  String[ ]
ConvertibleClassifierInt.isConvertible ( Object p1 ) [abstract] :  boolean
ConvertibleClassifierInt.setConvertible ( Class p1, int p2, boolean p3 ) [abstract] :  void

cdk-1.2.10.jar, Copyable.class
package org.omegahat.Environment.DataStructures
Copyable.copy ( ) [abstract] :  Object
Copyable.copy ( boolean p1 ) [abstract] :  Object

cdk-1.2.10.jar, CP.class
package jas
CP.CP ( )

cdk-1.2.10.jar, Database.class
package org.omegahat.Environment.Databases
Database.assign ( String p1, Object p2 ) [abstract] :  boolean
Database.attach ( Environment.Databases.DatabaseCustomer p1 ) [abstract] :  boolean
Database.clear ( ) [abstract] :  void
Database.detach ( Environment.Databases.DatabaseCustomer p1 ) [abstract] :  boolean
Database.exists ( String p1 ) [abstract] :  boolean
Database.get ( String p1 ) [abstract] :  Object
Database.getName ( ) [abstract] :  String
Database.objects ( ) [abstract] :  String[ ]
Database.remove ( String p1 ) [abstract] :  Object
Database.setName ( String p1 ) [abstract] :  String
Database.size ( ) [abstract] :  int

cdk-1.2.10.jar, DatabaseAssignEvent.class
package org.omegahat.Environment.Databases
DatabaseAssignEvent.DatabaseAssignEvent ( String p1, Environment.Databases.ObjectDatabase p2 )

cdk-1.2.10.jar, DatabaseAssignListener.class
package org.omegahat.Environment.Databases
DatabaseAssignListener.assignPerformed ( Environment.Databases.DatabaseAssignEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, DatabaseAttachEvent.class
package org.omegahat.Environment.Databases
DatabaseAttachEvent.DatabaseAttachEvent ( Environment.Databases.Database p1, Environment.Databases.SearchPath p2 )

cdk-1.2.10.jar, DatabaseAttachListener.class
package org.omegahat.Environment.Databases
DatabaseAttachListener.attachPerformed ( Environment.Databases.DatabaseAttachEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, DatabaseDetachEvent.class
package org.omegahat.Environment.Databases
DatabaseDetachEvent.DatabaseDetachEvent ( Environment.Databases.Database p1, Environment.Databases.SearchPath p2 )

cdk-1.2.10.jar, DatabaseDetachListener.class
package org.omegahat.Environment.Databases
DatabaseDetachListener.detachPerformed ( Environment.Databases.DatabaseDetachEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, DatabaseEvent.class
package org.omegahat.Environment.Databases
DatabaseEvent.database ( ) :  Environment.Databases.Database
DatabaseEvent.name ( ) :  String

cdk-1.2.10.jar, DatabaseListModel.class
DatabaseListModel.addListDataListener ( ListDataListener p1 ) :  void
DatabaseListModel.database ( ) :  Environment.Databases.Database
DatabaseListModel.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
DatabaseListModel.DatabaseListModel ( Environment.Databases.Database p1 )
DatabaseListModel.getElementAt ( int p1 ) :  Object
DatabaseListModel.getSize ( ) :  int
DatabaseListModel.removeListDataListener ( ListDataListener p1 ) :  void

cdk-1.2.10.jar, DatabaseNotifier.class
package org.omegahat.Environment.Databases
DatabaseNotifier.addAssignListener ( Environment.Databases.DatabaseAssignListener p1 ) [abstract] :  boolean
DatabaseNotifier.addListener ( int p1, Object p2 ) [abstract] :  boolean
DatabaseNotifier.addRemoveListener ( Environment.Databases.DatabaseRemoveListener p1 ) [abstract] :  boolean
DatabaseNotifier.assign ( String p1, Object p2, boolean p3 ) [abstract] :  boolean
DatabaseNotifier.remove ( String p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, DatabaseObjectEvent.class
package org.omegahat.Environment.Databases
DatabaseObjectEvent.DatabaseObjectEvent ( String p1, Environment.Databases.Database p2 )
DatabaseObjectEvent.name ( ) :  String
DatabaseObjectEvent.name ( String p1 ) :  String
DatabaseObjectEvent.object ( ) :  String

cdk-1.2.10.jar, DatabaseObjectRenderer.class
DatabaseObjectRenderer.database ( ) :  Environment.Databases.Database
DatabaseObjectRenderer.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
DatabaseObjectRenderer.DatabaseObjectRenderer ( )
DatabaseObjectRenderer.DatabaseObjectRenderer ( Environment.Databases.Database p1 )
DatabaseObjectRenderer.getListCellRendererComponent ( JList p1, Object p2, int p3, boolean p4, boolean p5 ) :  Component

cdk-1.2.10.jar, DatabaseRemoveEvent.class
package org.omegahat.Environment.Databases
DatabaseRemoveEvent.DatabaseRemoveEvent ( String p1, Environment.Databases.ObjectDatabase p2 )

cdk-1.2.10.jar, DatabaseRemoveListener.class
package org.omegahat.Environment.Databases
DatabaseRemoveListener.removePerformed ( Environment.Databases.DatabaseRemoveEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, DatabaseViewer.class
package org.omegahat.Environment.GUI
DatabaseViewer.assignPerformed ( Environment.Databases.DatabaseAssignEvent p1 ) :  void
DatabaseViewer.attachPerformed ( Environment.Databases.DatabaseAttachEvent p1 ) :  void
DatabaseViewer.database ( ) :  Environment.Databases.Database
DatabaseViewer.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
DatabaseViewer.DatabaseViewer ( Environment.Databases.Database p1 )
DatabaseViewer.DatabaseViewer ( Environment.Databases.Database p1, Environment.Interpreter.Evaluator p2 )
DatabaseViewer.defaultRenderer ( ) :  ListCellRenderer
DatabaseViewer.detachPerformed ( Environment.Databases.DatabaseDetachEvent p1 ) :  void
DatabaseViewer.make ( ) :  boolean
DatabaseViewer.removePerformed ( Environment.Databases.DatabaseRemoveEvent p1 ) :  void
DatabaseViewer.renderer ( ) :  ListCellRenderer
DatabaseViewer.renderer ( ListCellRenderer p1 ) :  ListCellRenderer

cdk-1.2.10.jar, DatabaseViewerFrame.class
package org.omegahat.Environment.GUI
DatabaseViewerFrame.DatabaseViewerFrame ( )
DatabaseViewerFrame.DatabaseViewerFrame ( Environment.Databases.Database p1 )
DatabaseViewerFrame.DatabaseViewerFrame ( Environment.GUI.DatabaseViewer p1 )

cdk-1.2.10.jar, DataLexer.class
package org.omegahat.Environment.Tools.DataScanner
DataLexer.addElement ( Object p1 ) :  int
DataLexer.addElement ( String p1, int p2 ) :  int
DataLexer.currentElements ( ) :  Vector
DataLexer.currentElements ( Vector p1 ) :  Vector
DataLexer.DataLexer ( InputBuffer p1 )
DataLexer.DataLexer ( InputStream p1 )
DataLexer.DataLexer ( Reader p1 )
DataLexer.endRecord ( ) :  Object
DataLexer.mDataWord ( boolean p1 ) :  void
DataLexer.mDOT ( boolean p1 ) :  void
DataLexer.mEXPONENT ( boolean p1 ) :  void
DataLexer.mFLOAT_SUFFIX ( boolean p1 ) :  void
DataLexer.mHEX_DIGIT ( boolean p1 ) :  void
DataLexer.mNUM_INT ( boolean p1 ) :  void
DataLexer.mNumber ( boolean p1 ) :  void
DataLexer.mQuoted ( boolean p1 ) :  void
DataLexer.mTerminator ( boolean p1 ) :  void
DataLexer.mWS ( boolean p1 ) :  void
DataLexer.nextToken ( ) :  Token

cdk-1.2.10.jar, DataScanner.class
package org.omegahat.Environment.Tools.DataScanner
DataScanner.currentRecord ( ) :  Object
DataScanner.DataScanner ( InputStream p1 )
DataScanner.DataScanner ( Reader p1 )
DataScanner.mEOF ( ) :  Object
DataScanner.nextRecord ( ) :  Object
DataScanner.nextRecord ( boolean p1 ) :  Object
DataScanner.nextToken ( ) :  Token
DataScanner.readRecords ( ) :  long
DataScanner.resetRecord ( ) :  Object

cdk-1.2.10.jar, DataTokenizer.class
package org.omegahat.Environment.Tools.DataScanner
DataTokenizer.currentRecord ( ) :  Object
DataTokenizer.DataTokenizer ( )
DataTokenizer.DataTokenizer ( InputStream p1 )
DataTokenizer.DataTokenizer ( Reader p1 )
DataTokenizer.endRecord ( ) :  Object
DataTokenizer.nextRecord ( ) :  Object
DataTokenizer.nextRecord ( boolean p1 ) :  Object
DataTokenizer.readRecords ( ) :  long
DataTokenizer.record ( ) :  Vector
DataTokenizer.record ( Vector p1 ) :  Vector

cdk-1.2.10.jar, DebugAminoAcid.class
package org.openscience.cdk.debug
DebugAminoAcid.addAtomParity ( IAtomParity parity ) :  void
DebugAminoAcid.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugAminoAcid.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugAtom.class
package org.openscience.cdk.debug
DebugAtom.getHydrogenCount ( ) :  Integer
DebugAtom.setHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.2.10.jar, DebugAtomContainer.class
package org.openscience.cdk.debug
DebugAtomContainer.addAtomParity ( IAtomParity parity ) :  void
DebugAtomContainer.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugAtomContainer.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugBioPolymer.class
package org.openscience.cdk.debug
DebugBioPolymer.addAtomParity ( IAtomParity parity ) :  void
DebugBioPolymer.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugBioPolymer.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugBond.class
package org.openscience.cdk.debug
DebugBond.DebugBond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo )
DebugBond.setStereo ( int stereo ) :  void

cdk-1.2.10.jar, DebugChemObjectBuilder.class
package org.openscience.cdk.debug
DebugChemObjectBuilder.getInstance ( ) [static] :  DebugChemObjectBuilder
DebugChemObjectBuilder.newAdductFormula ( ) :  IAdductFormula
DebugChemObjectBuilder.newAdductFormula ( IMolecularFormula formula ) :  IAdductFormula
DebugChemObjectBuilder.newAminoAcid ( ) :  IAminoAcid
DebugChemObjectBuilder.newAtom ( ) :  IAtom
DebugChemObjectBuilder.newAtom ( IElement element ) :  IAtom
DebugChemObjectBuilder.newAtom ( String elementSymbol ) :  IAtom
DebugChemObjectBuilder.newAtom ( String elementSymbol, Point2d point2d ) :  IAtom
DebugChemObjectBuilder.newAtom ( String elementSymbol, Point3d point3d ) :  IAtom
DebugChemObjectBuilder.newAtomContainer ( ) :  IAtomContainer
DebugChemObjectBuilder.newAtomContainer ( IAtomContainer container ) :  IAtomContainer
DebugChemObjectBuilder.newAtomContainer ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount ) :  IAtomContainer
DebugChemObjectBuilder.newAtomContainerSet ( ) :  IAtomContainerSet
DebugChemObjectBuilder.newAtomParity ( IAtom centralAtom, IAtom first, IAtom second, IAtom third, IAtom fourth, int parity ) :  IAtomParity
DebugChemObjectBuilder.newAtomType ( IElement element ) :  IAtomType
DebugChemObjectBuilder.newAtomType ( String elementSymbol ) :  IAtomType
DebugChemObjectBuilder.newAtomType ( String identifier, String elementSymbol ) :  IAtomType
DebugChemObjectBuilder.newBioPolymer ( ) :  IBioPolymer
DebugChemObjectBuilder.newBond ( ) :  IBond
DebugChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2 ) :  IBond
DebugChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order ) :  IBond
DebugChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo ) :  IBond
DebugChemObjectBuilder.newBond ( IAtom[ ] atoms ) :  IBond
DebugChemObjectBuilder.newBond ( IAtom[ ] atoms, IBond.Order order ) :  IBond
DebugChemObjectBuilder.newChemFile ( ) :  IChemFile
DebugChemObjectBuilder.newChemModel ( ) :  IChemModel
DebugChemObjectBuilder.newChemObject ( ) :  IChemObject
DebugChemObjectBuilder.newChemObject ( IChemObject object ) :  IChemObject
DebugChemObjectBuilder.newChemSequence ( ) :  IChemSequence
DebugChemObjectBuilder.newCrystal ( ) :  ICrystal
DebugChemObjectBuilder.newCrystal ( IAtomContainer container ) :  ICrystal
DebugChemObjectBuilder.newElectronContainer ( ) :  IElectronContainer
DebugChemObjectBuilder.newElement ( ) :  IElement
DebugChemObjectBuilder.newElement ( IElement element ) :  IElement
DebugChemObjectBuilder.newElement ( String symbol ) :  IElement
DebugChemObjectBuilder.newElement ( String symbol, int atomicNumber ) :  IElement
DebugChemObjectBuilder.newFragmentAtom ( ) :  IFragmentAtom
DebugChemObjectBuilder.newIsotope ( IElement element ) :  IIsotope
DebugChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, double exactMass, double abundance ) :  IIsotope
DebugChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, int massNumber, double exactMass, double abundance ) :  IIsotope
DebugChemObjectBuilder.newIsotope ( String elementSymbol ) :  IIsotope
DebugChemObjectBuilder.newIsotope ( String elementSymbol, int massNumber ) :  IIsotope
DebugChemObjectBuilder.newLonePair ( ) :  ILonePair
DebugChemObjectBuilder.newLonePair ( IAtom atom ) :  ILonePair
DebugChemObjectBuilder.newMapping ( IChemObject objectOne, IChemObject objectTwo ) :  IMapping
DebugChemObjectBuilder.newMolecularFormula ( ) :  IMolecularFormula
DebugChemObjectBuilder.newMolecularFormulaSet ( ) :  IMolecularFormulaSet
DebugChemObjectBuilder.newMolecularFormulaSet ( IMolecularFormula formula ) :  IMolecularFormulaSet
DebugChemObjectBuilder.newMolecule ( ) :  IMolecule
DebugChemObjectBuilder.newMolecule ( IAtomContainer container ) :  IMolecule
DebugChemObjectBuilder.newMolecule ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount ) :  IMolecule
DebugChemObjectBuilder.newMoleculeSet ( ) :  IMoleculeSet
DebugChemObjectBuilder.newMonomer ( ) :  IMonomer
DebugChemObjectBuilder.newPDBAtom ( IElement element ) :  IPDBAtom
DebugChemObjectBuilder.newPDBAtom ( String elementSymbol ) :  IPDBAtom
DebugChemObjectBuilder.newPDBAtom ( String elementSymbol, Point3d point3d ) :  IPDBAtom
DebugChemObjectBuilder.newPDBMonomer ( ) :  IPDBMonomer
DebugChemObjectBuilder.newPDBPolymer ( ) :  IPDBPolymer
DebugChemObjectBuilder.newPDBStructure ( ) :  IPDBStructure
DebugChemObjectBuilder.newPolymer ( ) :  IPolymer
DebugChemObjectBuilder.newPseudoAtom ( ) :  IPseudoAtom
DebugChemObjectBuilder.newPseudoAtom ( IAtom atom ) :  IPseudoAtom
DebugChemObjectBuilder.newPseudoAtom ( IElement element ) :  IPseudoAtom
DebugChemObjectBuilder.newPseudoAtom ( String label ) :  IPseudoAtom
DebugChemObjectBuilder.newPseudoAtom ( String label, Point2d point2d ) :  IPseudoAtom
DebugChemObjectBuilder.newPseudoAtom ( String label, Point3d point3d ) :  IPseudoAtom
DebugChemObjectBuilder.newReaction ( ) :  IReaction
DebugChemObjectBuilder.newReactionScheme ( ) :  IReactionScheme
DebugChemObjectBuilder.newReactionSet ( ) :  IReactionSet
DebugChemObjectBuilder.newRing ( ) :  IRing
DebugChemObjectBuilder.newRing ( IAtomContainer container ) :  IRing
DebugChemObjectBuilder.newRing ( int ringSize ) :  IRing
DebugChemObjectBuilder.newRing ( int ringSize, String elementSymbol ) :  IRing
DebugChemObjectBuilder.newRingSet ( ) :  IRingSet
DebugChemObjectBuilder.newSingleElectron ( ) :  ISingleElectron
DebugChemObjectBuilder.newSingleElectron ( IAtom atom ) :  ISingleElectron
DebugChemObjectBuilder.newStrand ( ) :  IStrand
DebugChemObjectBuilder.newStructure ( ) :  IPDBStructure

cdk-1.2.10.jar, DebugCrystal.class
package org.openscience.cdk.debug
DebugCrystal.addAtomParity ( IAtomParity parity ) :  void
DebugCrystal.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugCrystal.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugFragmentAtom.class
package org.openscience.cdk.debug
DebugFragmentAtom.getHydrogenCount ( ) :  Integer
DebugFragmentAtom.setHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.2.10.jar, Debugger.class
package org.omegahat.Environment.Debugger
Debugger.error ( Throwable p1, Environment.Parser.Parse.ExpressionInt p2 ) [abstract] :  Object

cdk-1.2.10.jar, DebugMolecule.class
package org.openscience.cdk.debug
DebugMolecule.addAtomParity ( IAtomParity parity ) :  void
DebugMolecule.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugMolecule.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugMonomer.class
package org.openscience.cdk.debug
DebugMonomer.addAtomParity ( IAtomParity parity ) :  void
DebugMonomer.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugMonomer.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugPolymer.class
package org.openscience.cdk.debug
DebugPolymer.addAtomParity ( IAtomParity parity ) :  void
DebugPolymer.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugPolymer.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugPseudoAtom.class
package org.openscience.cdk.debug
DebugPseudoAtom.getHydrogenCount ( ) :  Integer
DebugPseudoAtom.setHydrogenCount ( Integer hydrogenCount ) :  void

cdk-1.2.10.jar, DebugRing.class
package org.openscience.cdk.debug
DebugRing.addAtomParity ( IAtomParity parity ) :  void
DebugRing.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugRing.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, DebugStrand.class
package org.openscience.cdk.debug
DebugStrand.addAtomParity ( IAtomParity parity ) :  void
DebugStrand.addBond ( int atom1, int atom2, IBond.Order order, int stereo ) :  void
DebugStrand.getAtomParity ( IAtom atom ) :  IAtomParity

cdk-1.2.10.jar, Decrementable.class
package org.omegahat.Environment.DataStructures
Decrementable.decrement ( double p1 ) [abstract] :  Object
Decrementable.decrement ( int p1 ) [abstract] :  Object

cdk-1.2.10.jar, DefaultChemObjectBuilder.class
package org.openscience.cdk
DefaultChemObjectBuilder.getInstance ( ) [static] :  DefaultChemObjectBuilder
DefaultChemObjectBuilder.newAdductFormula ( ) :  IAdductFormula
DefaultChemObjectBuilder.newAdductFormula ( IMolecularFormula formula ) :  IAdductFormula
DefaultChemObjectBuilder.newAminoAcid ( ) :  IAminoAcid
DefaultChemObjectBuilder.newAtom ( ) :  IAtom
DefaultChemObjectBuilder.newAtom ( IElement element ) :  IAtom
DefaultChemObjectBuilder.newAtom ( String elementSymbol ) :  IAtom
DefaultChemObjectBuilder.newAtom ( String elementSymbol, Point2d point2d ) :  IAtom
DefaultChemObjectBuilder.newAtom ( String elementSymbol, Point3d point3d ) :  IAtom
DefaultChemObjectBuilder.newAtomContainer ( ) :  IAtomContainer
DefaultChemObjectBuilder.newAtomContainer ( IAtomContainer container ) :  IAtomContainer
DefaultChemObjectBuilder.newAtomContainer ( int atomCount, int bondCount, int lonePairCount, int singleElectronCount ) :  IAtomContainer
DefaultChemObjectBuilder.newAtomContainerSet ( ) :  IAtomContainerSet
DefaultChemObjectBuilder.newAtomParity ( IAtom centralAtom, IAtom first, IAtom second, IAtom third, IAtom fourth, int parity ) :  IAtomParity
DefaultChemObjectBuilder.newAtomType ( IElement element ) :  IAtomType
DefaultChemObjectBuilder.newAtomType ( String elementSymbol ) :  IAtomType
DefaultChemObjectBuilder.newAtomType ( String identifier, String elementSymbol ) :  IAtomType
DefaultChemObjectBuilder.newBioPolymer ( ) :  IBioPolymer
DefaultChemObjectBuilder.newBond ( ) :  IBond
DefaultChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2 ) :  IBond
DefaultChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order ) :  IBond
DefaultChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo ) :  IBond
DefaultChemObjectBuilder.newBond ( IAtom[ ] atoms ) :  IBond
DefaultChemObjectBuilder.newBond ( IAtom[ ] atoms, IBond.Order order ) :  IBond
DefaultChemObjectBuilder.newChemFile ( ) :  IChemFile
DefaultChemObjectBuilder.newChemModel ( ) :  IChemModel
DefaultChemObjectBuilder.newChemObject ( ) :  IChemObject
DefaultChemObjectBuilder.newChemObject ( IChemObject object ) :  IChemObject
DefaultChemObjectBuilder.newChemSequence ( ) :  IChemSequence
DefaultChemObjectBuilder.newCrystal ( ) :  ICrystal
DefaultChemObjectBuilder.newCrystal ( IAtomContainer container ) :  ICrystal
DefaultChemObjectBuilder.newElectronContainer ( ) :  IElectronContainer
DefaultChemObjectBuilder.newElement ( ) :  IElement
DefaultChemObjectBuilder.newElement ( IElement element ) :  IElement
DefaultChemObjectBuilder.newElement ( String symbol ) :  IElement
DefaultChemObjectBuilder.newElement ( String symbol, int atomicNumber ) :  IElement
DefaultChemObjectBuilder.newFragmentAtom ( ) :  IFragmentAtom
DefaultChemObjectBuilder.newIsotope ( IElement element ) :  IIsotope
DefaultChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, double exactMass, double abundance ) :  IIsotope
DefaultChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, int massNumber, double exactMass, double abundance ) :  IIsotope
DefaultChemObjectBuilder.newIsotope ( String elementSymbol ) :  IIsotope
DefaultChemObjectBuilder.newIsotope ( String elementSymbol, int massNumber ) :  IIsotope
DefaultChemObjectBuilder.newLonePair ( ) :  ILonePair
DefaultChemObjectBuilder.newLonePair ( IAtom atom ) :  ILonePair
DefaultChemObjectBuilder.newMapping ( IChemObject objectOne, IChemObject objectTwo ) :  IMapping
DefaultChemObjectBuilder.newMolecularFormula ( ) :  IMolecularFormula
DefaultChemObjectBuilder.newMolecularFormulaSet ( ) :  IMolecularFormulaSet
DefaultChemObjectBuilder.newMolecularFormulaSet ( IMolecularFormula formula ) :  IMolecularFormulaSet
DefaultChemObjectBuilder.newMolecule ( ) :  IMolecule
DefaultChemObjectBuilder.newMolecule ( IAtomContainer container ) :  IMolecule
DefaultChemObjectBuilder.newMolecule ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount ) :  IMolecule
DefaultChemObjectBuilder.newMoleculeSet ( ) :  IMoleculeSet
DefaultChemObjectBuilder.newMonomer ( ) :  IMonomer
DefaultChemObjectBuilder.newPDBAtom ( IElement element ) :  IPDBAtom
DefaultChemObjectBuilder.newPDBAtom ( String symbol ) :  IPDBAtom
DefaultChemObjectBuilder.newPDBAtom ( String symbol, Point3d coordinate ) :  IPDBAtom
DefaultChemObjectBuilder.newPDBMonomer ( ) :  IPDBMonomer
DefaultChemObjectBuilder.newPDBPolymer ( ) :  IPDBPolymer
DefaultChemObjectBuilder.newPDBStructure ( ) :  IPDBStructure
DefaultChemObjectBuilder.newPolymer ( ) :  IPolymer
DefaultChemObjectBuilder.newPseudoAtom ( ) :  IPseudoAtom
DefaultChemObjectBuilder.newPseudoAtom ( IAtom atom ) :  IPseudoAtom
DefaultChemObjectBuilder.newPseudoAtom ( IElement element ) :  IPseudoAtom
DefaultChemObjectBuilder.newPseudoAtom ( String label ) :  IPseudoAtom
DefaultChemObjectBuilder.newPseudoAtom ( String label, Point2d point2d ) :  IPseudoAtom
DefaultChemObjectBuilder.newPseudoAtom ( String label, Point3d point3d ) :  IPseudoAtom
DefaultChemObjectBuilder.newReaction ( ) :  IReaction
DefaultChemObjectBuilder.newReactionScheme ( ) :  IReactionScheme
DefaultChemObjectBuilder.newReactionSet ( ) :  IReactionSet
DefaultChemObjectBuilder.newRing ( ) :  IRing
DefaultChemObjectBuilder.newRing ( IAtomContainer container ) :  IRing
DefaultChemObjectBuilder.newRing ( int ringSize ) :  IRing
DefaultChemObjectBuilder.newRing ( int ringSize, String elementSymbol ) :  IRing
DefaultChemObjectBuilder.newRingSet ( ) :  IRingSet
DefaultChemObjectBuilder.newSingleElectron ( ) :  ISingleElectron
DefaultChemObjectBuilder.newSingleElectron ( IAtom atom ) :  ISingleElectron
DefaultChemObjectBuilder.newStrand ( ) :  IStrand

cdk-1.2.10.jar, DefaultErrorHandler.class
package org.omegahat.Environment.Debugger
DefaultErrorHandler.DefaultErrorHandler ( )
DefaultErrorHandler.DefaultErrorHandler ( Environment.Interpreter.Evaluator p1 )
DefaultErrorHandler.DefaultErrorHandler ( Throwable p1, String p2, Environment.Interpreter.Evaluator p3 )
DefaultErrorHandler.error ( Environment.Interpreter.EvaluationException p1 ) :  Object
DefaultErrorHandler.error ( Throwable p1, String p2 ) :  Object
DefaultErrorHandler.error ( Throwable p1, String p2, Environment.Parser.Parse.ExpressionInt p3 ) :  Object

cdk-1.2.10.jar, DefaultPromptSource.class
package org.omegahat.Environment.IO
DefaultPromptSource.count ( ) :  int
DefaultPromptSource.count ( int p1 ) :  int
DefaultPromptSource.DefaultPromptSource ( )
DefaultPromptSource.prompt ( ) :  String

cdk-1.2.10.jar, DeferredEagerURLClassLoader.class
package org.omegahat.Environment.System
DeferredEagerURLClassLoader.byteTable ( ) :  Hashtable
DeferredEagerURLClassLoader.byteTable ( Hashtable p1 ) :  Hashtable
DeferredEagerURLClassLoader.DeferredEagerURLClassLoader ( String p1 )
DeferredEagerURLClassLoader.DeferredEagerURLClassLoader ( URL p1 )
DeferredEagerURLClassLoader.defineClass ( String p1 ) :  Class
DeferredEagerURLClassLoader.defineClass ( String p1, byte[ ] p2 ) :  Class

cdk-1.2.10.jar, DirectoryFilter.class
package org.omegahat.Environment.IO
DirectoryFilter.accept ( ) :  boolean
DirectoryFilter.accept ( boolean p1 ) :  boolean
DirectoryFilter.accept ( File p1, String p2 ) :  boolean
DirectoryFilter.DirectoryFilter ( )
DirectoryFilter.DirectoryFilter ( boolean p1 )

cdk-1.2.10.jar, DirectoryNameFilter.class
package org.omegahat.Environment.IO
DirectoryNameFilter.accept ( File p1, String p2 ) :  boolean
DirectoryNameFilter.addName ( String p1 ) :  String
DirectoryNameFilter.DirectoryNameFilter ( )
DirectoryNameFilter.DirectoryNameFilter ( boolean p1 )
DirectoryNameFilter.DirectoryNameFilter ( String p1 )
DirectoryNameFilter.DirectoryNameFilter ( String[ ] p1 )

cdk-1.2.10.jar, DistributedTaskEvent.class
package org.omegahat.Environment.TaskManagement
DistributedTaskEvent.DistributedTaskEvent ( Environment.TaskManagement.TaskManager p1, int p2 )
DistributedTaskEvent.DistributedTaskEvent ( Environment.TaskManagement.TaskManager p1, int p2, Environment.TaskManagement.Task p3 )
DistributedTaskEvent.DistributedTaskEvent ( Environment.TaskManagement.TaskManager p1, int p2, Environment.TaskManagement.Task p3, Object p4 )
DistributedTaskEvent.DistributedTaskEvent ( Environment.TaskManagement.TaskManager p1, int p2, Object p3 )
DistributedTaskEvent.server ( ) :  Object
DistributedTaskEvent.server ( Object p1 ) :  Object
DistributedTaskEvent.task ( ) :  Environment.TaskManagement.Task
DistributedTaskEvent.task ( Environment.TaskManagement.Task p1 ) :  Environment.TaskManagement.Task

cdk-1.2.10.jar, DistributedTaskListener.class
package org.omegahat.Environment.TaskManagement
DistributedTaskListener.serverDiscarded ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean
DistributedTaskListener.serverPoolCleared ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean
DistributedTaskListener.serverRejected ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean
DistributedTaskListener.taskCompleted ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean
DistributedTaskListener.taskDispatched ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean
DistributedTaskListener.taskError ( Environment.TaskManagement.DistributedTaskEvent p1 ) [abstract] :  boolean

cdk-1.2.10.jar, Divisable.class
package org.omegahat.Environment.DataStructures
Divisable.divideValue ( Object p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, DoubleCP.class
package jas
DoubleCP.DoubleCP ( double n )

cdk-1.2.10.jar, DynamicClassLoader.class
package org.omegahat.Environment.System
DynamicClassLoader.classTable ( ) :  Hashtable
DynamicClassLoader.classTable ( Hashtable p1 ) :  Hashtable
DynamicClassLoader.defineClass ( Class p1 ) :  Class
DynamicClassLoader.defineClass ( Class p1, String p2 ) :  Class
DynamicClassLoader.defineClass ( ClassEnv p1, String p2 ) :  Class
DynamicClassLoader.defineClass ( Environment.GUITools.EvaluableInterfaceGenerator p1 ) :  Class
DynamicClassLoader.defineClass ( String p1 ) :  Class
DynamicClassLoader.defineClass ( String p1, ByteArrayOutputStream p2 ) :  Class
DynamicClassLoader.defineClass ( String p1, String p2 ) :  Class
DynamicClassLoader.defineClass ( String[ ] p1, String p2 ) :  Class
DynamicClassLoader.DynamicClassLoader ( )
DynamicClassLoader.DynamicClassLoader ( ClassLoader p1 )
DynamicClassLoader.DynamicClassLoader ( Hashtable p1 )
DynamicClassLoader.loadClass ( String p1, boolean p2 ) :  Class
DynamicClassLoader.removeClass ( Class p1 ) :  boolean

cdk-1.2.10.jar, DynamicCompiler.class
package org.omegahat.Environment.Compile
DynamicCompiler.accessorBody ( String p1, String p2, boolean p3, boolean p4 ) :  CodeAttr
DynamicCompiler.accessorBody ( String p1, String p2, boolean p3, boolean p4, CodeAttr p5 ) :  CodeAttr
DynamicCompiler.addConstructor ( Constructor p1 ) :  CodeAttr
DynamicCompiler.addField ( String p1, Class p2 ) :  Var
DynamicCompiler.addField ( String p1, Class p2, short p3 ) :  Var
DynamicCompiler.addField ( String p1, String p2 ) :  Var
DynamicCompiler.addField ( String p1, String p2, short p3 ) :  Var
DynamicCompiler.addField ( String p1, String p2, short p3, boolean p4 ) :  Var
DynamicCompiler.addField ( Var p1 ) :  Var
DynamicCompiler.addFieldAccessors ( String p1, String p2 ) :  boolean
DynamicCompiler.addFieldAccessors ( String p1, String p2, short p3 ) :  boolean
DynamicCompiler.addFieldAccessors ( String p1, String p2, short p3, int p4 ) :  boolean
DynamicCompiler.addInheritedConstructors ( ) :  int
DynamicCompiler.addReturn ( Class p1, CodeAttr p2 ) :  boolean
DynamicCompiler.addReturn ( Class p1, CodeAttr p2, boolean p3 ) :  boolean
DynamicCompiler.classDef ( ) :  ClassEnv
DynamicCompiler.classDef ( ClassEnv p1 ) :  ClassEnv
DynamicCompiler.className ( ) :  String
DynamicCompiler.className ( Class p1 ) :  String
DynamicCompiler.className ( Class p1, boolean p2 ) :  String
DynamicCompiler.className ( String p1 ) :  String
DynamicCompiler.Debug ( ) :  boolean
DynamicCompiler.Debug ( boolean p1 ) :  boolean
DynamicCompiler.DynamicCompiler ( )
DynamicCompiler.DynamicCompiler ( ClassEnv p1 )
DynamicCompiler.DynamicCompiler ( String p1 )
DynamicCompiler.DynamicCompiler ( String p1, String p2 )
DynamicCompiler.DynamicCompiler ( String p1, String p2, boolean p3 )
DynamicCompiler.DynamicCompiler ( String p1, String p2, String p3 )
DynamicCompiler.file ( ) :  File
DynamicCompiler.file ( File p1 ) :  File
DynamicCompiler.findClass ( Environment.Parser.Parse.Name p1 ) :  Class
DynamicCompiler.findClass ( String p1 ) :  Class
DynamicCompiler.initClassDef ( ) :  ClassEnv
DynamicCompiler.loadCode ( Class p1 ) :  int
DynamicCompiler.mapPrimitive ( Class p1 ) :  String
DynamicCompiler.packageName ( ) :  String
DynamicCompiler.packageName ( String p1 ) :  String
DynamicCompiler.primitiveLoadOp ( Class p1 ) :  short
DynamicCompiler.primitiveToClass ( Class p1 ) :  String
DynamicCompiler.returnPrimitive ( Class p1, CodeAttr p2 ) :  boolean
DynamicCompiler.returnPrimitive ( Class p1, CodeAttr p2, boolean p3 ) :  boolean
DynamicCompiler.superClassName ( ) :  String
DynamicCompiler.superClassName ( String p1 ) :  String
DynamicCompiler.warning ( String p1 ) :  boolean
DynamicCompiler.write ( ) :  boolean
DynamicCompiler.write ( DataOutputStream p1 ) :  boolean
DynamicCompiler.write ( File p1 ) :  boolean
DynamicCompiler.write ( OutputStream p1 ) :  boolean
DynamicCompiler.write ( String p1 ) :  boolean

cdk-1.2.10.jar, DynamicFieldAccess.class
package org.omegahat.Environment.Parser.Parse
DynamicFieldAccess.DynamicFieldAccess ( Environment.Parser.Parse.ExpressionInt p1, String p2 )
DynamicFieldAccess.DynamicFieldAccess ( Environment.Parser.Parse.Name p1 )
DynamicFieldAccess.DynamicFieldAccess ( String p1 )
DynamicFieldAccess.getFieldValue ( Object p1, Class p2, Environment.Interpreter.Evaluator p3 ) :  Object

cdk-1.2.10.jar, DynamicFieldAccessInt.class
package org.omegahat.Environment.Interpreter
DynamicFieldAccessInt.getDynamicField ( String p1 ) [abstract] :  Object
DynamicFieldAccessInt.setDynamicField ( String p1, Object p2 ) [abstract] :  Object

cdk-1.2.10.jar, DynamicFileFilter.class
package org.omegahat.Environment.Tools.FileLocator
DynamicFileFilter.accept ( File p1, String p2 ) :  boolean
DynamicFileFilter.DynamicFileFilter ( )
DynamicFileFilter.target ( ) :  String
DynamicFileFilter.target ( File p1 ) :  String
DynamicFileFilter.target ( String p1 ) :  String

cdk-1.2.10.jar, DynamicMethodAccessInt.class
package org.omegahat.Environment.Interpreter
DynamicMethodAccessInt.invoke ( String p1, Environment.Parser.Parse.List p2, Environment.Interpreter.Evaluator p3 ) [abstract] :  Object
DynamicMethodAccessInt.invoke ( String p1, Object[ ] p2, Environment.Interpreter.Evaluator p3 ) [abstract] :  Object

cdk-1.2.10.jar, EagerURLClassLoader.class
package org.omegahat.Environment.System
EagerURLClassLoader.EagerURLClassLoader ( String p1 )
EagerURLClassLoader.EagerURLClassLoader ( URL p1 )
EagerURLClassLoader.loadAll ( ) :  int

cdk-1.2.10.jar, ElectrostaticInteractions.class
package org.openscience.cdk.modeling.forcefield
ElectrostaticInteractions.ElectrostaticInteractions ( )
ElectrostaticInteractions.functionMMFF94SumEQ ( GVector coords3d ) :  double
ElectrostaticInteractions.getForHessianMMFF94SumEQ ( ) :  double[ ]
ElectrostaticInteractions.getGradientMMFF94SumEQ ( ) :  GVector
ElectrostaticInteractions.getHessianMMFF94SumEQ ( ) :  GMatrix
ElectrostaticInteractions.getInternuclearSeparation ( ) :  double[ ]
ElectrostaticInteractions.getInternuclearSeparationFirstDerivative ( ) :  double[ ][ ]
ElectrostaticInteractions.getInternuclearSeparationSecondDerivative ( ) :  double[ ][ ][ ]
ElectrostaticInteractions.setGradientMMFF94SumEQ ( GVector coords3d ) :  void
ElectrostaticInteractions.setHessianMMFF94SumEQ ( GVector coord3d ) :  void
ElectrostaticInteractions.setInternuclearSeparation ( GVector coords3d ) :  void
ElectrostaticInteractions.setInternuclearSeparationFirstOrderDerivative ( GVector coord3d ) :  void
ElectrostaticInteractions.setInternuclearSeparationSecondDerivative ( GVector coord3d ) :  void
ElectrostaticInteractions.setMMFF94ElectrostaticParameters ( IAtomContainer molecule, Map parameterSet ) :  void

cdk-1.2.10.jar, Element.class
package org.openscience.cdk
Element.Element ( String symbol, int atomicNumber )

cdk-1.2.10.jar, ElementAccess.class
package org.omegahat.Environment.Parser.Parse
ElementAccess.ElementAccess ( )
ElementAccess.ElementAccess ( Environment.Parser.Parse.ExpressionInt p1, String p2 )
ElementAccess.ElementAccess ( String p1 )
ElementAccess.elementName ( ) :  String
ElementAccess.elementName ( String p1 ) :  String
ElementAccess.getFirstChild ( ) :  AST
ElementAccess.isGlobal ( ) :  boolean
ElementAccess.isGlobal ( boolean p1 ) :  boolean
ElementAccess.isSuper ( ) :  boolean
ElementAccess.isSuper ( boolean p1 ) :  boolean
ElementAccess.qualifier ( ) :  Environment.Parser.Parse.ExpressionInt
ElementAccess.qualifier ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
ElementAccess.qualifierEval ( Environment.Interpreter.Evaluator p1 ) :  Object

cdk-1.2.10.jar, ElementAssignableSubset.class
package org.omegahat.Environment.DataStructures
ElementAssignableSubset.assign ( int p1, Object p2 ) [abstract] :  Object

cdk-1.2.10.jar, ElementPTFactory.class
package org.openscience.cdk.config
ElementPTFactory.configure ( PeriodicTableElement element ) :  PeriodicTableElement
ElementPTFactory.configureE ( PeriodicTableElement elementPT ) :  IElement
ElementPTFactory.getAtomicNumber ( PeriodicTableElement element ) :  double
ElementPTFactory.getCASid ( PeriodicTableElement element ) :  String
ElementPTFactory.getChemicalSerie ( PeriodicTableElement element ) :  String
ElementPTFactory.getCovalentRadius ( PeriodicTableElement element ) :  double
ElementPTFactory.getElement ( String symbol ) :  PeriodicTableElement
ElementPTFactory.getElements ( ) :  List
ElementPTFactory.getGroup ( PeriodicTableElement element ) :  int
ElementPTFactory.getInstance ( ) [static] :  ElementPTFactory
ElementPTFactory.getName ( PeriodicTableElement element ) :  String
ElementPTFactory.getPaulingEneg ( PeriodicTableElement element ) :  double
ElementPTFactory.getPeriod ( PeriodicTableElement element ) :  int
ElementPTFactory.getPhase ( PeriodicTableElement element ) :  String
ElementPTFactory.getSize ( ) :  int
ElementPTFactory.getVdwRadius ( PeriodicTableElement element ) :  double

cdk-1.2.10.jar, ElementPTHandler.class
package org.openscience.cdk.config.elements
ElementPTHandler.characters ( char[ ] chars, int start, int length ) :  void
ElementPTHandler.ElementPTHandler ( )
ElementPTHandler.endElement ( String uri, String local, String raw ) :  void
ElementPTHandler.getElements ( ) :  List
ElementPTHandler.startDocument ( ) :  void
ElementPTHandler.startElement ( String uri, String local, String raw, Attributes atts ) :  void

cdk-1.2.10.jar, ElementPTReader.class
package org.openscience.cdk.config.elements
ElementPTReader.ElementPTReader ( Reader input )
ElementPTReader.readElements ( ) :  List

cdk-1.2.10.jar, ElementSubsettable.class
package org.omegahat.Environment.DataStructures
ElementSubsettable.subset ( int p1 ) [abstract] :  Object

cdk-1.2.10.jar, EndSourceInputException.class
package org.omegahat.Environment.Interpreter
EndSourceInputException.EndSourceInputException ( String p1, Environment.Interpreter.Evaluator p2 )
EndSourceInputException.EndSourceInputException ( String p1, int p2, boolean p3, Environment.Interpreter.Evaluator p4 )
EndSourceInputException.EndSourceInputException ( String p1, int p2, Environment.Interpreter.Evaluator p3 )
EndSourceInputException.silent ( ) :  boolean
EndSourceInputException.silent ( boolean p1 ) :  boolean
EndSourceInputException.source ( ) :  Object
EndSourceInputException.source ( Object p1 ) :  Object
EndSourceInputException.toString ( ) :  String

cdk-1.2.10.jar, EnumeratedForLoop.class
package org.omegahat.Environment.Parser.Parse
EnumeratedForLoop.body ( ) :  Environment.Parser.Parse.ExpressionInt
EnumeratedForLoop.body ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
EnumeratedForLoop.EnumeratedForLoop ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.ExpressionInt p2, Object p3 )
EnumeratedForLoop.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
EnumeratedForLoop.getElementSource ( Environment.Interpreter.Evaluator p1 ) :  Object
EnumeratedForLoop.getElementSource ( Object p1 ) :  Object
EnumeratedForLoop.nextElement ( Object p1, int p2 ) :  Object
EnumeratedForLoop.terms ( ) :  Object
EnumeratedForLoop.terms ( Object p1 ) :  Object
EnumeratedForLoop.variable ( ) :  Environment.Parser.Parse.Name
EnumeratedForLoop.variable ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
EnumeratedForLoop.variable ( String p1 ) :  Environment.Parser.Parse.Name

cdk-1.2.10.jar, EOFException.class
package org.omegahat.Environment.Tools.DataScanner
EOFException.EOFException ( )
EOFException.EOFException ( String p1 )

cdk-1.2.10.jar, EqualityOperator.class
package org.omegahat.Environment.DataStructures
EqualityOperator.Equals ( Object p1 ) [abstract] :  Object
EqualityOperator.NotEquals ( Object p1 ) [abstract] :  Object

cdk-1.2.10.jar, ErrorHandler.class
package org.omegahat.Environment.Debugger
ErrorHandler.error ( Throwable p1, String p2, Environment.Parser.Parse.ExpressionInt p3 ) [abstract] :  Object

cdk-1.2.10.jar, Evaluable.class
package org.omegahat.Environment.Language
Evaluable.eval ( Environment.Interpreter.Evaluator p1 ) [abstract] :  Object
Evaluable.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) [abstract] :  Object

cdk-1.2.10.jar, EvaluableInterfaceGenerator.class
package org.omegahat.Environment.GUITools
EvaluableInterfaceGenerator.addConstructor ( Environment.GUITools.Signature p1 ) :  CodeAttr
EvaluableInterfaceGenerator.addConstructors ( ) :  boolean
EvaluableInterfaceGenerator.addDispatchCall ( CodeAttr p1, String p2, String p3, String p4 ) :  boolean
EvaluableInterfaceGenerator.addInterface ( Class p1 ) :  boolean
EvaluableInterfaceGenerator.addMethod ( Method p1 ) :  int
EvaluableInterfaceGenerator.addTarget ( Class p1 ) :  Class
EvaluableInterfaceGenerator.addTarget ( String p1 ) :  Class
EvaluableInterfaceGenerator.createArgumentList ( CodeAttr p1, Class[ ] p2, StringBuffer p3 ) :  int
EvaluableInterfaceGenerator.createArgumentList ( CodeAttr p1, Class[ ] p2, StringBuffer p3, boolean p4 ) :  int
EvaluableInterfaceGenerator.createArgumentList ( CodeAttr p1, Method p2, StringBuffer p3 ) :  int
EvaluableInterfaceGenerator.createArgumentList ( CodeAttr p1, Method p2, StringBuffer p3, boolean p4 ) :  int
EvaluableInterfaceGenerator.derivedClassName ( String p1 ) :  String
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( Class p1 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( Class p1, String p2 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String p1 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String p1, File p2 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String p1, File p2, boolean p3 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String p1, String p2 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String p1, String p2, boolean p3 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String[ ] p1, String p2 )
EvaluableInterfaceGenerator.EvaluableInterfaceGenerator ( String[ ] p1, String p2, boolean p3 )
EvaluableInterfaceGenerator.getStackSize ( ) :  int
EvaluableInterfaceGenerator.init ( String p1, String p2, boolean p3 ) :  void
EvaluableInterfaceGenerator.interfaces ( ) :  Vector
EvaluableInterfaceGenerator.make ( ) :  boolean
EvaluableInterfaceGenerator.make ( Class p1 ) :  boolean
EvaluableInterfaceGenerator.numLocalVariables ( int p1 ) :  int
EvaluableInterfaceGenerator.separator ( ) :  String
EvaluableInterfaceGenerator.superClassConstructors ( ) :  boolean
EvaluableInterfaceGenerator.superClassConstructors ( boolean p1 ) :  boolean

cdk-1.2.10.jar, EvaluationEvent.class
package org.omegahat.Environment.Interpreter
EvaluationEvent.EvaluationEvent ( Object p1 )
EvaluationEvent.getExpr ( ) :  Environment.Parser.Parse.ExpressionInt
EvaluationEvent.setExpr ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt

cdk-1.2.10.jar, EvaluationException.class
package org.omegahat.Environment.Interpreter
EvaluationException.errorExpression ( ) :  Environment.Parser.Parse.ExpressionInt
EvaluationException.errorExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
EvaluationException.EvaluationException ( String p1, Environment.Interpreter.Evaluator p2 )
EvaluationException.EvaluationException ( String p1, Environment.Parser.Parse.ExpressionInt p2, Environment.Interpreter.Evaluator p3 )
EvaluationException.EvaluationException ( String p1, Throwable p2, Environment.Parser.Parse.ExpressionInt p3, Environment.Interpreter.Evaluator p4 )
EvaluationException.evaluator ( ) :  Environment.Interpreter.Evaluator
EvaluationException.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
EvaluationException.getTargetException ( ) :  Throwable
EvaluationException.javaException ( ) :  Throwable
EvaluationException.javaException ( Throwable p1 ) :  Throwable
EvaluationException.message ( ) :  String
EvaluationException.message ( String p1 ) :  String
EvaluationException.toplevelExpression ( ) :  Environment.Parser.Parse.ExpressionInt
EvaluationException.toplevelExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt

cdk-1.2.10.jar, EvaluationFrame.class
package org.omegahat.Environment.Databases
EvaluationFrame.EvaluationFrame ( )
EvaluationFrame.EvaluationFrame ( int p1 )
EvaluationFrame.EvaluationFrame ( String p1 )

cdk-1.2.10.jar, EvaluationListener.class
package org.omegahat.Environment.Interpreter
EvaluationListener.nextEvaluation ( Environment.Interpreter.EvaluationEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, Evaluator.class
package org.omegahat.Environment.Interpreter
Evaluator.addEvaluationListener ( Environment.Interpreter.EvaluationListener p1 ) [abstract] :  int
Evaluator.addFunctionTable ( Object p1 ) [abstract] :  int
Evaluator.addMethod ( Environment.Language.Method p1, Environment.Parser.Parse.Name p2 ) [abstract] :  boolean
Evaluator.allowUnrestrictedAccess ( ) [abstract] :  boolean
Evaluator.asObject ( Environment.Parser.Parse.Name p1 ) [abstract] :  Object
Evaluator.asObjectName ( Environment.Parser.Parse.Name p1 ) [abstract] :  String
Evaluator.asPrimitiveClass ( String p1 ) [abstract] :  Class
Evaluator.assign ( String p1, Object p2 ) [abstract] :  boolean
Evaluator.assign ( String p1, Object p2, Environment.Databases.Database p3 ) [abstract] :  boolean
Evaluator.attach ( Environment.Databases.Database p1 ) [abstract] :  Environment.Databases.AttachedDatabase
Evaluator.attach ( Environment.Databases.Database p1, int p2 ) [abstract] :  Environment.Databases.AttachedDatabase
Evaluator.convertPrimitive ( Object p1, Class p2 ) [abstract] :  Object
Evaluator.currentExpression ( ) [abstract] :  Environment.Parser.Parse.ExpressionInt
Evaluator.currentExpression ( Environment.Parser.Parse.ExpressionInt p1 ) [abstract] :  Environment.Parser.Parse.ExpressionInt
Evaluator.Debug ( ) [abstract] :  boolean
Evaluator.Debug ( Object p1 ) [abstract] :  boolean
Evaluator.defaultDatabase ( ) [abstract] :  Environment.Databases.Database
Evaluator.defaultDatabase ( Environment.Databases.Database p1 ) [abstract] :  Environment.Databases.Database
Evaluator.detach ( Environment.Databases.Database p1 ) [abstract] :  int
Evaluator.detach ( int p1 ) [abstract] :  int
Evaluator.error ( String p1 ) [abstract] :  Exception
Evaluator.error ( Throwable p1, String p2 ) [abstract] :  Exception
Evaluator.evaluate ( Environment.Parser.Parse.ExpressionInt p1 ) [abstract] :  Object
Evaluator.evaluate ( String p1 ) [abstract] :  Object
Evaluator.exists ( String p1 ) [abstract] :  boolean
Evaluator.exit ( int p1 ) [abstract] :  void
Evaluator.findClass ( Environment.Parser.Parse.Name p1 ) [abstract] :  Class
Evaluator.findClass ( String p1 ) [abstract] :  Class
Evaluator.findFunctionOrMethod ( String p1 ) [abstract] :  Environment.Language.Evaluable
Evaluator.functionTableList ( ) [abstract] :  Environment.Utils.OrderedTable
Evaluator.get ( String p1 ) [abstract] :  Object
Evaluator.get ( String p1, Class p2 ) [abstract] :  Object
Evaluator.newDatabase ( String p1 ) [abstract] :  Environment.Databases.Database
Evaluator.objects ( int p1 ) [abstract] :  String[ ]
Evaluator.options ( ) [abstract] :  Environment.Interpreter.Options
Evaluator.options ( Environment.Interpreter.Options p1 ) [abstract] :  Environment.Interpreter.Options
Evaluator.parse ( String p1 ) [abstract] :  Environment.Parser.Parse.ExpressionInt
Evaluator.q ( ) [abstract] :  boolean
Evaluator.remove ( String p1 ) [abstract] :  boolean
Evaluator.removeFunctionTable ( Object p1 ) [abstract] :  boolean
Evaluator.searchPath ( ) [abstract] :  Environment.Databases.SearchPath
Evaluator.searchPath ( Environment.Databases.SearchPath p1 ) [abstract] :  Environment.Databases.SearchPath
Evaluator.source ( File p1 ) [abstract] :  Object
Evaluator.source ( Object p1 ) [abstract] :  Object
Evaluator.source ( String p1 ) [abstract] :  Object
Evaluator.source ( URL p1 ) [abstract] :  Object
Evaluator.sourceStack ( ) [abstract] :  Stack
Evaluator.stderr ( ) [abstract] :  PrintWriter
Evaluator.stdout ( ) [abstract] :  PrintWriter
Evaluator.toplevelExpression ( ) [abstract] :  Environment.Parser.Parse.ExpressionInt
Evaluator.warning ( String p1 ) [abstract] :  void
Evaluator.warning ( String p1, boolean p2 ) [abstract] :  void
Evaluator.warning ( Throwable p1, String p2 ) [abstract] :  void
Evaluator.where ( String p1 ) [abstract] :  Environment.Databases.Database[ ]
Evaluator.which ( String p1 ) [abstract] :  Environment.Databases.Database

cdk-1.2.10.jar, EvaluatorDebugger.class
package org.omegahat.Environment.Debugger
EvaluatorDebugger.error ( Throwable p1, Environment.Parser.Parse.ExpressionInt p2 ) :  Object
EvaluatorDebugger.error ( Throwable p1, String p2, Environment.Parser.Parse.ExpressionInt p3 ) :  Object
EvaluatorDebugger.EvaluatorDebugger ( Environment.Interpreter.Evaluator p1 )
EvaluatorDebugger.nextEvaluation ( Environment.Interpreter.EvaluationEvent p1 ) :  void

cdk-1.2.10.jar, EvaluatorInputConsumer.class
package org.omegahat.Environment.IO
EvaluatorInputConsumer.evaluator ( ) :  Environment.Interpreter.Evaluator
EvaluatorInputConsumer.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
EvaluatorInputConsumer.EvaluatorInputConsumer ( Environment.Interpreter.Evaluator p1 )
EvaluatorInputConsumer.inputReady ( Environment.IO.InputSupplier p1 ) :  boolean
EvaluatorInputConsumer.inputReady ( String p1 ) :  boolean

cdk-1.2.10.jar, EvaluatorJPanel.class
package org.omegahat.Environment.GUI
EvaluatorJPanel.evaluator ( ) :  Environment.Interpreter.Evaluator
EvaluatorJPanel.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
EvaluatorJPanel.EvaluatorJPanel ( )
EvaluatorJPanel.EvaluatorJPanel ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, EvaluatorManager.class
package org.omegahat.Environment.Interpreter
EvaluatorManager.addEvaluator ( Environment.Interpreter.ManagedEvaluatorInt p1 ) :  Environment.Interpreter.ManagedEvaluatorInt
EvaluatorManager.commandLine ( ) :  String[ ]
EvaluatorManager.commandLine ( String[ ] p1 ) :  String[ ]
EvaluatorManager.createEvaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( boolean p1 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( String p1 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( String p1, Environment.Interpreter.Evaluator p2 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.evaluator ( Thread p1 ) :  Environment.Interpreter.Evaluator
EvaluatorManager.EvaluatorManager ( )
EvaluatorManager.EvaluatorManager ( Environment.Interpreter.ManagedEvaluatorInt p1 )
EvaluatorManager.EvaluatorManager ( Environment.Interpreter.Options p1 )
EvaluatorManager.EvaluatorManager ( String[ ] p1 )
EvaluatorManager.evaluators ( ) :  Vector
EvaluatorManager.evaluatorThreads ( ) :  Hashtable
EvaluatorManager.exit ( Environment.Interpreter.Evaluator p1 ) :  void
EvaluatorManager.exit ( Environment.Interpreter.Evaluator p1, int p2 ) :  void
EvaluatorManager.exit ( int p1 ) :  void
EvaluatorManager.fileLocator ( ) :  Environment.Tools.FileLocator.FileLocatorInt
EvaluatorManager.fileLocator ( Environment.Tools.FileLocator.FileLocatorInt p1 ) :  Environment.Tools.FileLocator.FileLocatorInt
EvaluatorManager.findFile ( String p1 ) :  Object
EvaluatorManager.manager ( Environment.Interpreter.Evaluator p1 ) :  int
EvaluatorManager.options ( ) :  Environment.Interpreter.Options
EvaluatorManager.options ( Environment.Interpreter.Options p1 ) :  Environment.Interpreter.Options
EvaluatorManager.q ( Environment.Interpreter.Evaluator p1 ) :  boolean
EvaluatorManager.q ( Environment.Interpreter.Evaluator p1, boolean p2 ) :  boolean

cdk-1.2.10.jar, EvaluatorOutput.class
package org.omegahat.Environment.GUI
EvaluatorOutput.createDisplayAttributes ( ) :  boolean
EvaluatorOutput.display ( Environment.Interpreter.Task p1 ) :  boolean
EvaluatorOutput.display ( Object p1 ) :  boolean
EvaluatorOutput.display ( Object p1, long p2 ) :  boolean
EvaluatorOutput.EvaluatorOutput ( Environment.Interpreter.Evaluator p1 )
EvaluatorOutput.make ( ) :  boolean
EvaluatorOutput.toString ( Object p1 ) :  String
EvaluatorOutput.toWriter ( Object p1 ) :  Writer
EvaluatorOutput.writer ( ) :  Writer

cdk-1.2.10.jar, EvaluatorStatusBar.class
package org.omegahat.Environment.GUI
EvaluatorStatusBar.EvaluatorStatusBar ( Environment.Interpreter.Evaluator p1 )
EvaluatorStatusBar.make ( ) :  boolean

cdk-1.2.10.jar, EventDataScanner.class
package org.omegahat.Environment.Tools.DataScanner
EventDataScanner.addListener ( Environment.Tools.DataScanner.RecordStreamListener p1 ) :  int
EventDataScanner.addListener ( Environment.Tools.DataScanner.RecordStreamListener p1, boolean p2 ) :  int
EventDataScanner.currentRecord ( ) :  Object
EventDataScanner.endRecord ( ) :  Object
EventDataScanner.EventDataScanner ( )
EventDataScanner.EventDataScanner ( Environment.Tools.DataScanner.RecordLexer p1 )
EventDataScanner.EventDataScanner ( Environment.Tools.DataScanner.RecordLexer p1, long p2 )
EventDataScanner.EventDataScanner ( Reader p1 )
EventDataScanner.EventDataScanner ( Reader p1, long p2 )
EventDataScanner.lexer ( ) :  Environment.Tools.DataScanner.RecordLexer
EventDataScanner.lexer ( Environment.Tools.DataScanner.RecordLexer p1 ) :  Environment.Tools.DataScanner.RecordLexer
EventDataScanner.listeners ( ) :  Vector
EventDataScanner.listeners ( Vector p1 ) :  Vector
EventDataScanner.maximumRecords ( ) :  long
EventDataScanner.maximumRecords ( long p1 ) :  long
EventDataScanner.nextRecord ( ) :  Object
EventDataScanner.nextRecord ( boolean p1 ) :  Object
EventDataScanner.notify ( Object p1 ) :  void
EventDataScanner.readRecords ( ) :  long
EventDataScanner.readRecords ( boolean p1 ) :  long
EventDataScanner.removeListener ( Environment.Tools.DataScanner.RecordStreamListener p1 ) :  boolean

cdk-1.2.10.jar, ExceptAttr.class
package jas
ExceptAttr.addException ( CP cp ) :  void
ExceptAttr.ExceptAttr ( )

cdk-1.2.10.jar, ExpressionInt.class
package org.omegahat.Environment.Parser.Parse
ExpressionInt.error ( String p1, Environment.Interpreter.Evaluator p2 ) [abstract] :  Exception
ExpressionInt.resolve ( Environment.Interpreter.Evaluator p1 ) [abstract] :  Environment.Parser.Parse.ExpressionInt
ExpressionInt.substitute ( Hashtable p1 ) [abstract] :  Environment.Parser.Parse.ExpressionInt

cdk-1.2.10.jar, ExpressionList.class
package org.omegahat.Environment.Debugger.ParserViewer
ExpressionList.add ( Object p1 ) :  int
ExpressionList.clear ( ) :  void
ExpressionList.ExpressionList ( )

cdk-1.2.10.jar, ExpressionTraceTree.class
package org.omegahat.Environment.Debugger.ParserViewer
ExpressionTraceTree.addExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  TreePath
ExpressionTraceTree.addVisited ( Environment.Parser.Parse.ExpressionInt p1 ) :  TreePath
ExpressionTraceTree.ExpressionTraceTree ( TreeModel p1 )
ExpressionTraceTree.path ( ) :  TreePath
ExpressionTraceTree.path ( TreePath p1 ) :  TreePath
ExpressionTraceTree.setModel ( TreeModel p1 ) :  void
ExpressionTraceTree.visited ( ) :  Vector

cdk-1.2.10.jar, ExpressionTreeRenderer.class
package org.omegahat.Environment.Debugger.ParserViewer
ExpressionTreeRenderer.color ( Object p1 ) :  Color
ExpressionTreeRenderer.colorTable ( ) :  Graphics.Utils.ColorTable
ExpressionTreeRenderer.colorTable ( Graphics.Utils.ColorTable p1 ) :  Graphics.Utils.ColorTable
ExpressionTreeRenderer.ExpressionTreeRenderer ( )
ExpressionTreeRenderer.getTreeCellRendererComponent ( JTree p1, Object p2, boolean p3, boolean p4, boolean p5, int p6, boolean p7 ) :  Component
ExpressionTreeRenderer.icon ( ) :  Icon

cdk-1.2.10.jar, ExpressionTreeWindow.class
package org.omegahat.Environment.Debugger.ParserViewer
ExpressionTreeWindow.activeExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Interpreter.Evaluator p2 ) :  void
ExpressionTreeWindow.expressionList ( ) :  Environment.Debugger.ParserViewer.ExpressionList
ExpressionTreeWindow.expressionList ( Environment.Debugger.ParserViewer.ExpressionList p1 ) :  Environment.Debugger.ParserViewer.ExpressionList
ExpressionTreeWindow.ExpressionTreeWindow ( )
ExpressionTreeWindow.ExpressionTreeWindow ( Environment.Interpreter.Evaluator p1 )
ExpressionTreeWindow.ExpressionTreeWindow ( Environment.Interpreter.Evaluator p1, Environment.Parser.Parse.ExpressionInt p2 )
ExpressionTreeWindow.make ( ) :  boolean
ExpressionTreeWindow.make ( Environment.Parser.Parse.ExpressionInt p1 ) :  boolean
ExpressionTreeWindow.nextEvaluation ( Environment.Interpreter.EvaluationEvent p1 ) :  void
ExpressionTreeWindow.panel ( ) :  Environment.Debugger.ParserViewer.JTreeASTPanel
ExpressionTreeWindow.panel ( Environment.Debugger.ParserViewer.JTreeASTPanel p1 ) :  Environment.Debugger.ParserViewer.JTreeASTPanel
ExpressionTreeWindow.taskExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Interpreter.Evaluator p2 ) :  void
ExpressionTreeWindow.treeModel ( ) :  Environment.Debugger.ParserViewer.JTreeASTModel
ExpressionTreeWindow.treeModel ( Environment.Debugger.ParserViewer.JTreeASTModel p1 ) :  Environment.Debugger.ParserViewer.JTreeASTModel
ExpressionTreeWindow.treeModel ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Debugger.ParserViewer.JTreeASTModel

cdk-1.2.10.jar, ExtensionFilenameFilter.class
package org.omegahat.Environment.IO
ExtensionFilenameFilter.accept ( File p1, String p2 ) :  boolean
ExtensionFilenameFilter.extension ( ) :  String
ExtensionFilenameFilter.extension ( String p1 ) :  String
ExtensionFilenameFilter.ExtensionFilenameFilter ( String p1 )

cdk-1.2.10.jar, FactoryTable.class
package org.omegahat.Environment.Tools.Factory
FactoryTable.asFile ( String p1 ) :  File
FactoryTable.FactoryTable ( )
FactoryTable.FactoryTable ( Environment.Utils.TrimmedProperties p1 )
FactoryTable.FactoryTable ( File p1 )
FactoryTable.FactoryTable ( String p1 )
FactoryTable.load ( Hashtable p1 ) :  int
FactoryTable.load ( String p1 ) :  int

cdk-1.2.10.jar, FieldAccess.class
package org.omegahat.Environment.Parser.Parse
FieldAccess.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
FieldAccess.FieldAccess ( )
FieldAccess.FieldAccess ( boolean p1, String p2 )
FieldAccess.FieldAccess ( Environment.Parser.Parse.ExpressionInt p1, String p2 )
FieldAccess.FieldAccess ( Environment.Parser.Parse.Name p1 )
FieldAccess.FieldAccess ( String p1 )
FieldAccess.fieldName ( ) :  String
FieldAccess.fieldName ( String p1 ) :  String
FieldAccess.findMethod ( Object p1, Class p2, Environment.Interpreter.Evaluator p3 ) :  Object
FieldAccess.getField ( Environment.Interpreter.Evaluator p1 ) :  Field
FieldAccess.getFieldValue ( Object p1, Class p2, Environment.Interpreter.Evaluator p3 ) :  Object
FieldAccess.getFieldValue ( Object p1, Environment.Interpreter.Evaluator p2 ) :  Object
FieldAccess.getReferencedVariables ( boolean p1, Vector p2 ) :  Vector
FieldAccess.getTargetObject ( Environment.Interpreter.Evaluator p1 ) :  Object
FieldAccess.toString ( ) :  String

cdk-1.2.10.jar, FieldCP.class
package jas
FieldCP.FieldCP ( String clazz, String name, String sig )

cdk-1.2.10.jar, FileLocator.class
package org.omegahat.Environment.Tools.FileLocator
FileLocator.add ( Object p1 ) :  boolean
FileLocator.add ( String p1 ) :  boolean
FileLocator.add ( String[ ] p1 ) :  boolean
FileLocator.asString ( ) :  String
FileLocator.createElement ( String p1 ) :  Object
FileLocator.FileLocator ( )
FileLocator.FileLocator ( String p1 )
FileLocator.FileLocator ( String[ ] p1 )
FileLocator.FileLocator ( Vector p1 )
FileLocator.filter ( ) :  Environment.Tools.FileLocator.DynamicFileFilter
FileLocator.filter ( FilenameFilter p1 ) :  Environment.Tools.FileLocator.DynamicFileFilter
FileLocator.find ( File p1 ) :  Object
FileLocator.find ( File p1, boolean p2 ) :  Object
FileLocator.find ( String p1 ) :  Object
FileLocator.findIn ( File p1, File p2 ) :  Object
FileLocator.findIn ( ZipFile p1, File p2 ) :  Object
FileLocator.isArchive ( File p1 ) :  boolean
FileLocator.matches ( ZipEntry p1, File p2 ) :  boolean
FileLocator.matches ( ZipEntry p1, String p2 ) :  boolean
FileLocator.searchPath ( ) :  Vector
FileLocator.searchPath ( String p1 ) :  Vector
FileLocator.searchPath ( String[ ] p1 ) :  Vector
FileLocator.searchPath ( Vector p1 ) :  Vector
FileLocator.where ( File p1 ) :  Object
FileLocator.where ( String p1 ) :  Object

cdk-1.2.10.jar, FileLocatorInt.class
package org.omegahat.Environment.Tools.FileLocator
FileLocatorInt.find ( File p1 ) [abstract] :  Object
FileLocatorInt.find ( String p1 ) [abstract] :  Object
FileLocatorInt.where ( File p1 ) [abstract] :  Object
FileLocatorInt.where ( String p1 ) [abstract] :  Object

cdk-1.2.10.jar, FloatCP.class
package jas
FloatCP.FloatCP ( float n )

cdk-1.2.10.jar, FlowControl.class
package org.omegahat.Environment.Parser.Parse
FlowControl.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
FlowControl.expression ( ) :  Environment.Parser.Parse.ExpressionInt
FlowControl.expression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Object
FlowControl.FlowControl ( int p1, Object p2 )
FlowControl.toString ( ) :  String
FlowControl.type ( ) :  int
FlowControl.type ( int p1 ) :  int

cdk-1.2.10.jar, ForceField.class
package org.openscience.cdk.modeling.forcefield
ForceField.ForceField ( )
ForceField.ForceField ( Molecule molecule )
ForceField.minimize ( ) :  void
ForceField.setPotentialFunction ( String potentialName ) :  void
ForceField.setUsedGMMethods ( boolean sdm, boolean cgm, boolean nrm ) :  void

cdk-1.2.10.jar, ForceFieldTools.class
package org.openscience.cdk.modeling.forcefield
ForceFieldTools.angleBetweenTwoBonds ( IAtom atomi, IAtom atomj, IAtom atomk ) [static] :  double
ForceFieldTools.angleBetweenTwoBondsFrom3xNCoordinates ( GVector coords3d, int atomiPosition, int atomjPosition, int atomkPosition ) [static] :  double
ForceFieldTools.assignCoordinatesToMolecule ( GVector moleculeCoords, IAtomContainer molecule ) [static] :  IAtomContainer
ForceFieldTools.distanceBetweenTwoAtomFromTwo3xNCoordinates ( GVector atomsCoordinatesVector1, GVector atomsCoordinatesVector2, int atomNumM1, int atomNumM2 ) [static] :  double
ForceFieldTools.distanceBetweenTwoAtoms ( IAtom atom1, IAtom atom2 ) [static] :  double
ForceFieldTools.distanceBetweenTwoAtomsFrom3xNCoordinates ( GVector coords3d, int atom1Position, int atom2Position ) [static] :  double
ForceFieldTools.distanceBetweenTwoAtomsFromNCoordinates3d ( Vector atoms3dCoordinates, int atomNum1, int atomNum2 ) [static] :  double
ForceFieldTools.ForceFieldTools ( )
ForceFieldTools.getCoordinates3xNVector ( IAtomContainer molecule ) [static] :  GVector
ForceFieldTools.getPoint3dCoordinates ( IAtomContainer molecule ) [static] :  Vector
ForceFieldTools.toDegrees ( double angleRad ) [static] :  double
ForceFieldTools.torsionAngle ( IAtom atomi, IAtom atomj, IAtom atomk, IAtom atoml ) [static] :  double
ForceFieldTools.torsionAngleFrom3xNCoordinates ( GVector coords3d, int atomiPosition, int atomjPosition, int atomkPosition, int atomlPosition ) [static] :  double

cdk-1.2.10.jar, ForeignReference.class
package org.omegahat.Interfaces.NativeInterface
ForeignReference.convertResult ( Object p1, String p2 ) :  Object
ForeignReference.eval ( Environment.Parser.Parse.List p1, String p2, String p3, String[ ] p4 ) :  Object
ForeignReference.ForeignReference ( Interfaces.NativeInterface.ForeignReference p1 )
ForeignReference.ForeignReference ( Interfaces.NativeInterface.ForeignReference p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
ForeignReference.ForeignReference ( String p1 )
ForeignReference.ForeignReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
ForeignReference.getEvaluator ( ) :  Interfaces.NativeInterface.OmegaInterfaceManager
ForeignReference.getReferenceName ( ) :  String
ForeignReference.processArg ( Object p1 ) :  Object
ForeignReference.processArgs ( Environment.Parser.Parse.List p1 ) :  Object[ ]
ForeignReference.removeTemporaryAnonymousReferences ( Object[ ] p1, Environment.Parser.Parse.List p2 ) :  int
ForeignReference.setEvaluator ( Interfaces.NativeInterface.OmegaInterfaceManager p1 ) :  Interfaces.NativeInterface.OmegaInterfaceManager
ForeignReference.setReferenceName ( String p1 ) :  String
ForeignReference.toString ( ) :  String

cdk-1.2.10.jar, ForeignReferenceClassGenerator.class
package org.omegahat.Interfaces.NativeInterface
ForeignReferenceClassGenerator.addDispatchCall ( CodeAttr p1, String p2, String p3, String p4 ) :  boolean
ForeignReferenceClassGenerator.addMethod ( Method p1 ) :  int
ForeignReferenceClassGenerator.ForeignReferenceClassGenerator ( )
ForeignReferenceClassGenerator.ForeignReferenceClassGenerator ( String p1, String p2 )
ForeignReferenceClassGenerator.ForeignReferenceClassGenerator ( String p1, String p2, boolean p3 )
ForeignReferenceClassGenerator.ForeignReferenceClassGenerator ( String[ ] p1, String p2 )
ForeignReferenceClassGenerator.numLocalVariables ( int p1 ) :  int

cdk-1.2.10.jar, ForeignReferenceInt.class
package org.omegahat.Interfaces.NativeInterface
ForeignReferenceInt.eval ( Environment.Parser.Parse.List p1, String p2, String p3, String[ ] p4 ) [abstract] :  Object
ForeignReferenceInt.getReferenceName ( ) [abstract] :  String

cdk-1.2.10.jar, ForLoop.class
package org.omegahat.Environment.Parser.Parse
ForLoop.conditionIsTrue ( Environment.Interpreter.Evaluator p1 ) :  boolean
ForLoop.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ForLoop.ForLoop ( Object p1, Object p2, Object p3, Object p4 )
ForLoop.getFirstChild ( ) :  AST
ForLoop.toString ( ) :  String

cdk-1.2.10.jar, FormalComment.class
package org.omegahat.Environment.Parser.Parse
FormalComment.FormalComment ( String p1 )
FormalComment.toString ( ) :  String

cdk-1.2.10.jar, Function.class
package org.omegahat.Environment.Language
Function.addArgument ( Environment.Parser.Parse.AssignExpression p1 ) :  String
Function.addArgument ( Environment.Parser.Parse.AssignExpression p1, Environment.Interpreter.Evaluator p2 ) :  String
Function.addArgument ( Environment.Parser.Parse.MethodParameter p1 ) :  String
Function.addArgument ( Environment.Parser.Parse.MethodParameter p1, Environment.Interpreter.Evaluator p2 ) :  String
Function.addArgument ( Environment.Parser.Parse.MethodParameter p1, Object p2 ) :  String
Function.addArgument ( Environment.Parser.Parse.MethodParameter p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  String
Function.addArgumentName ( String p1 ) :  String
Function.argList ( ) :  Environment.Databases.Database
Function.argList ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
Function.argList ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Environment.Databases.Database
Function.argumentName ( int p1 ) :  String
Function.argumentNames ( ) :  Vector
Function.argumentNames ( Vector p1 ) :  Vector
Function.assignArgument ( Environment.Databases.Database p1, Object p2, String p3, String p4, Environment.Interpreter.Evaluator p5 ) :  Object
Function.assignNamedArgument ( Environment.Databases.Database p1, Environment.Parser.Parse.AssignExpression p2, String p3, String p4, Environment.Interpreter.Evaluator p5 ) :  Object
Function.body ( ) :  Environment.Language.Evaluable
Function.body ( Environment.Language.Evaluable p1 ) :  Environment.Language.Evaluable
Function.body ( Environment.Parser.Parse.StatementList p1 ) :  Environment.Language.Evaluable
Function.callFrame ( Environment.Interpreter.Evaluator p1 ) :  Environment.Databases.Database
Function.checkReturnType ( Object p1, Environment.Interpreter.Evaluator p2 ) :  boolean
Function.createCallFrame ( Environment.Interpreter.Evaluator p1 ) :  Environment.Databases.Database
Function.createVariable ( Environment.Parser.Parse.LocalVariable p1, Environment.Databases.Database p2, Environment.Interpreter.Evaluator p3 ) :  int
Function.eval ( Environment.Databases.Database p1, boolean p2, Environment.Interpreter.Evaluator p3 ) :  Object
Function.eval ( Environment.Databases.Database p1, Environment.Interpreter.Evaluator p2 ) :  Object
Function.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
Function.eval ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Object
Function.eval ( Object p1, Environment.Interpreter.Evaluator p2 ) :  Object
Function.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
Function.evalBody ( Environment.Interpreter.Evaluator p1 ) :  Object
Function.exceptions ( ) :  Vector
Function.exceptions ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Vector
Function.exceptions ( Vector p1 ) :  Vector
Function.frame ( Environment.Interpreter.Evaluator p1 ) :  Environment.Databases.Database
Function.Function ( )
Function.Function ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Interpreter.Evaluator p6 )
Function.Function ( Environment.Parser.Parse.MethodDefinition p1 )
Function.functionName ( Environment.Interpreter.Evaluator p1 ) :  String
Function.getDocumentation ( ) :  String
Function.getFirstChild ( ) :  AST
Function.hasVariableArguments ( ) :  boolean
Function.hasVariableArguments ( boolean p1 ) :  boolean
Function.isSynchronized ( ) :  boolean
Function.lazy ( Environment.Interpreter.Evaluator p1 ) :  boolean
Function.matchArgument ( Environment.Databases.Database p1, Object p2, Vector p3, int p4, Environment.Interpreter.Evaluator p5 ) :  int
Function.matchArguments ( Environment.Databases.Database p1, Environment.Parser.Parse.List p2, Environment.Interpreter.Evaluator p3 ) :  Environment.Databases.Database
Function.matchArguments ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Environment.Databases.Database
Function.name ( ) :  String
Function.name ( String p1 ) :  String
Function.parameterTypes ( ) :  Class[ ]
Function.returnType ( ) :  Class
Function.returnType ( Class p1 ) :  Class
Function.setDocumentation ( Environment.Parser.Parse.Comment p1 ) :  String
Function.setDocumentation ( String p1 ) :  String
Function.showArg ( String p1, Environment.Databases.Database p2, StringBuffer p3 ) :  StringBuffer
Function.showArguments ( ) :  String
Function.showArguments ( StringBuffer p1 ) :  String
Function.signature ( ) :  Environment.Language.Signature
Function.templateArgument ( Environment.Language.Evaluable p1, String p2, Environment.Interpreter.Evaluator p3 ) :  Object
Function.toString ( ) :  String

cdk-1.2.10.jar, FunctionCall.class
package org.omegahat.Environment.Parser.Parse
FunctionCall.args ( ) :  Environment.Parser.Parse.List
FunctionCall.args ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
FunctionCall.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
FunctionCall.FunctionCall ( )
FunctionCall.FunctionCall ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2 )
FunctionCall.getReferencedVariables ( boolean p1, AbstractCollection p2 ) :  AbstractCollection
FunctionCall.qualifier ( ) :  Environment.Parser.Parse.ExpressionInt
FunctionCall.qualifier ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
FunctionCall.toString ( ) :  String

cdk-1.2.10.jar, FunctionCallArguments.class
package org.omegahat.Environment.Language
FunctionCallArguments.addArgument ( boolean p1 ) :  void
FunctionCallArguments.addArgument ( byte p1 ) :  void
FunctionCallArguments.addArgument ( char p1 ) :  void
FunctionCallArguments.addArgument ( double p1 ) :  void
FunctionCallArguments.addArgument ( float p1 ) :  void
FunctionCallArguments.addArgument ( int p1 ) :  void
FunctionCallArguments.addArgument ( long p1 ) :  void
FunctionCallArguments.addArgument ( Object p1 ) :  void
FunctionCallArguments.addArgument ( short p1 ) :  void
FunctionCallArguments.FunctionCallArguments ( )
FunctionCallArguments.FunctionCallArguments ( int p1 )

cdk-1.2.10.jar, FunctionExpression.class
package org.omegahat.Environment.Parser.Parse
FunctionExpression.args ( ) :  Environment.Parser.Parse.List
FunctionExpression.body ( ) :  Environment.Parser.Parse.ExpressionInt
FunctionExpression.body ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
FunctionExpression.createFunction ( ) :  Environment.Language.Function
FunctionExpression.createFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5 ) :  Environment.Language.Function
FunctionExpression.createFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6 ) :  Environment.Language.Function
FunctionExpression.createFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Interpreter.Evaluator p7 ) :  Environment.Language.Function
FunctionExpression.createFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 ) :  Environment.Language.Function
FunctionExpression.createFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7, Environment.Interpreter.Evaluator p8 ) :  Environment.Language.Function
FunctionExpression.documentation ( ) :  Environment.Parser.Parse.Comment
FunctionExpression.documentation ( Environment.Parser.Parse.Comment p1 ) :  Environment.Parser.Parse.Comment
FunctionExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
FunctionExpression.function ( ) :  Environment.Language.Function
FunctionExpression.function ( Environment.Language.Function p1 ) :  Environment.Language.Function
FunctionExpression.FunctionExpression ( )
FunctionExpression.FunctionExpression ( Environment.Language.Function p1 )
FunctionExpression.FunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5 )
FunctionExpression.FunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6 )
FunctionExpression.FunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 )
FunctionExpression.getName ( ) :  String
FunctionExpression.hasLazyArguments ( Environment.Parser.Parse.List p1 ) :  boolean
FunctionExpression.isClosure ( Environment.Parser.Parse.ExpressionInt p1 ) :  boolean
FunctionExpression.isStaticVariable ( Environment.Parser.Parse.LocalVariable p1 ) :  boolean
FunctionExpression.isTailRecursive ( Environment.Parser.Parse.ExpressionInt p1, String p2 ) :  boolean
FunctionExpression.setName ( String p1 ) :  String
FunctionExpression.toString ( ) :  String

cdk-1.2.10.jar, FunctionListener.class
package org.omegahat.Environment.GUITools
FunctionListener.addArgument ( boolean p1 ) :  void
FunctionListener.addArgument ( byte p1 ) :  void
FunctionListener.addArgument ( char p1 ) :  void
FunctionListener.addArgument ( double p1 ) :  void
FunctionListener.addArgument ( float p1 ) :  void
FunctionListener.addArgument ( int p1 ) :  void
FunctionListener.addArgument ( long p1 ) :  void
FunctionListener.addArgument ( Object p1 ) :  void
FunctionListener.addArgument ( short p1 ) :  void
FunctionListener.arguments ( ) :  Environment.Parser.Parse.List
FunctionListener.arguments ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
FunctionListener.eval ( ) :  Object
FunctionListener.eval ( Environment.Parser.Parse.List p1 ) :  Object
FunctionListener.FunctionListener ( )
FunctionListener.FunctionListener ( double p1, int[ ][ ] p2, Vector p3 )
FunctionListener.FunctionListener ( Environment.Language.Function p1 )
FunctionListener.FunctionListener ( Environment.Language.Function p1, Environment.Interpreter.Evaluator p2 )

cdk-1.2.10.jar, FunctionParameterModifier.class
package org.omegahat.Environment.Parser.Parse
FunctionParameterModifier.FunctionParameterModifier ( boolean p1 )
FunctionParameterModifier.FunctionParameterModifier ( boolean p1, boolean p2 )
FunctionParameterModifier.FunctionParameterModifier ( int p1 )
FunctionParameterModifier.FunctionParameterModifier ( int p1, boolean p2 )
FunctionParameterModifier.isLazy ( ) :  boolean
FunctionParameterModifier.lazy ( ) :  int
FunctionParameterModifier.lazy ( int p1 ) :  int
FunctionParameterModifier.op ( ) :  String
FunctionParameterModifier.toString ( ) :  String

cdk-1.2.10.jar, FunctionType.class
package org.omegahat.Environment.Parser.Parse
FunctionType.FunctionType ( int p1 )
FunctionType.isFunction ( ) :  boolean
FunctionType.isMethod ( ) :  boolean
FunctionType.type ( ) :  int
FunctionType.type ( int p1 ) :  int

cdk-1.2.10.jar, GenerateFragments.class
package org.openscience.cdk.tools
GenerateFragments.GenerateFragments ( )
GenerateFragments.generateMurckoFragments ( IMolecule molecule, boolean sidechainHetatoms, boolean exocyclicDoubleBonds, int minimumRingSize ) :  void
GenerateFragments.generateRingFragments ( IMolecule molecule ) :  void
GenerateFragments.getLinkerFragments ( ) :  List
GenerateFragments.getLinkerFragmentsAsSmileArray ( ) :  String[ ]
GenerateFragments.getMurckoFrameworks ( ) :  List
GenerateFragments.getMurckoFrameworksAsSmileArray ( ) :  String[ ]
GenerateFragments.getRingFragments ( ) :  List
GenerateFragments.getRingFragmentsAsSmileArray ( ) :  String[ ]
GenerateFragments.isSmilesToUpperCase ( ) :  boolean
GenerateFragments.setSmilesToUpperCase ( boolean smilesToUpperCase ) :  void

cdk-1.2.10.jar, GenericAttr.class
package jas
GenericAttr.GenericAttr ( CP name, byte[ ] data )
GenericAttr.GenericAttr ( String name, byte[ ] data )

cdk-1.2.10.jar, GenericFrame.class
package org.omegahat.Environment.GUITools
GenericFrame.actionPerformed ( ActionEvent p1 ) :  void
GenericFrame.component ( Component p1 ) :  Component
GenericFrame.component ( Component p1, boolean p2 ) :  Component
GenericFrame.createMenu ( String p1, String[ ] p2, ActionListener p3 ) :  JMenu
GenericFrame.createMenuBar ( ) :  JMenuBar
GenericFrame.createMenuBar ( boolean p1 ) :  JMenuBar
GenericFrame.defaultBounds ( ) :  Rectangle
GenericFrame.GenericFrame ( )
GenericFrame.GenericFrame ( Component p1 )
GenericFrame.GenericFrame ( Component p1, boolean p2 )
GenericFrame.GenericFrame ( Component p1, boolean p2, String p3 )
GenericFrame.GenericFrame ( String p1 )
GenericFrame.GenericFrame ( String p1, boolean p2 )
GenericFrame.init ( ) :  void
GenericFrame.menuBar ( ) :  JMenuBar
GenericFrame.menuBar ( JMenuBar p1 ) :  JMenuBar

cdk-1.2.10.jar, GeometricMinimizer.class
package org.openscience.cdk.modeling.forcefield
GeometricMinimizer.checkConvergence ( double convergenceCriterion ) :  void
GeometricMinimizer.conjugateGradientMinimization ( GVector initialCoordinates, IPotentialFunction forceField ) :  void
GeometricMinimizer.GeometricMinimizer ( )
GeometricMinimizer.getConjugateGradientMinimum ( ) :  GVector
GeometricMinimizer.getConvergenceParametersForCGM ( ) :  double[ ]
GeometricMinimizer.getConvergenceParametersForNRM ( ) :  double[ ]
GeometricMinimizer.getConvergenceParametersForSDM ( ) :  double[ ]
GeometricMinimizer.getMinimumFunctionValueCGM ( ) :  double
GeometricMinimizer.getMolecule ( ) :  IMolecule
GeometricMinimizer.getNewtonRaphsonMinimum ( ) :  GVector
GeometricMinimizer.getPotentialParameterSet ( ) :  Map
GeometricMinimizer.getSteepestDescentsMinimum ( ) :  GVector
GeometricMinimizer.gradientSmallEnough ( double function, GVector gradient ) :  void
GeometricMinimizer.initializeMinimizationParameters ( GVector initialCoord ) :  void
GeometricMinimizer.newtonRaphsonMinimization ( GVector initialCoordinates, IPotentialFunction forceField ) :  void
GeometricMinimizer.rootMeanSquareGradient ( GVector gradient ) :  double
GeometricMinimizer.setConvergenceParametersForCGM ( int changeCGMaximumIteration, double changeCGConvergenceCriterion ) :  void
GeometricMinimizer.setConvergenceParametersForNRM ( int changeNRMaximumIteration, double changeNRConvergenceCriterion ) :  void
GeometricMinimizer.setConvergenceParametersForSDM ( int changeSDMaximumIteration, double changeSDConvergenceCriterion ) :  void
GeometricMinimizer.setkplus1Coordinates ( GVector direction, double stepSize ) :  void
GeometricMinimizer.setMMFF94Tables ( IAtomContainer molecule ) :  void
GeometricMinimizer.setMolecule ( IMolecule mol, boolean clone ) :  void
GeometricMinimizer.steepestDescentsMinimization ( GVector initialCoordinates, IPotentialFunction forceField ) :  void

cdk-1.2.10.jar, GlobalName.class
package org.omegahat.Environment.Parser.Parse
GlobalName.GlobalName ( )

cdk-1.2.10.jar, Globals.class
package org.omegahat.Environment.System
Globals.applet ( ) [static] :  Applet
Globals.applet ( Applet p1 ) [static] :  Applet
Globals.args ( ) [static] :  String[ ]
Globals.args ( String[ ] p1 ) [static] :  String[ ]
Globals.error ( String p1 ) [static] :  void
Globals.evaluator ( ) [static] :  Environment.Interpreter.Evaluator
Globals.evaluator ( boolean p1 ) [static] :  Environment.Interpreter.Evaluator
Globals.evaluator ( Environment.Interpreter.Evaluator p1 ) [static] :  Environment.Interpreter.Evaluator
Globals.Globals ( )
Globals.manager ( ) [static] :  Environment.Interpreter.EvaluatorManager
Globals.manager ( Environment.Interpreter.EvaluatorManager p1 ) [static] :  Environment.Interpreter.EvaluatorManager
Globals.stringList ( String p1 ) [static] :  String[ ]
Globals.stringList ( String p1, char p2 ) [static] :  String[ ]
Globals.warning ( String p1 ) [static] :  void

cdk-1.2.10.jar, GroupedClassLocator.class
package org.omegahat.Environment.Tools.ClassList
GroupedClassLocator.add ( String p1 ) :  Object
GroupedClassLocator.add ( String p1, boolean p2 ) :  Object
GroupedClassLocator.findClasses ( String p1, Vector p2 ) :  Vector
GroupedClassLocator.GroupedClassLocator ( )
GroupedClassLocator.GroupedClassLocator ( String[ ] p1 )
GroupedClassLocator.GroupedClassLocator ( Vector p1 )
GroupedClassLocator.isPackage ( String p1 ) :  boolean
GroupedClassLocator.newSubList ( ) :  Environment.Tools.ClassList.ObjectList

cdk-1.2.10.jar, GUIHelpEvaluator.class
package org.omegahat.Environment.Interpreter
GUIHelpEvaluator.GUIHelpEvaluator ( )
GUIHelpEvaluator.GUIHelpEvaluator ( Environment.Interpreter.Evaluator p1 )
GUIHelpEvaluator.GUIHelpEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
GUIHelpEvaluator.GUIHelpEvaluator ( Environment.Interpreter.Options p1 )
GUIHelpEvaluator.help ( ) :  Object
GUIHelpEvaluator.help ( HelpSet p1, String p2 ) :  Object
GUIHelpEvaluator.help ( String p1 ) :  Object
GUIHelpEvaluator.help ( String p1, String p2 ) :  Object
GUIHelpEvaluator.help ( URL p1, String p2 ) :  Object

cdk-1.2.10.jar, HelpSystem.class
package org.omegahat.Environment.System.Functions
HelpSystem.helpSet ( String p1 ) :  HelpSet
HelpSystem.HelpSystem ( )
HelpSystem.HelpSystem ( HelpSet p1 )
HelpSystem.HelpSystem ( String p1 )

cdk-1.2.10.jar, HelpTOC.class
package org.omegahat.Environment.System.Functions
HelpTOC.createNavigator ( HelpModel p1 ) :  Component
HelpTOC.HelpTOC ( HelpSet p1, String p2, String p3, Hashtable p4 )
HelpTOC.HelpTOC ( HelpSet p1, String p2, String p3, Locale p4, Hashtable p5 )

cdk-1.2.10.jar, HierarchyGenerator.class
package org.omegahat.Environment.Tools.ClassHierarchy
HierarchyGenerator.addClass ( Class p1 ) :  Environment.Tools.ClassHierarchy.ClassNode
HierarchyGenerator.addClass ( Class p1, Environment.Tools.ClassHierarchy.ClassNode p2 ) :  Environment.Tools.ClassHierarchy.ClassNode
HierarchyGenerator.addClass ( Environment.Tools.ClassHierarchy.ClassNode p1 ) :  Environment.Tools.ClassHierarchy.ClassNode
HierarchyGenerator.addClass ( String p1 ) :  Environment.Tools.ClassHierarchy.ClassNode
HierarchyGenerator.addClasses ( String[ ] p1 ) :  int
HierarchyGenerator.compute ( ) :  Vector
HierarchyGenerator.compute ( boolean p1 ) :  Vector
HierarchyGenerator.evaluator ( ) :  Environment.Interpreter.Evaluator
HierarchyGenerator.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
HierarchyGenerator.findClass ( String p1 ) :  Class
HierarchyGenerator.getClass ( String p1 ) :  Class
HierarchyGenerator.HierarchyGenerator ( )
HierarchyGenerator.HierarchyGenerator ( String[ ] p1 )
HierarchyGenerator.listChildren ( PrintStream p1 ) :  int
HierarchyGenerator.listClasses ( PrintStream p1 ) :  void
HierarchyGenerator.listElements ( PrintStream p1, boolean p2 ) :  int
HierarchyGenerator.listParents ( PrintStream p1 ) :  int

cdk-1.2.10.jar, HomogeneousTypedDatabase.class
package org.omegahat.Environment.Databases
HomogeneousTypedDatabase.HomogeneousTypedDatabase ( )
HomogeneousTypedDatabase.HomogeneousTypedDatabase ( int p1 )
HomogeneousTypedDatabase.HomogeneousTypedDatabase ( String p1 )

cdk-1.2.10.jar, IAtom.class
package org.openscience.cdk.interfaces
IAtom.getHydrogenCount ( ) [abstract] :  Integer
IAtom.setHydrogenCount ( Integer p1 ) [abstract] :  void

cdk-1.2.10.jar, IAtomContainer.class
package org.openscience.cdk.interfaces
IAtomContainer.addAtomParity ( IAtomParity p1 ) [abstract] :  void
IAtomContainer.addBond ( int p1, int p2, IBond.Order p3, int p4 ) [abstract] :  void
IAtomContainer.getAtomParity ( IAtom p1 ) [abstract] :  IAtomParity

cdk-1.2.10.jar, IBond.class
package org.openscience.cdk.interfaces
IBond.getStereo ( ) [abstract] :  int
IBond.setStereo ( int p1 ) [abstract] :  void

cdk-1.2.10.jar, IChemObjectBuilder.class
package org.openscience.cdk.interfaces
IChemObjectBuilder.newAdductFormula ( ) [abstract] :  IAdductFormula
IChemObjectBuilder.newAdductFormula ( IMolecularFormula p1 ) [abstract] :  IAdductFormula
IChemObjectBuilder.newAminoAcid ( ) [abstract] :  IAminoAcid
IChemObjectBuilder.newAtom ( ) [abstract] :  IAtom
IChemObjectBuilder.newAtom ( IElement p1 ) [abstract] :  IAtom
IChemObjectBuilder.newAtom ( String p1 ) [abstract] :  IAtom
IChemObjectBuilder.newAtom ( String p1, Point2d p2 ) [abstract] :  IAtom
IChemObjectBuilder.newAtom ( String p1, Point3d p2 ) [abstract] :  IAtom
IChemObjectBuilder.newAtomContainer ( ) [abstract] :  IAtomContainer
IChemObjectBuilder.newAtomContainer ( IAtomContainer p1 ) [abstract] :  IAtomContainer
IChemObjectBuilder.newAtomContainer ( int p1, int p2, int p3, int p4 ) [abstract] :  IAtomContainer
IChemObjectBuilder.newAtomContainerSet ( ) [abstract] :  IAtomContainerSet
IChemObjectBuilder.newAtomParity ( IAtom p1, IAtom p2, IAtom p3, IAtom p4, IAtom p5, int p6 ) [abstract] :  IAtomParity
IChemObjectBuilder.newAtomType ( IElement p1 ) [abstract] :  IAtomType
IChemObjectBuilder.newAtomType ( String p1 ) [abstract] :  IAtomType
IChemObjectBuilder.newAtomType ( String p1, String p2 ) [abstract] :  IAtomType
IChemObjectBuilder.newBioPolymer ( ) [abstract] :  IBioPolymer
IChemObjectBuilder.newBond ( ) [abstract] :  IBond
IChemObjectBuilder.newBond ( IAtom p1, IAtom p2 ) [abstract] :  IBond
IChemObjectBuilder.newBond ( IAtom p1, IAtom p2, IBond.Order p3 ) [abstract] :  IBond
IChemObjectBuilder.newBond ( IAtom p1, IAtom p2, IBond.Order p3, int p4 ) [abstract] :  IBond
IChemObjectBuilder.newBond ( IAtom[ ] p1 ) [abstract] :  IBond
IChemObjectBuilder.newBond ( IAtom[ ] p1, IBond.Order p2 ) [abstract] :  IBond
IChemObjectBuilder.newChemFile ( ) [abstract] :  IChemFile
IChemObjectBuilder.newChemModel ( ) [abstract] :  IChemModel
IChemObjectBuilder.newChemObject ( ) [abstract] :  IChemObject
IChemObjectBuilder.newChemObject ( IChemObject p1 ) [abstract] :  IChemObject
IChemObjectBuilder.newChemSequence ( ) [abstract] :  IChemSequence
IChemObjectBuilder.newCrystal ( ) [abstract] :  ICrystal
IChemObjectBuilder.newCrystal ( IAtomContainer p1 ) [abstract] :  ICrystal
IChemObjectBuilder.newElectronContainer ( ) [abstract] :  IElectronContainer
IChemObjectBuilder.newElement ( ) [abstract] :  IElement
IChemObjectBuilder.newElement ( IElement p1 ) [abstract] :  IElement
IChemObjectBuilder.newElement ( String p1 ) [abstract] :  IElement
IChemObjectBuilder.newElement ( String p1, int p2 ) [abstract] :  IElement
IChemObjectBuilder.newFragmentAtom ( ) [abstract] :  IFragmentAtom
IChemObjectBuilder.newIsotope ( IElement p1 ) [abstract] :  IIsotope
IChemObjectBuilder.newIsotope ( int p1, String p2, double p3, double p4 ) [abstract] :  IIsotope
IChemObjectBuilder.newIsotope ( int p1, String p2, int p3, double p4, double p5 ) [abstract] :  IIsotope
IChemObjectBuilder.newIsotope ( String p1 ) [abstract] :  IIsotope
IChemObjectBuilder.newIsotope ( String p1, int p2 ) [abstract] :  IIsotope
IChemObjectBuilder.newLonePair ( ) [abstract] :  ILonePair
IChemObjectBuilder.newLonePair ( IAtom p1 ) [abstract] :  ILonePair
IChemObjectBuilder.newMapping ( IChemObject p1, IChemObject p2 ) [abstract] :  IMapping
IChemObjectBuilder.newMolecularFormula ( ) [abstract] :  IMolecularFormula
IChemObjectBuilder.newMolecularFormulaSet ( ) [abstract] :  IMolecularFormulaSet
IChemObjectBuilder.newMolecularFormulaSet ( IMolecularFormula p1 ) [abstract] :  IMolecularFormulaSet
IChemObjectBuilder.newMolecule ( ) [abstract] :  IMolecule
IChemObjectBuilder.newMolecule ( IAtomContainer p1 ) [abstract] :  IMolecule
IChemObjectBuilder.newMolecule ( int p1, int p2, int p3, int p4 ) [abstract] :  IMolecule
IChemObjectBuilder.newMoleculeSet ( ) [abstract] :  IMoleculeSet
IChemObjectBuilder.newMonomer ( ) [abstract] :  IMonomer
IChemObjectBuilder.newPDBAtom ( IElement p1 ) [abstract] :  IPDBAtom
IChemObjectBuilder.newPDBAtom ( String p1 ) [abstract] :  IPDBAtom
IChemObjectBuilder.newPDBAtom ( String p1, Point3d p2 ) [abstract] :  IPDBAtom
IChemObjectBuilder.newPDBMonomer ( ) [abstract] :  IPDBMonomer
IChemObjectBuilder.newPDBPolymer ( ) [abstract] :  IPDBPolymer
IChemObjectBuilder.newPDBStructure ( ) [abstract] :  IPDBStructure
IChemObjectBuilder.newPolymer ( ) [abstract] :  IPolymer
IChemObjectBuilder.newPseudoAtom ( ) [abstract] :  IPseudoAtom
IChemObjectBuilder.newPseudoAtom ( IElement p1 ) [abstract] :  IPseudoAtom
IChemObjectBuilder.newPseudoAtom ( String p1 ) [abstract] :  IPseudoAtom
IChemObjectBuilder.newPseudoAtom ( String p1, Point2d p2 ) [abstract] :  IPseudoAtom
IChemObjectBuilder.newPseudoAtom ( String p1, Point3d p2 ) [abstract] :  IPseudoAtom
IChemObjectBuilder.newReaction ( ) [abstract] :  IReaction
IChemObjectBuilder.newReactionScheme ( ) [abstract] :  IReactionScheme
IChemObjectBuilder.newReactionSet ( ) [abstract] :  IReactionSet
IChemObjectBuilder.newRing ( ) [abstract] :  IRing
IChemObjectBuilder.newRing ( IAtomContainer p1 ) [abstract] :  IRing
IChemObjectBuilder.newRing ( int p1 ) [abstract] :  IRing
IChemObjectBuilder.newRing ( int p1, String p2 ) [abstract] :  IRing
IChemObjectBuilder.newRingSet ( ) [abstract] :  IRingSet
IChemObjectBuilder.newSingleElectron ( ) [abstract] :  ISingleElectron
IChemObjectBuilder.newSingleElectron ( IAtom p1 ) [abstract] :  ISingleElectron
IChemObjectBuilder.newStrand ( ) [abstract] :  IStrand

cdk-1.2.10.jar, IfElseExpression.class
package org.omegahat.Environment.Parser.Parse
IfElseExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
IfElseExpression.getFirstChild ( ) :  AST
IfElseExpression.IfElseExpression ( Object p1, Object p2 )
IfElseExpression.IfElseExpression ( Object p1, Object p2, Object p3 )
IfElseExpression.otherwise ( ) :  Object
IfElseExpression.otherwise ( Object p1 ) :  Object
IfElseExpression.prefix ( ) :  String
IfElseExpression.toString ( ) :  String

cdk-1.2.10.jar, IInchiGenerator.class
package net.sf.jniinchi
IInchiGenerator.getAuxInfo ( ) [abstract] :  String
IInchiGenerator.getInchi ( ) [abstract] :  String
IInchiGenerator.getLog ( ) [abstract] :  String
IInchiGenerator.getMessage ( ) [abstract] :  String
IInchiGenerator.getReturnStatus ( ) [abstract] :  INCHI_RET

cdk-1.2.10.jar, IincInsn.class
package jas
IincInsn.IincInsn ( int vindex, int increment )

cdk-1.2.10.jar, IModel.class
package org.openscience.cdk.qsar.model
IModel.build ( ) [abstract] :  void
IModel.predict ( ) [abstract] :  void

cdk-1.2.10.jar, ImportExpression.class
package org.omegahat.Environment.Parser.Parse
ImportExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ImportExpression.ImportExpression ( )
ImportExpression.ImportExpression ( Environment.Parser.Parse.Name p1 )
ImportExpression.ImportExpression ( String p1 )

cdk-1.2.10.jar, INCHI_BOND_STEREO.class
package net.sf.jniinchi
INCHI_BOND_STEREO.toString ( ) :  String

cdk-1.2.10.jar, INCHI_BOND_TYPE.class
package net.sf.jniinchi
INCHI_BOND_TYPE.toString ( ) :  String

cdk-1.2.10.jar, INCHI_KEY.class
package net.sf.jniinchi
INCHI_KEY.getList ( ) [static] :  List
INCHI_KEY.toString ( ) :  String

cdk-1.2.10.jar, INCHI_KEY_STATUS.class
package net.sf.jniinchi
INCHI_KEY_STATUS.getList ( ) [static] :  List
INCHI_KEY_STATUS.toString ( ) :  String

cdk-1.2.10.jar, INCHI_OPTION.class
package net.sf.jniinchi
INCHI_OPTION.getLowercaseMap ( ) [static] :  Map
INCHI_OPTION.getName ( ) :  String
INCHI_OPTION.toString ( ) :  String

cdk-1.2.10.jar, INCHI_PARITY.class
package net.sf.jniinchi
INCHI_PARITY.toString ( ) :  String

cdk-1.2.10.jar, INCHI_RADICAL.class
package net.sf.jniinchi
INCHI_RADICAL.toString ( ) :  String

cdk-1.2.10.jar, INCHI_RET.class
package net.sf.jniinchi
INCHI_RET.getList ( ) [static] :  List
INCHI_RET.toString ( ) :  String

cdk-1.2.10.jar, INCHI_STEREOTYPE.class
package net.sf.jniinchi
INCHI_STEREOTYPE.toString ( ) :  String

cdk-1.2.10.jar, IncompleteExpression.class
package org.omegahat.Environment.Parser.AntlrParser
IncompleteExpression.IncompleteExpression ( )
IncompleteExpression.IncompleteExpression ( String p1 )

cdk-1.2.10.jar, IncompleteInputException.class
package org.omegahat.Environment.IO
IncompleteInputException.IncompleteInputException ( )
IncompleteInputException.IncompleteInputException ( String p1 )

cdk-1.2.10.jar, IncorrectTypeException.class
package org.omegahat.Environment.Databases
IncorrectTypeException.assigned ( ) :  Class
IncorrectTypeException.assigned ( Class p1 ) :  Class
IncorrectTypeException.IncorrectTypeException ( )
IncorrectTypeException.IncorrectTypeException ( String p1 )
IncorrectTypeException.IncorrectTypeException ( String p1, Class p2, Class p3 )
IncorrectTypeException.IncorrectTypeException ( String p1, Environment.Databases.IncorrectTypeException p2 )
IncorrectTypeException.type ( ) :  Class
IncorrectTypeException.type ( Class p1 ) :  Class
IncorrectTypeException.variable ( ) :  String
IncorrectTypeException.variable ( String p1 ) :  String

cdk-1.2.10.jar, Incrementable.class
package org.omegahat.Environment.DataStructures
Incrementable.increment ( double p1 ) [abstract] :  Object
Incrementable.increment ( int p1 ) [abstract] :  Object

cdk-1.2.10.jar, InputConsumer.class
package org.omegahat.Environment.IO
InputConsumer.inputReady ( Environment.IO.InputSupplier p1 ) [abstract] :  boolean
InputConsumer.inputReady ( String p1 ) [abstract] :  boolean

cdk-1.2.10.jar, InputFile.class
package org.omegahat.Environment.IO
InputFile.asURL ( ) :  URL
InputFile.getContents ( ) :  String
InputFile.getInputStream ( ) :  InputStream
InputFile.InputFile ( File p1 )
InputFile.InputFile ( String p1 )
InputFile.readStream ( InputStream p1 ) :  String

cdk-1.2.10.jar, InputFileInt.class
package org.omegahat.Environment.IO
InputFileInt.asURL ( ) [abstract] :  URL
InputFileInt.canRead ( ) [abstract] :  boolean
InputFileInt.getContents ( ) [abstract] :  String
InputFileInt.getInputStream ( ) [abstract] :  InputStream
InputFileInt.getName ( ) [abstract] :  String

cdk-1.2.10.jar, InputReader.class
package org.omegahat.Environment.IO
InputReader.addInputConsumer ( Environment.IO.InputConsumer p1 ) :  boolean
InputReader.defaultPrompt ( ) :  String
InputReader.getInput ( ) :  Object
InputReader.InputReader ( )
InputReader.InputReader ( Environment.IO.PromptSource p1 )
InputReader.InputReader ( InputStream p1 )
InputReader.InputReader ( InputStreamReader p1 )
InputReader.notifyConsumers ( String p1 ) :  void
InputReader.prompt ( ) :  String
InputReader.promptSource ( ) :  Environment.IO.PromptSource
InputReader.promptSource ( Environment.IO.PromptSource p1 ) :  Environment.IO.PromptSource
InputReader.removeInputConsumer ( Environment.IO.InputConsumer p1 ) :  boolean
InputReader.run ( ) :  void

cdk-1.2.10.jar, InputSupplier.class
package org.omegahat.Environment.IO
InputSupplier.getInput ( ) [abstract] :  Object

cdk-1.2.10.jar, Insn.class
package jas
Insn.Insn ( int opc )
Insn.Insn ( int opc, CP arg )
Insn.Insn ( int opc, int val )
Insn.Insn ( int opc, Label target )

cdk-1.2.10.jar, InstanceOfExpression.class
package org.omegahat.Environment.Parser.Parse
InstanceOfExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
InstanceOfExpression.InstanceOfExpression ( Object p1, Object p2 )

cdk-1.2.10.jar, integer.class
package org.omegahat.Environment.DataStructures
integer.Data ( ) :  long[ ]
integer.data ( int p1 ) :  Object
integer.data ( long p1 ) :  Object
integer.data ( long[ ] p1 ) :  Object
integer.getElement ( int p1 ) :  int
integer.integer ( )
integer.integer ( int p1 )
integer.integer ( long p1 )
integer.integer ( long[ ] p1 )
integer.setData ( int[ ] p1 ) :  int
integer.valueOf ( String p1 ) [static] :  long
package org.omegahat.Environment.ObjectDataStructures
integer.convertElement ( Object p1 ) :  Object
integer.getElement ( int p1 ) :  int
integer.integer ( )
integer.integer ( Environment.ObjectDataStructures.integer p1, boolean p2 )
integer.integer ( int p1 )
integer.integer ( int p1, int p2 )
integer.integer ( int p1, int p2, int p3 )
integer.integer ( long p1 )
integer.integer ( long p1, boolean p2 )
integer.integer ( long[ ] p1 )
integer.primitiveData ( ) :  int[ ]
integer.setData ( int[ ] p1 ) :  int
integer.setData ( long[ ] p1 ) :  int
integer.targetClass ( ) :  Class
integer.valueOf ( String p1 ) [static] :  long

cdk-1.2.10.jar, IntegerCP.class
package jas
IntegerCP.IntegerCP ( int n )

cdk-1.2.10.jar, InteractiveEvaluator.class
package org.omegahat.Environment.Interpreter
InteractiveEvaluator.currentExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
InteractiveEvaluator.deserialize ( File p1 ) :  Object
InteractiveEvaluator.deserialize ( File p1, boolean p2 ) :  Object
InteractiveEvaluator.deserialize ( InputStream p1 ) :  Object
InteractiveEvaluator.deserialize ( ObjectInputStream p1 ) :  Object
InteractiveEvaluator.deserialize ( String p1 ) :  Object
InteractiveEvaluator.deserialize ( String p1, boolean p2 ) :  Object
InteractiveEvaluator.evaluate ( Object p1, String p2 ) :  Object
InteractiveEvaluator.inputReady ( Environment.IO.InputSupplier p1 ) :  boolean
InteractiveEvaluator.inputReady ( String p1 ) :  boolean
InteractiveEvaluator.InteractiveEvaluator ( )
InteractiveEvaluator.InteractiveEvaluator ( Environment.Interpreter.Evaluator p1 )
InteractiveEvaluator.InteractiveEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
InteractiveEvaluator.InteractiveEvaluator ( Environment.Interpreter.Options p1 )
InteractiveEvaluator.interrupt ( ) :  boolean
InteractiveEvaluator.notify_listeners ( ) :  boolean
InteractiveEvaluator.notify_listeners ( boolean p1 ) :  boolean
InteractiveEvaluator.notifyListeners ( Environment.Parser.Parse.ExpressionInt p1, boolean p2 ) :  int
InteractiveEvaluator.parserError ( Exception p1 ) :  void
InteractiveEvaluator.prompt ( ) :  String
InteractiveEvaluator.promptExpression ( ) :  Environment.Language.Evaluable
InteractiveEvaluator.promptExpression ( Environment.Language.Evaluable p1 ) :  Environment.Language.Evaluable
InteractiveEvaluator.promptExpression ( String p1 ) :  Environment.Language.Evaluable
InteractiveEvaluator.serialize ( Object p1, File p2 ) :  ObjectOutputStream
InteractiveEvaluator.serialize ( Object p1, ObjectOutputStream p2 ) :  ObjectOutputStream
InteractiveEvaluator.serialize ( Object p1, OutputStream p2 ) :  ObjectOutputStream
InteractiveEvaluator.serialize ( Object p1, String p2 ) :  ObjectOutputStream

cdk-1.2.10.jar, InterfaceCP.class
package jas
InterfaceCP.InterfaceCP ( String cname, String varname, String sig )

cdk-1.2.10.jar, InterfaceDatabase.class
package org.omegahat.Interfaces.NativeInterface
InterfaceDatabase.get ( String p1, String p2 ) :  Object
InterfaceDatabase.getId ( ) :  String

cdk-1.2.10.jar, InterfaceNode.class
package org.omegahat.Environment.Tools.ClassHierarchy
InterfaceNode.findParents ( ) :  int
InterfaceNode.InterfaceNode ( Class p1, Environment.Tools.ClassHierarchy.ClassNodeAgent p2 )

cdk-1.2.10.jar, InterfaceReference.class
package org.omegahat.Interfaces.NativeInterface
InterfaceReference.database ( ) :  Environment.Databases.Database
InterfaceReference.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
InterfaceReference.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
InterfaceReference.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
InterfaceReference.getClassName ( ) :  String
InterfaceReference.InterfaceReference ( )
InterfaceReference.InterfaceReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
InterfaceReference.InterfaceReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2, Environment.Databases.Database p3 )
InterfaceReference.InterfaceReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2, Environment.Databases.Database p3, String p4 )
InterfaceReference.key ( ) :  String
InterfaceReference.key ( String p1 ) :  String
InterfaceReference.manager ( ) :  Interfaces.NativeInterface.OmegaInterfaceManager
InterfaceReference.manager ( Interfaces.NativeInterface.OmegaInterfaceManager p1 ) :  Interfaces.NativeInterface.OmegaInterfaceManager
InterfaceReference.setClassName ( String p1 ) :  String
InterfaceReference.toString ( ) :  String

cdk-1.2.10.jar, InterruptButton.class
package org.omegahat.Environment.Interpreter
InterruptButton.actionPerformed ( ActionEvent p1 ) :  void
InterruptButton.defaultBounds ( ) :  Rectangle
InterruptButton.getEvaluator ( ) :  Environment.Interpreter.Evaluator
InterruptButton.InterruptButton ( )
InterruptButton.InterruptButton ( Environment.Interpreter.Evaluator p1 )
InterruptButton.make ( ) :  boolean
InterruptButton.setEvaluator ( Environment.Interpreter.Evaluator p1 ) :  void

cdk-1.2.10.jar, InvokeinterfaceInsn.class
package jas
InvokeinterfaceInsn.InvokeinterfaceInsn ( CP cpe, int nargs )

cdk-1.2.10.jar, IPotentialFunction.class
package org.openscience.cdk.modeling.forcefield
IPotentialFunction.energyFunction ( GVector p1 ) [abstract] :  double
IPotentialFunction.getEnergyGradient ( ) [abstract] :  GVector
IPotentialFunction.getEnergyHessian ( ) [abstract] :  GMatrix
IPotentialFunction.getForEnergyHessian ( ) [abstract] :  double[ ]
IPotentialFunction.setEnergyGradient ( GVector p1 ) [abstract] :  void
IPotentialFunction.setEnergyHessian ( GVector p1 ) [abstract] :  void

cdk-1.2.10.jar, JarClassLoader.class
package org.omegahat.Environment.System
JarClassLoader.JarClassLoader ( File p1 )
JarClassLoader.JarClassLoader ( File p1, ZipFile p2 )
JarClassLoader.zipFile ( File p1 ) :  ZipFile

cdk-1.2.10.jar, jasError.class
package jas
jasError.jasError ( )
jasError.jasError ( String s )

cdk-1.2.10.jar, JniInchiOutputKey.class
package net.sf.jniinchi
JniInchiOutputKey.getCheckChar ( ) :  char
JniInchiOutputKey.getFirstBlock ( ) :  String
JniInchiOutputKey.getFlagChar ( ) :  char
JniInchiOutputKey.getFlagFixedH ( ) :  boolean
JniInchiOutputKey.getFlagIsotopic ( ) :  boolean
JniInchiOutputKey.getFlagStereo ( ) :  boolean
JniInchiOutputKey.getFlagVersion ( ) :  int
JniInchiOutputKey.getSecondBlock ( ) :  String

cdk-1.2.10.jar, JniInchiWrapper.class
package net.sf.jniinchi
JniInchiWrapper.checkInChIKey ( String key ) [static] :  INCHI_KEY_STATUS
JniInchiWrapper.getInChIKey ( String inchi ) [static] :  JniInchiOutputKey

cdk-1.2.10.jar, JTreeASTModel.class
package org.omegahat.Environment.Debugger.ParserViewer
JTreeASTModel.addTreeModelListener ( TreeModelListener p1 ) :  void
JTreeASTModel.getChild ( Object p1, int p2 ) :  Object
JTreeASTModel.getChildCount ( Object p1 ) :  int
JTreeASTModel.getIndexOfChild ( Object p1, Object p2 ) :  int
JTreeASTModel.getRoot ( ) :  Object
JTreeASTModel.isLeaf ( Object p1 ) :  boolean
JTreeASTModel.JTreeASTModel ( AST p1 )
JTreeASTModel.removeTreeModelListener ( TreeModelListener p1 ) :  void
JTreeASTModel.valueForPathChanged ( TreePath p1, Object p2 ) :  void

cdk-1.2.10.jar, JTreeASTPanel.class
package org.omegahat.Environment.Debugger.ParserViewer
JTreeASTPanel.JTreeASTPanel ( JTree p1, TreeSelectionListener p2 )
JTreeASTPanel.JTreeASTPanel ( TreeModel p1 )
JTreeASTPanel.JTreeASTPanel ( TreeModel p1, TreeSelectionListener p2 )
JTreeASTPanel.make ( ) :  boolean
JTreeASTPanel.make ( TreeSelectionListener p1 ) :  boolean
JTreeASTPanel.model ( TreeModel p1 ) :  TreeModel
JTreeASTPanel.tree ( ) :  JTree
JTreeASTPanel.tree ( JTree p1 ) :  JTree
JTreeASTPanel.tree ( TreeModel p1 ) :  JTree

cdk-1.2.10.jar, Label.class
package jas
Label.Label ( String tag )
Label.toString ( ) :  String

cdk-1.2.10.jar, LazyArgument.class
package org.omegahat.Environment.Language
LazyArgument.database ( Environment.Interpreter.Evaluator p1 ) :  Environment.Databases.Database
LazyArgument.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
LazyArgument.expression ( ) :  Environment.Parser.Parse.ExpressionInt
LazyArgument.expression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
LazyArgument.LazyArgument ( )
LazyArgument.LazyArgument ( String p1 )
LazyArgument.LazyArgument ( String p1, Environment.Parser.Parse.ExpressionInt p2 )
LazyArgument.name ( ) :  String
LazyArgument.name ( String p1 ) :  String
LazyArgument.toString ( ) :  String

cdk-1.2.10.jar, LazyFunction.class
package org.omegahat.Environment.Language
LazyFunction.addArgument ( Environment.Parser.Parse.MethodParameter p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  String
LazyFunction.assignArgument ( Environment.Databases.Database p1, Object p2, String p3, String p4, Environment.Interpreter.Evaluator p5 ) :  Object
LazyFunction.assignNamedArgument ( Environment.Databases.Database p1, Environment.Parser.Parse.AssignExpression p2, String p3, String p4, Environment.Interpreter.Evaluator p5 ) :  Object
LazyFunction.createCallFrame ( Environment.Interpreter.Evaluator p1 ) :  Environment.Databases.Database
LazyFunction.defaultIsLazy ( ) :  boolean
LazyFunction.defaultIsLazy ( boolean p1 ) :  boolean
LazyFunction.defaultIsLazy ( Environment.Parser.Parse.FunctionParameterModifier p1 ) :  boolean
LazyFunction.isLazy ( String p1 ) :  boolean
LazyFunction.isLazy ( String p1, int p2 ) :  boolean
LazyFunction.LazyFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Interpreter.Evaluator p6 )
LazyFunction.LazyFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Interpreter.Evaluator p7 )
LazyFunction.templateArgument ( Environment.Language.Evaluable p1, String p2, Environment.Interpreter.Evaluator p3 ) :  Object

cdk-1.2.10.jar, LazyFunctionDatabase.class
package org.omegahat.Environment.Databases
LazyFunctionDatabase.assign ( String p1, Object p2 ) :  boolean
LazyFunctionDatabase.evaluator ( ) :  Environment.Interpreter.Evaluator
LazyFunctionDatabase.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
LazyFunctionDatabase.Function ( ) :  Environment.Language.LazyFunction
LazyFunctionDatabase.Function ( Environment.Language.LazyFunction p1 ) :  Environment.Language.LazyFunction
LazyFunctionDatabase.get ( String p1 ) :  Object
LazyFunctionDatabase.get ( String p1, boolean p2 ) :  Object
LazyFunctionDatabase.get ( String p1, boolean p2, boolean p3 ) :  Object
LazyFunctionDatabase.get ( String p1, Environment.Interpreter.Evaluator p2 ) :  Object
LazyFunctionDatabase.isLazy ( String p1 ) :  boolean
LazyFunctionDatabase.LazyFunctionDatabase ( )
LazyFunctionDatabase.LazyFunctionDatabase ( Environment.Language.LazyFunction p1 )
LazyFunctionDatabase.LazyFunctionDatabase ( Environment.Language.LazyFunction p1, Environment.Interpreter.Evaluator p2 )
LazyFunctionDatabase.LazyFunctionDatabase ( String p1 )
LazyFunctionDatabase.templateDB ( ) :  Environment.Databases.Database

cdk-1.2.10.jar, LinearRegressionModel.class
package org.openscience.cdk.qsar.model.R
LinearRegressionModel.build ( ) :  void
LinearRegressionModel.finalize ( ) :  void
LinearRegressionModel.getFitCoefficients ( ) :  double[ ]
LinearRegressionModel.getFitDFResidual ( ) :  int
LinearRegressionModel.getFitFitted ( ) :  double[ ]
LinearRegressionModel.getFitRank ( ) :  int
LinearRegressionModel.getFitResiduals ( ) :  double[ ]
LinearRegressionModel.getPredictDF ( ) :  int
LinearRegressionModel.getPredictLowerBound ( ) :  double[ ]
LinearRegressionModel.getPredictPredicted ( ) :  double[ ]
LinearRegressionModel.getPredictResidualScale ( ) :  double
LinearRegressionModel.getPredictSEPredictions ( ) :  double[ ]
LinearRegressionModel.getPredictUpperBound ( ) :  double[ ]
LinearRegressionModel.LinearRegressionModel ( )
LinearRegressionModel.LinearRegressionModel ( double[ ][ ] xx, double[ ] yy )
LinearRegressionModel.LinearRegressionModel ( double[ ][ ] xx, double[ ] yy, double[ ] weights )
LinearRegressionModel.loadModel ( String fileName ) :  void
LinearRegressionModel.loadModel ( String serializedModel, String modelName ) :  void
LinearRegressionModel.predict ( ) :  void
LinearRegressionModel.setParameters ( String key, Object obj ) :  void
LinearRegressionModel.summary ( ) :  R.LinearRegressionModelSummary
package org.openscience.cdk.qsar.model.R2
LinearRegressionModel.build ( ) :  void
LinearRegressionModel.getAssign ( ) :  int[ ]
LinearRegressionModel.getCoefficients ( ) :  double[ ]
LinearRegressionModel.getDfResidual ( ) :  int
LinearRegressionModel.getEffects ( ) :  double[ ]
LinearRegressionModel.getFittedValues ( ) :  double[ ]
LinearRegressionModel.getModel ( ) :  JRI.RList
LinearRegressionModel.getModelPredict ( ) :  JRI.RList
LinearRegressionModel.getQr ( ) :  JRI.RList
LinearRegressionModel.getRank ( ) :  int
LinearRegressionModel.getResiduals ( ) :  double[ ]
LinearRegressionModel.getXlevels ( ) :  JRI.RList
LinearRegressionModel.LinearRegressionModel ( )
LinearRegressionModel.LinearRegressionModel ( double[ ][ ] xx, double[ ] yy )
LinearRegressionModel.LinearRegressionModel ( double[ ][ ] xx, double[ ] yy, double[ ] weights )
LinearRegressionModel.loadModel ( String fileName ) :  void
LinearRegressionModel.loadModel ( String serializedModel, String modelName ) :  void
LinearRegressionModel.predict ( ) :  void
LinearRegressionModel.setParameters ( String key, Object obj ) :  void
LinearRegressionModel.summary ( ) :  JRI.RList

cdk-1.2.10.jar, LinearRegressionModelFit.class
package org.openscience.cdk.qsar.model.R
LinearRegressionModelFit.getCoefficients ( ) :  double[ ]
LinearRegressionModelFit.getdfResidual ( ) :  int
LinearRegressionModelFit.getFitted ( ) :  double[ ]
LinearRegressionModelFit.getRank ( ) :  int
LinearRegressionModelFit.getResiduals ( ) :  double[ ]
LinearRegressionModelFit.LinearRegressionModelFit ( double[ ] coeff, double[ ] res, double[ ] fitted, int rank, int degreesOfFreedom )
LinearRegressionModelFit.setCoefficients ( double[ ] coeff ) :  void
LinearRegressionModelFit.setdfResidual ( int degreesOfFreedom ) :  void
LinearRegressionModelFit.setFitted ( double[ ] fitted ) :  void
LinearRegressionModelFit.setRank ( int rank ) :  void
LinearRegressionModelFit.setResiduals ( double[ ] residuals ) :  void

cdk-1.2.10.jar, LinearRegressionModelPredict.class
package org.openscience.cdk.qsar.model.R
LinearRegressionModelPredict.getDF ( ) :  int
LinearRegressionModelPredict.getLower ( ) :  double[ ]
LinearRegressionModelPredict.getPredicted ( ) :  double[ ]
LinearRegressionModelPredict.getResidualScale ( ) :  double
LinearRegressionModelPredict.getSEFit ( ) :  double[ ]
LinearRegressionModelPredict.getUpper ( ) :  double[ ]
LinearRegressionModelPredict.LinearRegressionModelPredict ( double predicted, double standardErrors, double lowerBounds, double upperBounds, int degreesOfFreedom, double residualScale )
LinearRegressionModelPredict.LinearRegressionModelPredict ( double[ ] predicted, double[ ] standardErrors, double[ ] lowerBounds, double[ ] upperBounds, int degreesOfFreedom, double residualScale )
LinearRegressionModelPredict.setDF ( int degreesOfFreedom ) :  void
LinearRegressionModelPredict.setLower ( double[ ] lowerBounds ) :  void
LinearRegressionModelPredict.setPredicted ( double[ ] predicted ) :  void
LinearRegressionModelPredict.setResidualScale ( double scale ) :  void
LinearRegressionModelPredict.setSEFit ( double[ ] standardErrors ) :  void
LinearRegressionModelPredict.setUpper ( double[ ] upperBounds ) :  void

cdk-1.2.10.jar, LinearRegressionModelSummary.class
package org.openscience.cdk.qsar.model.R
LinearRegressionModelSummary.getAdjRSQ ( ) :  double
LinearRegressionModelSummary.getCoeff ( ) :  double[ ][ ]
LinearRegressionModelSummary.getFStatistic ( ) :  double
LinearRegressionModelSummary.getFStatisticDF ( ) :  int[ ]
LinearRegressionModelSummary.getResiduals ( ) :  double[ ]
LinearRegressionModelSummary.getRSQ ( ) :  double
LinearRegressionModelSummary.getSigma ( ) :  double[ ]
LinearRegressionModelSummary.LinearRegressionModelSummary ( double[ ] residuals, double[ ] coeff, double sigma, double rsq, double adjrsq, int df, double[ ] fstat, String[ ] coeffRowNames, String[ ] coeffColNames )

cdk-1.2.10.jar, LineSearch.class
package org.openscience.cdk.modeling.forcefield
LineSearch.bracketingTheMinimum ( ) :  void
LineSearch.brentsMethod ( ) :  void
LineSearch.dbrentsMethod ( ) :  void
LineSearch.f ( double lambda ) :  double
LineSearch.getStepSize ( ) :  double
LineSearch.LineSearch ( )
LineSearch.setLineStep ( GVector kPoint, GVector searchDirection, IPotentialFunction forceFieldFunction ) :  void
LineSearch.sign ( double a, double b ) :  double
LineSearch.wolfeConditions ( double lambda ) :  boolean

cdk-1.2.10.jar, LineSearchForTheWolfeConditions.class
package org.openscience.cdk.modeling.forcefield
LineSearchForTheWolfeConditions.cubicInterpolation ( double alphai, double linearFunctionInAlphai, double linearFunctionDerivativeInAlphai, double alphaiMinus1, double linearFunctionInAlphaiMinus1, double linearFunctionDerivativeInAlphaiMinus1, double a, double b ) :  double
LineSearchForTheWolfeConditions.initialize ( GVector xUser, double fxUser, GVector dfxUser, GVector directionUser, double linearFunctionDerivativeUser, double alphaInitialStepUser ) :  void
LineSearchForTheWolfeConditions.lineSearchAlgorithm ( double alphaMax ) :  void
LineSearchForTheWolfeConditions.LineSearchForTheWolfeConditions ( IPotentialFunction pfUser, String method )

cdk-1.2.10.jar, LineTableAttr.class
package jas
LineTableAttr.addEntry ( Label l, int line ) :  void
LineTableAttr.LineTableAttr ( )

cdk-1.2.10.jar, list.class
package org.omegahat.Environment.DataStructures
list.addElement ( Object p1 ) :  int
list.data ( int p1 ) :  Object
list.data ( Object[ ] p1 ) :  Object
list.getElement ( int p1 ) :  Object
list.list ( )
list.list ( int p1 )
list.list ( Object[ ] p1 )
list.setData ( Object[ ] p1 ) :  int
list.setElement ( Object p1, int p2 ) :  int
package org.omegahat.Environment.ObjectDataStructures
list.convertElement ( Object p1 ) :  Object
list.list ( )
list.list ( Environment.ObjectDataStructures.list p1 )
list.list ( Environment.ObjectDataStructures.list p1, boolean p2 )
list.list ( int p1 )
list.list ( int p1, boolean p2 )
list.list ( Object[ ] p1 )
list.setData ( Object[ ] p1 ) :  int
list.setElement ( Object p1, int p2 ) :  int
list.targetClass ( ) :  Class

cdk-1.2.10.jar, List.class
package org.omegahat.Environment.Parser.Parse
List.addElement ( Object p1 ) :  void
List.addElements ( AST p1 ) :  int
List.addElements ( AST p1, boolean p2 ) :  int
List.addElements ( Environment.Parser.Parse.List p1 ) :  int
List.addResult ( Object p1, int p2, Object p3 ) :  Object
List.asString ( ) :  String
List.asString ( boolean p1 ) :  String
List.asString ( boolean p1, String p2 ) :  String
List.clear ( ) :  void
List.clone ( ) :  Object
List.contains ( Object p1 ) :  boolean
List.copyElements ( Environment.Parser.Parse.List p1 ) :  void
List.elementAt ( int p1 ) :  Object
List.elements ( ) :  Enumeration
List.elementToString ( Object p1, boolean p2, StringBuffer p3 ) :  void
List.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
List.eval ( Environment.Interpreter.Evaluator p1, boolean p2 ) :  Object
List.evalElement ( Object p1, int p2, Environment.Interpreter.Evaluator p3 ) :  Object
List.evalElement ( Object p1, int p2, Object p3, Environment.Interpreter.Evaluator p4 ) :  Object
List.evalResult ( Environment.Interpreter.Evaluator p1 ) :  Object
List.getFirstChild ( ) :  AST
List.getReferencedVariables ( boolean p1, AbstractCollection p2 ) :  AbstractCollection
List.lastElement ( ) :  Object
List.List ( )
List.List ( AST p1 )
List.List ( AST p1, boolean p2 )
List.List ( Environment.Parser.Parse.List p1 )
List.List ( int p1 )
List.List ( Object p1 )
List.List ( Object[ ] p1 )
List.parent ( Environment.Parser.Parse.TreeNodeInt p1 ) :  Environment.Parser.Parse.TreeNodeInt
List.separator ( ) :  String
List.separator ( String p1 ) :  String
List.setElementAt ( Object p1, int p2 ) :  Object
List.size ( ) :  int
List.size ( int p1 ) :  int
List.subset ( int p1 ) :  Environment.Parser.Parse.List
List.subset ( int[ ] p1 ) :  Environment.Parser.Parse.List
List.subset ( Object p1, boolean p2 ) :  Object
List.toArray ( ) :  Object[ ]
List.toString ( ) :  String
List.toString ( boolean p1 ) :  String

cdk-1.2.10.jar, ListListener.class
package org.omegahat.Environment.Utils
ListListener.assignPerformed ( Environment.Utils.OrderedListEvent p1 ) [abstract] :  void
ListListener.removePerformed ( Environment.Utils.OrderedListEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, LocalClassList.class
package org.omegahat.Environment.Tools.ClassList
LocalClassList.classLoader ( ) :  ClassLoader
LocalClassList.classLoader ( ClassLoader p1 ) :  ClassLoader
LocalClassList.classLoader ( File p1 ) :  ClassLoader
LocalClassList.loadClass ( String p1 ) :  Class
LocalClassList.LocalClassList ( )
LocalClassList.LocalClassList ( File p1 )
LocalClassList.LocalClassList ( File p1, ClassLoader p2 )

cdk-1.2.10.jar, LocalClassLocator.class
package org.omegahat.Environment.Tools.ClassList
LocalClassLocator.classList ( File p1 ) :  Environment.Tools.ClassList.ClassList
LocalClassLocator.classList ( URL p1 ) :  Environment.Tools.ClassList.ClassList
LocalClassLocator.LocalClassLocator ( )
LocalClassLocator.LocalClassLocator ( File p1 )
LocalClassLocator.LocalClassLocator ( URL p1 )

cdk-1.2.10.jar, LocalURLClassList.class
package org.omegahat.Environment.Tools.ClassList
LocalURLClassList.classLoader ( ) :  ClassLoader
LocalURLClassList.classLoader ( ClassLoader p1 ) :  ClassLoader
LocalURLClassList.loadClass ( String p1 ) :  Class
LocalURLClassList.LocalURLClassList ( URL p1 )
LocalURLClassList.LocalURLClassList ( URL p1, ClassLoader p2 )

cdk-1.2.10.jar, LocalVarEntry.class
package jas
LocalVarEntry.LocalVarEntry ( Label startLabel, Label endLabel, CP name, CP sig, int slot )
LocalVarEntry.LocalVarEntry ( Label startLabel, Label endLabel, String name, String sig, int slot )

cdk-1.2.10.jar, LocalVariable.class
package org.omegahat.Environment.Parser.Parse
LocalVariable.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
LocalVariable.elements ( ) :  Environment.Parser.Parse.List
LocalVariable.elements ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
LocalVariable.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
LocalVariable.getFirstChild ( ) :  AST
LocalVariable.getTypeClass ( Environment.Interpreter.Evaluator p1 ) :  Class
LocalVariable.LocalVariable ( AST p1 )
LocalVariable.LocalVariable ( Object p1, Object p2 )
LocalVariable.LocalVariable ( Object p1, Object p2, boolean p3 )
LocalVariable.LocalVariable ( Object p1, Object p2, Environment.Parser.Parse.Modifier p3 )
LocalVariable.modifiers ( ) :  Environment.Parser.Parse.Modifier
LocalVariable.modifiers ( Environment.Parser.Parse.Modifier p1 ) :  Environment.Parser.Parse.Modifier
LocalVariable.toString ( ) :  String
LocalVariable.type ( ) :  Environment.Parser.Parse.Name
LocalVariable.type ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name

cdk-1.2.10.jar, LocalVarTableAttr.class
package jas
LocalVarTableAttr.addEntry ( LocalVarEntry e ) :  void
LocalVarTableAttr.LocalVarTableAttr ( )

cdk-1.2.10.jar, LoggingTool.class
package org.openscience.cdk.tools
LoggingTool.debug ( Object obj, Object obj2, Object obj3 ) :  void
LoggingTool.debug ( Object obj, Object obj2, Object obj3, Object obj4 ) :  void
LoggingTool.debug ( Object obj, Object obj2, Object obj3, Object obj4, Object obj5 ) :  void
LoggingTool.debug ( Object object, boolean bool ) :  void
LoggingTool.debug ( Object object, double number ) :  void
LoggingTool.debug ( Object object, int number ) :  void
LoggingTool.debug ( Object object, Object object2 ) :  void
LoggingTool.error ( Object obj, Object obj2, Object obj3 ) :  void
LoggingTool.error ( Object obj, Object obj2, Object obj3, Object obj4 ) :  void
LoggingTool.error ( Object obj, Object obj2, Object obj3, Object obj4, Object obj5 ) :  void
LoggingTool.error ( Object object, boolean bool ) :  void
LoggingTool.error ( Object object, double number ) :  void
LoggingTool.error ( Object object, int number ) :  void
LoggingTool.error ( Object object, Object object2 ) :  void
LoggingTool.info ( Object obj, Object obj2, Object obj3 ) :  void
LoggingTool.info ( Object obj, Object obj2, Object obj3, Object obj4 ) :  void
LoggingTool.info ( Object obj, Object obj2, Object obj3, Object obj4, Object obj5 ) :  void
LoggingTool.info ( Object object, boolean bool ) :  void
LoggingTool.info ( Object object, double number ) :  void
LoggingTool.info ( Object object, int number ) :  void
LoggingTool.info ( Object object, Object object2 ) :  void
LoggingTool.warn ( Object obj, Object obj2, Object obj3 ) :  void
LoggingTool.warn ( Object obj, Object obj2, Object obj3, Object obj4 ) :  void
LoggingTool.warn ( Object obj, Object obj2, Object obj3, Object obj4, Object obj5 ) :  void
LoggingTool.warn ( Object object, boolean bool ) :  void
LoggingTool.warn ( Object object, double number ) :  void
LoggingTool.warn ( Object object, int number ) :  void
LoggingTool.warn ( Object object, Object object2 ) :  void

cdk-1.2.10.jar, logical.class
package org.omegahat.Environment.DataStructures
logical.addElement ( Object p1 ) :  int
logical.data ( boolean p1 ) :  Object
logical.data ( boolean[ ] p1 ) :  Object
logical.data ( byte p1 ) :  Object
logical.data ( byte[ ] p1 ) :  Object
logical.data ( int p1 ) :  Object
logical.getElement ( int p1 ) :  boolean
logical.logical ( )
logical.logical ( boolean p1 )
logical.logical ( boolean[ ] p1 )
logical.logical ( byte p1 )
logical.logical ( byte[ ] p1 )
logical.logical ( int p1 )
logical.setData ( boolean[ ] p1 ) :  int
logical.setElement ( Object p1, int p2 ) :  int
logical.valueOf ( String p1 ) [static] :  byte
package org.omegahat.Environment.ObjectDataStructures
logical.convertElement ( Object p1 ) :  Object
logical.data ( boolean p1 ) :  Vector
logical.data ( boolean[ ] p1 ) :  Vector
logical.data ( byte p1 ) :  Vector
logical.data ( byte[ ] p1 ) :  Vector
logical.logical ( )
logical.logical ( boolean p1 )
logical.logical ( boolean[ ] p1 )
logical.logical ( byte p1 )
logical.logical ( byte[ ] p1 )
logical.logical ( int p1 )
logical.setData ( boolean[ ] p1 ) :  int
logical.setElement ( Object p1, int p2 ) :  int
logical.targetClass ( ) :  Class
logical.valueOf ( String p1 ) [static] :  byte

cdk-1.2.10.jar, LogicalExpression.class
package org.omegahat.Environment.Parser.Parse
LogicalExpression.asLogical ( Object p1 ) :  boolean
LogicalExpression.dontDoBoth ( ) :  boolean
LogicalExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
LogicalExpression.LogicalExpression ( Object p1, Object p2, int p3 )
LogicalExpression.operate ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
LogicalExpression.operate ( String[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
LogicalExpression.separator ( ) :  String

cdk-1.2.10.jar, LongCP.class
package jas
LongCP.LongCP ( long n )

cdk-1.2.10.jar, LookupswitchInsn.class
package jas
LookupswitchInsn.LookupswitchInsn ( Label def, int[ ] match, Label[ ] target )

cdk-1.2.10.jar, ManagedEvaluatorInt.class
package org.omegahat.Environment.Interpreter
ManagedEvaluatorInt.manager ( ) [abstract] :  Environment.Interpreter.EvaluatorManager
ManagedEvaluatorInt.manager ( Environment.Interpreter.EvaluatorManager p1 ) [abstract] :  Environment.Interpreter.EvaluatorManager

cdk-1.2.10.jar, MathExpression.class
package org.omegahat.Environment.Parser.Parse
MathExpression.arrayOperation ( Object p1, Object p2 ) :  Object
MathExpression.computeNumeric ( double[ ] p1 ) :  double
MathExpression.doSpecialInterface ( Environment.DataStructures.MathOperable p1, Object p2 ) :  Object
MathExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
MathExpression.MathExpression ( int p1, AST p2 )
MathExpression.MathExpression ( Object p1, Object p2, int p3 )
MathExpression.numericComputation ( Object[ ] p1 ) :  Object
MathExpression.operate ( Object[ ] p1 ) :  Object
MathExpression.toString ( ) :  String

cdk-1.2.10.jar, MDLWriter.class
package org.openscience.cdk.io
MDLWriter.accepts ( Class classObject ) :  boolean
MDLWriter.close ( ) :  void
MDLWriter.customizeJob ( ) :  void
MDLWriter.getFormat ( ) :  IResourceFormat
MDLWriter.getIOSettings ( ) :  IOSetting[ ]
MDLWriter.MDLWriter ( )
MDLWriter.MDLWriter ( OutputStream output )
MDLWriter.MDLWriter ( Writer out )
MDLWriter.setWriter ( OutputStream output ) :  void
MDLWriter.setWriter ( Writer out ) :  void
MDLWriter.write ( IChemObject object ) :  void
MDLWriter.writeMolecule ( IAtomContainer container ) :  void

cdk-1.2.10.jar, MenuDescription.class
package org.omegahat.Environment.GUI
MenuDescription.MenuDescription ( String[ ] p1 )
MenuDescription.menuItem ( int p1 ) :  JMenuItem
MenuDescription.setItems ( String[ ] p1 ) :  int
MenuDescription.setItems ( String[ ] p1, boolean p2 ) :  int

cdk-1.2.10.jar, MergableHashtable.class
package org.omegahat.Environment.Utils
MergableHashtable.getNames ( ) :  String[ ]
MergableHashtable.MergableHashtable ( )
MergableHashtable.MergableHashtable ( int p1 )
MergableHashtable.merge ( Hashtable p1 ) :  int
MergableHashtable.merge ( Hashtable p1, boolean p2 ) :  int

cdk-1.2.10.jar, MergableInt.class
package org.omegahat.Environment.Databases
MergableInt.merge ( Environment.Databases.Database p1, boolean p2 ) [abstract] :  int
MergableInt.merge ( Hashtable p1, boolean p2 ) [abstract] :  int

cdk-1.2.10.jar, MetaForeignReference.class
package org.omegahat.Interfaces.NativeInterface
MetaForeignReference.defineClass ( String p1, String[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Class
MetaForeignReference.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
MetaForeignReference.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
MetaForeignReference.getName ( ) :  String
MetaForeignReference.getTargetClass ( ) :  String
MetaForeignReference.MetaForeignReference ( String p1 )
MetaForeignReference.MetaForeignReference ( String p1, String p2 )
MetaForeignReference.MetaForeignReference ( String p1, String p2, String[ ] p3 )
MetaForeignReference.MetaForeignReference ( String p1, String p2, String[ ] p3, Environment.Interpreter.Evaluator p4 )
MetaForeignReference.setName ( String p1 ) :  String
MetaForeignReference.setTargetClass ( String p1 ) :  String

cdk-1.2.10.jar, Method.class
package jas
Method.Method ( short macc, CP name, CP sig, CodeAttr cd, ExceptAttr ex )
package org.omegahat.Environment.Language
Method.addElement ( Object p1 ) :  void
Method.compile ( ) :  Class
Method.createDispatchClass ( String p1 ) :  Class
Method.createJavaMethods ( ClassEnv p1 ) :  int
Method.dispatchClass ( ) :  Class
Method.dispatchClass ( boolean p1 ) :  Class
Method.dispatchClass ( Class p1 ) :  Class
Method.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
Method.eval ( Environment.Language.Function p1, Environment.Parser.Parse.List p2, Object p3, Environment.Interpreter.Evaluator p4 ) :  Object
Method.eval ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Object
Method.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
Method.eval ( String p1, Environment.Parser.Parse.List p2, Object p3, Environment.Interpreter.Evaluator p4 ) :  Object
Method.frame ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2, Class[ ] p3, Vector p4 ) :  Environment.Databases.TypedDatabase
Method.functionKey ( Environment.Language.Function p1 ) :  String
Method.jasBody ( String p1, int p2 ) :  CodeAttr
Method.jasDefaultConstructor ( ClassEnv p1 ) :  void
Method.jasMethod ( Environment.Language.Function p1, String p2, ClassEnv p3 ) :  Method
Method.jasSignature ( Environment.Language.Function p1 ) :  Vector
Method.load ( String p1, ClassEnv p2 ) :  Class
Method.loader ( ) :  Environment.System.DynamicClassLoader
Method.locateMethod ( Environment.Databases.Database p1, Class[ ] p2, Vector p3, Environment.Interpreter.Evaluator p4 ) :  Environment.Language.Function
Method.lookupAndDispatch ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Object
Method.Method ( )
Method.Method ( Environment.Language.Function p1 )
Method.Method ( Environment.Language.Method p1 )
Method.Method ( String p1, Environment.Language.Function p2 )
Method.name ( ) :  String
Method.name ( String p1 ) :  String
Method.put ( Environment.Language.Function p1 ) :  void
Method.put ( Environment.Language.Method p1 ) :  void

cdk-1.2.10.jar, MethodAlias.class
package org.omegahat.Environment.Language
MethodAlias.MethodAlias ( Object p1, Method p2 )
MethodAlias.This ( ) :  Object
MethodAlias.This ( Object p1 ) :  Object

cdk-1.2.10.jar, MethodAliasException.class
package org.omegahat.Environment.Language
MethodAliasException.alias ( ) :  Environment.Language.MethodAlias
MethodAliasException.fieldName ( ) :  String
MethodAliasException.MethodAliasException ( String p1, Class p2 )
MethodAliasException.MethodAliasException ( String p1, Class p2, Environment.Language.MethodAlias p3 )
MethodAliasException.sourceClass ( ) :  Class

cdk-1.2.10.jar, MethodCall.class
package org.omegahat.Environment.Parser.Parse
MethodCall.argList ( Environment.Interpreter.Evaluator p1 ) :  Environment.Parser.Parse.List
MethodCall.args ( ) :  Environment.Parser.Parse.List
MethodCall.args ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
MethodCall.args ( Object[ ] p1 ) :  Environment.Parser.Parse.List
MethodCall.argumentClasses ( Object[ ] p1 ) :  Vector
MethodCall.children ( ) :  Vector
MethodCall.elementName ( String p1 ) :  String
MethodCall.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
MethodCall.evalArgs ( ) :  boolean
MethodCall.evalArgs ( boolean p1 ) :  boolean
MethodCall.evalFunction ( Environment.Language.Function p1, Environment.Interpreter.Evaluator p2 ) :  Object
MethodCall.evalFunction ( Environment.Language.Method p1, Environment.Interpreter.Evaluator p2 ) :  Object
MethodCall.evaluatorMethod ( ) :  boolean
MethodCall.evaluatorMethod ( boolean p1 ) :  boolean
MethodCall.findEvalMethod ( Environment.Interpreter.Evaluator p1, boolean p2 ) :  Object
MethodCall.findEvalMethod ( Environment.Parser.Parse.List p1, Object p2, Environment.Interpreter.Evaluator p3, boolean p4 ) :  Object
MethodCall.findEvalMethod ( Object p1, Environment.Interpreter.Evaluator p2 ) :  Object
MethodCall.findEvalMethod ( Object p1, Environment.Interpreter.Evaluator p2, boolean p3 ) :  Object
MethodCall.fullName ( ) :  Environment.Parser.Parse.Name
MethodCall.getFirstChild ( ) :  AST
MethodCall.implicitNew ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) :  Object
MethodCall.implicitNew ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
MethodCall.isStatic ( ) :  boolean
MethodCall.isStatic ( boolean p1 ) :  boolean
MethodCall.isStatic ( Method p1 ) :  boolean
MethodCall.MethodCall ( )
MethodCall.MethodCall ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2 )
MethodCall.MethodCall ( Environment.Parser.Parse.ExpressionInt p1, String p2, Environment.Parser.Parse.List p3 )
MethodCall.MethodCall ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2 )
MethodCall.MethodCall ( String p1, Environment.Parser.Parse.List p2 )
MethodCall.MethodCall ( String p1, String[ ] p2 )
MethodCall.methodInvoke ( Method p1, Object p2, Object[ ] p3, Environment.Interpreter.Evaluator p4 ) :  Object
MethodCall.methodLocator ( ) :  Environment.Parser.Parse.MethodLocator
MethodCall.methodLocator ( Environment.Parser.Parse.MethodLocator p1 ) :  Environment.Parser.Parse.MethodLocator
MethodCall.methodName ( ) :  String
MethodCall.methodName ( Environment.Parser.Parse.Name p1 ) :  String
MethodCall.methodName ( String p1 ) :  String
MethodCall.Quote ( Environment.Interpreter.Evaluator p1 ) :  Environment.Parser.Parse.ExpressionInt
MethodCall.replaceChild ( Environment.Parser.Parse.TreeNodeInt p1, Environment.Parser.Parse.TreeNodeInt p2 ) :  int
MethodCall.resolveMethod ( Object[ ] p1, Object p2, Environment.Interpreter.Evaluator p3 ) :  Method
MethodCall.returnsVoid ( Method p1 ) :  boolean
MethodCall.setAccessible ( Method p1, Object p2 ) :  Method
MethodCall.substitute ( Hashtable p1, boolean p2 ) :  Environment.Parser.Parse.ExpressionInt
MethodCall.toString ( ) :  String
MethodCall.transformArguments ( Class[ ] p1, Object[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Object[ ]
MethodCall.transformArguments ( Method p1, Object[ ] p2, Environment.Interpreter.Evaluator p3 ) :  Object[ ]
MethodCall.unqualifiedCall ( Environment.Interpreter.Evaluator p1 ) :  Object

cdk-1.2.10.jar, MethodCP.class
package jas
MethodCP.MethodCP ( String cname, String varname, String sig )

cdk-1.2.10.jar, MethodDefinition.class
package org.omegahat.Environment.Parser.Parse
MethodDefinition.MethodDefinition ( )
MethodDefinition.MethodDefinition ( Environment.Parser.Parse.MethodHeader p1, Environment.Parser.Parse.StatementList p2 )
MethodDefinition.toString ( ) :  String

cdk-1.2.10.jar, MethodExpression.class
package org.omegahat.Environment.Parser.Parse
MethodExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
MethodExpression.MethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 )
MethodExpression.MethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 )
MethodExpression.MethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Parser.Parse.FunctionParameterModifier p6 )
MethodExpression.name ( ) :  Environment.Parser.Parse.Name
MethodExpression.name ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name

cdk-1.2.10.jar, MethodHeader.class
package org.omegahat.Environment.Parser.Parse
MethodHeader.emptyBody ( ) :  boolean
MethodHeader.emptyBody ( boolean p1 ) :  boolean
MethodHeader.exceptions ( ) :  Environment.Parser.Parse.ClassList
MethodHeader.exceptions ( Environment.Parser.Parse.ClassList p1 ) :  Environment.Parser.Parse.ClassList
MethodHeader.MethodHeader ( String p1, Environment.Parser.Parse.List p2 )
MethodHeader.MethodHeader ( String p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.ClassList p4 )
MethodHeader.modifiers ( ) :  Object
MethodHeader.modifiers ( Object p1 ) :  Object
MethodHeader.returnType ( ) :  Environment.Parser.Parse.Name
MethodHeader.returnType ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
MethodHeader.returnType ( String p1 ) :  Environment.Parser.Parse.Name
MethodHeader.toString ( ) :  String

cdk-1.2.10.jar, MethodLocator.class
package org.omegahat.Environment.Parser.Parse
MethodLocator.isCast ( Environment.Parser.Parse.List p1 ) :  boolean[ ]
MethodLocator.matchClass ( Class p1, Class p2 ) [static] :  Class
MethodLocator.matchClass ( Class p1, Class p2, boolean p3 ) [static] :  Class
MethodLocator.matchClasses ( Class[ ] p1, Class[ ] p2 ) :  Class[ ]
MethodLocator.matchClasses ( Class[ ] p1, Class[ ] p2, boolean[ ] p3, Environment.Interpreter.Evaluator p4 ) :  Class[ ]
MethodLocator.matchClasses ( Class[ ] p1, Class[ ] p2, Environment.Parser.Parse.List p3, Environment.Interpreter.Evaluator p4 ) :  Class[ ]
MethodLocator.matchInterfaces ( Class p1, Class p2 ) [static] :  Class
MethodLocator.matchMethod ( Method p1, Class[ ] p2, boolean[ ] p3, Environment.Interpreter.Evaluator p4 ) :  Class[ ]
MethodLocator.MethodLocator ( )
MethodLocator.searchMethods ( Class p1, String p2, Object[ ] p3, Environment.Parser.Parse.List p4, Environment.Interpreter.Evaluator p5 ) :  Method
MethodLocator.searchMethods ( Class p1, String p2, Object[ ] p3, Environment.Parser.Parse.List p4, Environment.Interpreter.Evaluator p5, Class p6 ) :  Method
MethodLocator.searchMethods ( Object p1, String p2, Object[ ] p3, Environment.Parser.Parse.List p4, Environment.Interpreter.Evaluator p5 ) :  Method
MethodLocator.searchMethods ( Object p1, String p2, Object[ ] p3, Environment.Parser.Parse.List p4, Environment.Interpreter.Evaluator p5, boolean p6 ) :  Method
MethodLocator.searchMethods ( String p1, Environment.Parser.Parse.List p2, Class[ ] p3, Method[ ] p4, Environment.Interpreter.Evaluator p5 ) :  Method
MethodLocator.toClasses ( Object[ ] p1, Environment.Parser.Parse.List p2 ) :  Class[ ]

cdk-1.2.10.jar, MethodParameter.class
package org.omegahat.Environment.Parser.Parse
MethodParameter.Class ( Environment.Interpreter.Evaluator p1 ) :  Class
MethodParameter.isLazy ( ) :  boolean
MethodParameter.lazy ( ) :  int
MethodParameter.MethodParameter ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.Name p2 )
MethodParameter.MethodParameter ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.Name p2, Environment.Parser.Parse.FunctionParameterModifier p3 )
MethodParameter.MethodParameter ( String p1, Environment.Parser.Parse.Name p2 )
MethodParameter.MethodParameter ( String p1, Environment.Parser.Parse.Name p2, Environment.Parser.Parse.FunctionParameterModifier p3 )
MethodParameter.MethodParameter ( String p1, String p2 )
MethodParameter.MethodParameter ( String p1, String p2, Environment.Parser.Parse.FunctionParameterModifier p3 )
MethodParameter.modifier ( ) :  Environment.Parser.Parse.FunctionParameterModifier
MethodParameter.modifier ( Environment.Parser.Parse.FunctionParameterModifier p1 ) :  Environment.Parser.Parse.FunctionParameterModifier
MethodParameter.name ( ) :  String
MethodParameter.name ( String p1 ) :  String
MethodParameter.toString ( ) :  String

cdk-1.2.10.jar, MethodsCollection.class
package org.omegahat.Environment.Language.UserClasses
MethodsCollection.dispatchAndEval ( String p1, String p2, Environment.Language.FunctionCallArguments p3, Object p4 ) :  Object
MethodsCollection.dispatchAndEval ( String p1, String p2, Environment.Language.FunctionCallArguments p3, Object p4, Environment.Interpreter.Evaluator p5 ) :  Object
MethodsCollection.evaluator ( ) :  Environment.Interpreter.Evaluator
MethodsCollection.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
MethodsCollection.MethodsCollection ( )
MethodsCollection.MethodsCollection ( int p1 )
MethodsCollection.MethodsCollection ( String p1 )

cdk-1.2.10.jar, MethodTreeModel.class
package org.omegahat.Environment.GUITools.MethodViewer
MethodTreeModel.addTreeModelListener ( TreeModelListener p1 ) :  void
MethodTreeModel.constructors ( ) :  Constructor[ ]
MethodTreeModel.copyTo ( Object p1, Object p2 ) :  Object
MethodTreeModel.fields ( ) :  Field[ ]
MethodTreeModel.getChild ( Object p1, int p2 ) :  Object
MethodTreeModel.getChildCount ( Object p1 ) :  int
MethodTreeModel.getElements ( int p1 ) :  Object
MethodTreeModel.getIndexOfChild ( Object p1, Object p2 ) :  int
MethodTreeModel.getRoot ( ) :  Object
MethodTreeModel.isLeaf ( Object p1 ) :  boolean
MethodTreeModel.methods ( ) :  Method[ ]
MethodTreeModel.MethodTreeModel ( Class p1 )
MethodTreeModel.MethodTreeModel ( Class p1, boolean p2 )
MethodTreeModel.nonPublic ( ) :  boolean
MethodTreeModel.nonPublic ( boolean p1 ) :  boolean
MethodTreeModel.removeTreeModelListener ( TreeModelListener p1 ) :  void
MethodTreeModel.source ( ) :  Class
MethodTreeModel.source ( Class p1 ) :  Class
MethodTreeModel.valueForPathChanged ( TreePath p1, Object p2 ) :  void

cdk-1.2.10.jar, MethodTreeRenderer.class
package org.omegahat.Environment.GUITools.MethodViewer
MethodTreeRenderer.asString ( Class p1 ) :  String
MethodTreeRenderer.asString ( Constructor p1 ) :  String
MethodTreeRenderer.asString ( Field p1 ) :  String
MethodTreeRenderer.asString ( Method p1 ) :  String
MethodTreeRenderer.asString ( Object p1 ) :  String
MethodTreeRenderer.asString ( String p1, Class p2, Class[ ] p3 ) :  String
MethodTreeRenderer.color ( Object p1 ) :  Color
MethodTreeRenderer.getTreeCellRendererComponent ( JTree p1, Object p2, boolean p3, boolean p4, boolean p5, int p6, boolean p7 ) :  Component
MethodTreeRenderer.icon ( Object p1 ) :  Icon
MethodTreeRenderer.MethodTreeRenderer ( )

cdk-1.2.10.jar, MethodViewer.class
package org.omegahat.Environment.GUITools.MethodViewer
MethodViewer.defaultModel ( Class p1 ) :  TreeModel
MethodViewer.defaultRenderer ( ) :  TreeCellRenderer
MethodViewer.MethodViewer ( )
MethodViewer.MethodViewer ( Class p1 )
MethodViewer.MethodViewer ( TreeModel p1 )
MethodViewer.setClass ( Class p1 ) :  Class

cdk-1.2.10.jar, MethodViewerFrame.class
package org.omegahat.Environment.GUITools.MethodViewer
MethodViewerFrame.actionPerformed ( ActionEvent p1 ) :  void
MethodViewerFrame.evaluator ( ) :  Environment.Interpreter.Evaluator
MethodViewerFrame.getClass ( String p1 ) :  Class
MethodViewerFrame.init ( Environment.GUITools.MethodViewer.MethodViewer p1 ) :  void
MethodViewerFrame.MethodViewerFrame ( Class p1 )
MethodViewerFrame.MethodViewerFrame ( Class p1, boolean p2 )
MethodViewerFrame.MethodViewerFrame ( Environment.GUITools.MethodViewer.MethodViewer p1 )
MethodViewerFrame.setClass ( String p1 ) :  Class
MethodViewerFrame.valueChanged ( ListSelectionEvent p1 ) :  void
MethodViewerFrame.viewer ( ) :  Environment.GUITools.MethodViewer.MethodViewer
MethodViewerFrame.viewer ( Environment.GUITools.MethodViewer.MethodViewer p1 ) :  Environment.GUITools.MethodViewer.MethodViewer

cdk-1.2.10.jar, MissingMethodException.class
package org.omegahat.R.Java
MissingMethodException.getMethodName ( ) :  String
MissingMethodException.MissingMethodException ( String p1 )
MissingMethodException.MissingMethodException ( String p1, Class p2 )

cdk-1.2.10.jar, MMFF94EnergyFunction.class
package org.openscience.cdk.modeling.forcefield
MMFF94EnergyFunction.energyFunction ( GVector coords3d ) :  double
MMFF94EnergyFunction.energyFunctionOfAMolecule ( IAtomContainer molecule ) :  double
MMFF94EnergyFunction.getEnergyGradient ( ) :  GVector
MMFF94EnergyFunction.getEnergyHessian ( ) :  GMatrix
MMFF94EnergyFunction.getForEnergyHessian ( ) :  double[ ]
MMFF94EnergyFunction.getOrder2ndErrorApproximateEnergyGradient ( ) :  GVector
MMFF94EnergyFunction.getOrder5thErrorApproximateEnergyGradient ( ) :  GVector
MMFF94EnergyFunction.MMFF94EnergyFunction ( IAtomContainer molecule, Map mmff94Tables )
MMFF94EnergyFunction.setEnergyGradient ( GVector coords3d ) :  void
MMFF94EnergyFunction.setEnergyHessian ( GVector coords3d ) :  void
MMFF94EnergyFunction.setOrder2ndErrorApproximateEnergyGradient ( GVector coords3d ) :  void
MMFF94EnergyFunction.setOrder5thErrorApproximateEnergyGradient ( GVector coords3d ) :  void

cdk-1.2.10.jar, Modifier.class
package org.omegahat.Environment.Parser.Parse
Modifier.access ( ) :  int
Modifier.access ( int p1 ) :  int
Modifier.access ( String p1 ) :  int
Modifier.addModifier ( int p1 ) :  int
Modifier.isStatic ( ) :  boolean
Modifier.isStatic ( boolean p1 ) :  boolean
Modifier.Modifier ( )
Modifier.Modifier ( boolean p1 )
Modifier.Modifier ( int p1 )
Modifier.Modifier ( String p1 )
Modifier.Modifier ( String p1, boolean p2 )
Modifier.toString ( ) :  String

cdk-1.2.10.jar, MultiarrayInsn.class
package jas
MultiarrayInsn.MultiarrayInsn ( CP cpe, int sz )

cdk-1.2.10.jar, MultiLineComment.class
package org.omegahat.Environment.Parser.Parse
MultiLineComment.MultiLineComment ( )
MultiLineComment.MultiLineComment ( String p1 )
MultiLineComment.toString ( ) :  String

cdk-1.2.10.jar, MultiMethodAliasException.class
package org.omegahat.Environment.Language
MultiMethodAliasException.aliases ( ) :  Vector
MultiMethodAliasException.MultiMethodAliasException ( String p1, Class p2, Vector p3 )

cdk-1.2.10.jar, Multiplicable.class
package org.omegahat.Environment.DataStructures
Multiplicable.multiplyValue ( Object p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, Mutex.class
package org.rosuda.JRI
Mutex.lock ( ) :  void
Mutex.lockWithTimeout ( long p1 ) :  boolean
Mutex.Mutex ( )
Mutex.safeLock ( ) :  boolean
Mutex.safeLockWithTimeout ( long p1 ) :  boolean
Mutex.toString ( ) :  String
Mutex.tryLock ( ) :  int
Mutex.unlock ( ) :  void

cdk-1.2.10.jar, Name.class
package org.omegahat.Environment.Parser.Parse
Name.addElements ( AST p1 ) :  int
Name.append ( Environment.Parser.Parse.Name p1 ) :  int
Name.asClass ( ) :  Object
Name.asClass ( Environment.Interpreter.Evaluator p1 ) :  Object
Name.asObject ( Environment.Interpreter.Evaluator p1 ) :  Object
Name.asString ( ) :  String
Name.collapse ( ) :  String
Name.collapse ( String p1 ) :  String
Name.element ( int p1 ) :  String
Name.equals ( Object p1 ) :  boolean
Name.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
Name.getReferencedVariables ( boolean p1, AbstractCollection p2 ) :  AbstractCollection
Name.hashCode ( ) :  int
Name.Name ( )
Name.Name ( AST p1 )
Name.Name ( Environment.Parser.Parse.FieldAccess p1 )
Name.Name ( Environment.Parser.Parse.Name p1 )
Name.Name ( int p1 )
Name.Name ( String p1 )
Name.Name ( String p1, String p2 )
Name.Name ( String[ ] p1 )
Name.subset ( int p1, int p2 ) :  Environment.Parser.Parse.Name
Name.substitute ( Hashtable p1, boolean p2 ) :  Environment.Parser.Parse.ExpressionInt
Name.toString ( ) :  String

cdk-1.2.10.jar, Named.class
package org.omegahat.Environment.Utils
Named.getName ( ) [abstract] :  String

cdk-1.2.10.jar, NamedReference.class
package org.omegahat.Interfaces.NativeInterface
NamedReference.NamedReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
NamedReference.NamedReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2, Environment.Databases.Database p3, String p4 )

cdk-1.2.10.jar, NamedServerPool.class
package org.omegahat.Environment.TaskManagement
NamedServerPool.objects ( ) [abstract] :  String[ ]

cdk-1.2.10.jar, NameTypeCP.class
package jas
NameTypeCP.NameTypeCP ( String name, String sig )

cdk-1.2.10.jar, NameTypeSearchFilter.class
package org.omegahat.Environment.Databases
NameTypeSearchFilter.accept ( String p1, Object p2 ) :  boolean
NameTypeSearchFilter.classes ( ) :  Vector
NameTypeSearchFilter.classes ( Class p1 ) :  Vector
NameTypeSearchFilter.classes ( Vector p1 ) :  Vector
NameTypeSearchFilter.name ( ) :  String
NameTypeSearchFilter.name ( String p1 ) :  String
NameTypeSearchFilter.NameTypeSearchFilter ( )
NameTypeSearchFilter.NameTypeSearchFilter ( String p1 )
NameTypeSearchFilter.NameTypeSearchFilter ( String p1, Class p2 )
NameTypeSearchFilter.NameTypeSearchFilter ( String p1, String p2 )
NameTypeSearchFilter.NameTypeSearchFilter ( String p1, Vector p2 )
NameTypeSearchFilter.strictMatch ( ) :  boolean
NameTypeSearchFilter.strictMatch ( boolean p1 ) :  boolean

cdk-1.2.10.jar, NativeArtefactLocator.class
package net.sf.jnati.deploy
NativeArtefactLocator.findArtefact ( String id, String version ) [static] :  ArtefactLocation

cdk-1.2.10.jar, NewtonRaphsonMethod.class
package org.openscience.cdk.modeling.forcefield
NewtonRaphsonMethod.determinat ( GVector gradientk, GMatrix hessiank ) :  void
NewtonRaphsonMethod.getGradientPerInverseHessian ( ) :  GVector
NewtonRaphsonMethod.gradientPerInverseHessian ( GVector gradientk, GMatrix hessiank ) :  void
NewtonRaphsonMethod.hessianEigenValues ( double[ ] forMatrix, int size ) :  void
NewtonRaphsonMethod.NewtonRaphsonMethod ( )

cdk-1.2.10.jar, NNBond.class
package org.openscience.cdk.nonotify
NNBond.NNBond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo )

cdk-1.2.10.jar, NoNotificationChemObjectBuilder.class
package org.openscience.cdk.nonotify
NoNotificationChemObjectBuilder.getInstance ( ) [static] :  NoNotificationChemObjectBuilder
NoNotificationChemObjectBuilder.newAdductFormula ( ) :  IAdductFormula
NoNotificationChemObjectBuilder.newAdductFormula ( IMolecularFormula formula ) :  IAdductFormula
NoNotificationChemObjectBuilder.newAminoAcid ( ) :  IAminoAcid
NoNotificationChemObjectBuilder.newAtom ( ) :  IAtom
NoNotificationChemObjectBuilder.newAtom ( IElement element ) :  IAtom
NoNotificationChemObjectBuilder.newAtom ( String elementSymbol ) :  IAtom
NoNotificationChemObjectBuilder.newAtom ( String elementSymbol, Point2d point2d ) :  IAtom
NoNotificationChemObjectBuilder.newAtom ( String elementSymbol, Point3d point3d ) :  IAtom
NoNotificationChemObjectBuilder.newAtomContainer ( ) :  IAtomContainer
NoNotificationChemObjectBuilder.newAtomContainer ( IAtomContainer container ) :  IAtomContainer
NoNotificationChemObjectBuilder.newAtomContainer ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount ) :  IAtomContainer
NoNotificationChemObjectBuilder.newAtomContainerSet ( ) :  IAtomContainerSet
NoNotificationChemObjectBuilder.newAtomParity ( IAtom centralAtom, IAtom first, IAtom second, IAtom third, IAtom fourth, int parity ) :  IAtomParity
NoNotificationChemObjectBuilder.newAtomType ( IElement element ) :  IAtomType
NoNotificationChemObjectBuilder.newAtomType ( String elementSymbol ) :  IAtomType
NoNotificationChemObjectBuilder.newAtomType ( String identifier, String elementSymbol ) :  IAtomType
NoNotificationChemObjectBuilder.newBioPolymer ( ) :  IBioPolymer
NoNotificationChemObjectBuilder.newBond ( ) :  IBond
NoNotificationChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2 ) :  IBond
NoNotificationChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order ) :  IBond
NoNotificationChemObjectBuilder.newBond ( IAtom atom1, IAtom atom2, IBond.Order order, int stereo ) :  IBond
NoNotificationChemObjectBuilder.newBond ( IAtom[ ] atoms ) :  IBond
NoNotificationChemObjectBuilder.newBond ( IAtom[ ] atoms, IBond.Order order ) :  IBond
NoNotificationChemObjectBuilder.newChemFile ( ) :  IChemFile
NoNotificationChemObjectBuilder.newChemModel ( ) :  IChemModel
NoNotificationChemObjectBuilder.newChemObject ( ) :  IChemObject
NoNotificationChemObjectBuilder.newChemObject ( IChemObject object ) :  IChemObject
NoNotificationChemObjectBuilder.newChemSequence ( ) :  IChemSequence
NoNotificationChemObjectBuilder.newCrystal ( ) :  ICrystal
NoNotificationChemObjectBuilder.newCrystal ( IAtomContainer container ) :  ICrystal
NoNotificationChemObjectBuilder.newElectronContainer ( ) :  IElectronContainer
NoNotificationChemObjectBuilder.newElement ( ) :  IElement
NoNotificationChemObjectBuilder.newElement ( IElement element ) :  IElement
NoNotificationChemObjectBuilder.newElement ( String symbol ) :  IElement
NoNotificationChemObjectBuilder.newElement ( String symbol, int atomicNumber ) :  IElement
NoNotificationChemObjectBuilder.newFragmentAtom ( ) :  IFragmentAtom
NoNotificationChemObjectBuilder.newIsotope ( IElement element ) :  IIsotope
NoNotificationChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, double exactMass, double abundance ) :  IIsotope
NoNotificationChemObjectBuilder.newIsotope ( int atomicNumber, String elementSymbol, int massNumber, double exactMass, double abundance ) :  IIsotope
NoNotificationChemObjectBuilder.newIsotope ( String elementSymbol ) :  IIsotope
NoNotificationChemObjectBuilder.newIsotope ( String elementSymbol, int massNumber ) :  IIsotope
NoNotificationChemObjectBuilder.newLonePair ( ) :  ILonePair
NoNotificationChemObjectBuilder.newLonePair ( IAtom atom ) :  ILonePair
NoNotificationChemObjectBuilder.newMapping ( IChemObject objectOne, IChemObject objectTwo ) :  IMapping
NoNotificationChemObjectBuilder.newMolecularFormula ( ) :  IMolecularFormula
NoNotificationChemObjectBuilder.newMolecularFormulaSet ( ) :  IMolecularFormulaSet
NoNotificationChemObjectBuilder.newMolecularFormulaSet ( IMolecularFormula formula ) :  IMolecularFormulaSet
NoNotificationChemObjectBuilder.newMolecule ( ) :  IMolecule
NoNotificationChemObjectBuilder.newMolecule ( IAtomContainer container ) :  IMolecule
NoNotificationChemObjectBuilder.newMolecule ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount ) :  IMolecule
NoNotificationChemObjectBuilder.newMoleculeSet ( ) :  IMoleculeSet
NoNotificationChemObjectBuilder.newMonomer ( ) :  IMonomer
NoNotificationChemObjectBuilder.newPDBAtom ( IElement element ) :  IPDBAtom
NoNotificationChemObjectBuilder.newPDBAtom ( String elementSymbol ) :  IPDBAtom
NoNotificationChemObjectBuilder.newPDBAtom ( String elementSymbol, Point3d point3d ) :  IPDBAtom
NoNotificationChemObjectBuilder.newPDBMonomer ( ) :  IPDBMonomer
NoNotificationChemObjectBuilder.newPDBPolymer ( ) :  IPDBPolymer
NoNotificationChemObjectBuilder.newPDBStructure ( ) :  IPDBStructure
NoNotificationChemObjectBuilder.newPolymer ( ) :  IPolymer
NoNotificationChemObjectBuilder.newPseudoAtom ( ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newPseudoAtom ( IAtom atom ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newPseudoAtom ( IElement element ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newPseudoAtom ( String label ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newPseudoAtom ( String label, Point2d point2d ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newPseudoAtom ( String label, Point3d point3d ) :  IPseudoAtom
NoNotificationChemObjectBuilder.newReaction ( ) :  IReaction
NoNotificationChemObjectBuilder.newReactionScheme ( ) :  IReactionScheme
NoNotificationChemObjectBuilder.newReactionSet ( ) :  IReactionSet
NoNotificationChemObjectBuilder.newRing ( ) :  IRing
NoNotificationChemObjectBuilder.newRing ( IAtomContainer container ) :  IRing
NoNotificationChemObjectBuilder.newRing ( int ringSize ) :  IRing
NoNotificationChemObjectBuilder.newRing ( int ringSize, String elementSymbol ) :  IRing
NoNotificationChemObjectBuilder.newRingSet ( ) :  IRingSet
NoNotificationChemObjectBuilder.newSingleElectron ( ) :  ISingleElectron
NoNotificationChemObjectBuilder.newSingleElectron ( IAtom atom ) :  ISingleElectron
NoNotificationChemObjectBuilder.newStrand ( ) :  IStrand

cdk-1.2.10.jar, Normalizer.class
package org.openscience.cdk.tools
Normalizer.normalize ( IAtomContainer ac, Document doc ) [static] :  boolean
Normalizer.Normalizer ( )

cdk-1.2.10.jar, NotImplementedException.class
package org.omegahat.Environment.System
NotImplementedException.NotImplementedException ( )

cdk-1.2.10.jar, NumberedInputReader.class
package org.omegahat.Environment.IO
NumberedInputReader.defaultPrompt ( ) :  String
NumberedInputReader.lineNumber ( ) :  int
NumberedInputReader.lineNumber ( int p1 ) :  int
NumberedInputReader.NumberedInputReader ( )
NumberedInputReader.NumberedInputReader ( Environment.IO.PromptSource p1 )
NumberedInputReader.NumberedInputReader ( InputStream p1 )
NumberedInputReader.NumberedInputReader ( InputStreamReader p1 )

cdk-1.2.10.jar, NumberExpression.class
package org.omegahat.Environment.Parser.Parse
NumberExpression.asBoolean ( Object p1 ) :  boolean
NumberExpression.asInt ( Object p1 ) :  int
NumberExpression.asInteger ( Object p1 ) :  Integer
NumberExpression.asNumber ( Object p1 ) [static] :  double
NumberExpression.isNumber ( Object p1 ) :  boolean
NumberExpression.NumberExpression ( )
NumberExpression.toInteger ( double p1 ) :  Integer
NumberExpression.toInteger ( int p1 ) :  Integer
NumberExpression.toNumber ( double p1, Object[ ] p2 ) :  Object

cdk-1.2.10.jar, numeric.class
package org.omegahat.Environment.DataStructures
numeric.addValue ( Object p1, boolean p2 ) :  Object
numeric.assignSubset ( Object p1, Object p2 ) :  Object
numeric.data ( ) :  Object
numeric.data ( double p1 ) :  Object
numeric.data ( double[ ] p1 ) :  Object
numeric.data ( int p1 ) :  Object
numeric.divideValue ( Object p1, boolean p2 ) :  Object
numeric.getElement ( int p1 ) :  double
numeric.length ( ) :  int
numeric.mathOperation ( Environment.DataStructures.numeric p1, boolean p2, int p3 ) :  Object
numeric.mathOperation ( Object p1, boolean p2, int p3 ) :  Object
numeric.max ( ) :  double
numeric.min ( ) :  double
numeric.multiplyValue ( Object p1, boolean p2 ) :  Object
numeric.numeric ( )
numeric.numeric ( double p1 )
numeric.numeric ( double[ ] p1 )
numeric.numeric ( double[ ] p1, boolean p2 )
numeric.numeric ( Environment.DataStructures.numeric p1 )
numeric.numeric ( Environment.DataStructures.numeric p1, boolean p2 )
numeric.numeric ( int p1 )
numeric.setData ( double[ ] p1 ) :  int
numeric.setData ( double[ ] p1, boolean p2 ) :  int
numeric.sort ( boolean p1 ) :  Environment.DataStructures.numeric
numeric.subset ( Environment.Parser.Parse.List p1, boolean p2 ) :  Object
numeric.subset ( Number p1, boolean p2 ) :  Object
numeric.subset ( Object p1, boolean p2 ) :  Object
numeric.subtractValue ( Object p1, boolean p2 ) :  Object
numeric.toString ( ) :  String
numeric.valueOf ( String p1 ) [static] :  double
package org.omegahat.Environment.ObjectDataStructures
numeric.convertElement ( Object p1 ) :  Object
numeric.data ( double p1 ) :  Vector
numeric.data ( double[ ] p1 ) :  Vector
numeric.numeric ( )
numeric.numeric ( double p1 )
numeric.numeric ( double[ ] p1 )
numeric.numeric ( Environment.ObjectDataStructures.numeric p1, boolean p2 )
numeric.numeric ( int p1 )
numeric.numeric ( Integer p1 )
numeric.setData ( double[ ] p1 ) :  int
numeric.targetClass ( ) :  Class
numeric.valueOf ( String p1 ) [static] :  double

cdk-1.2.10.jar, ObjectDatabase.class
package org.omegahat.Environment.Databases
ObjectDatabase.addAssignListener ( Environment.Databases.DatabaseAssignListener p1 ) :  boolean
ObjectDatabase.addAttachListener ( Environment.Databases.DatabaseAttachListener p1 ) :  boolean
ObjectDatabase.addDetachListener ( Environment.Databases.DatabaseDetachListener p1 ) :  boolean
ObjectDatabase.addListener ( int p1, Object p2 ) :  boolean
ObjectDatabase.addRemoveListener ( Environment.Databases.DatabaseRemoveListener p1 ) :  boolean
ObjectDatabase.assign ( String p1, Object p2 ) :  boolean
ObjectDatabase.assign ( String p1, Object p2, boolean p3 ) :  boolean
ObjectDatabase.attach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
ObjectDatabase.clear ( ) :  void
ObjectDatabase.detach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
ObjectDatabase.exists ( String p1 ) :  boolean
ObjectDatabase.get ( String p1 ) :  Object
ObjectDatabase.getDynamicField ( String p1 ) :  Object
ObjectDatabase.getName ( ) :  String
ObjectDatabase.getState ( ) :  int
ObjectDatabase.getTable ( ) :  Hashtable
ObjectDatabase.merge ( Environment.Databases.Database p1, boolean p2 ) :  int
ObjectDatabase.merge ( Hashtable p1, boolean p2 ) :  int
ObjectDatabase.notify ( Environment.Databases.DatabaseEvent p1, int p2 ) :  void
ObjectDatabase.ObjectDatabase ( )
ObjectDatabase.ObjectDatabase ( Hashtable p1 )
ObjectDatabase.ObjectDatabase ( Hashtable p1, String p2 )
ObjectDatabase.ObjectDatabase ( int p1 )
ObjectDatabase.ObjectDatabase ( String p1 )
ObjectDatabase.ObjectDatabase ( String p1, int p2 )
ObjectDatabase.objects ( ) :  String[ ]
ObjectDatabase.put ( Object p1, Object p2 ) :  Object
ObjectDatabase.readOnly ( ) :  boolean
ObjectDatabase.readOnly ( boolean p1 ) :  boolean
ObjectDatabase.readSerialized ( File p1 ) [static] :  Environment.Databases.ObjectDatabase
ObjectDatabase.readSerialized ( InputStream p1 ) [static] :  Environment.Databases.ObjectDatabase
ObjectDatabase.readSerialized ( String p1 ) [static] :  Environment.Databases.ObjectDatabase
ObjectDatabase.remove ( String p1 ) :  Object
ObjectDatabase.remove ( String p1, boolean p2 ) :  Object
ObjectDatabase.setDynamicField ( String p1, Object p2 ) :  Object
ObjectDatabase.setName ( String p1 ) :  String
ObjectDatabase.setState ( int p1 ) :  int
ObjectDatabase.setTable ( Hashtable p1 ) :  Hashtable
ObjectDatabase.size ( ) :  int
ObjectDatabase.subset ( Object p1, boolean p2 ) :  Object
ObjectDatabase.table ( ) :  Hashtable
ObjectDatabase.table ( Hashtable p1 ) :  Hashtable

cdk-1.2.10.jar, ObjectDisplayFilter.class
package org.omegahat.Environment.IO
ObjectDisplayFilter.display ( Object p1 ) [abstract] :  boolean
ObjectDisplayFilter.display ( Object p1, long p2 ) [abstract] :  boolean
ObjectDisplayFilter.toString ( Object p1 ) [abstract] :  String
ObjectDisplayFilter.toWriter ( Object p1 ) [abstract] :  Writer
ObjectDisplayFilter.writer ( ) [abstract] :  Writer

cdk-1.2.10.jar, ObjectIncrementable.class
package org.omegahat.Environment.DataStructures
ObjectIncrementable.increment ( Object p1 ) [abstract] :  Object

cdk-1.2.10.jar, ObjectList.class
package org.omegahat.Environment.Tools.ClassList
ObjectList.add ( ZipEntry p1 ) :  Object
ObjectList.add ( ZipEntry p1, boolean p2 ) :  Object
ObjectList.addElement ( Object p1 ) :  void
ObjectList.archive ( boolean p1 ) :  boolean
ObjectList.checkIsArchive ( String p1 ) :  boolean
ObjectList.computeTime ( ) :  long
ObjectList.computeTime ( boolean p1 ) :  long
ObjectList.directoryFilter ( ) :  Environment.IO.DirectoryFilter
ObjectList.directoryFilter ( Environment.IO.DirectoryFilter p1 ) :  Environment.IO.DirectoryFilter
ObjectList.doneSearch ( ) :  boolean
ObjectList.doneSearch ( boolean p1 ) :  boolean
ObjectList.entries ( ) :  Vector
ObjectList.file ( ) :  File
ObjectList.file ( File p1 ) :  File
ObjectList.file ( File p1, boolean p2 ) :  File
ObjectList.fileSeparator ( ) [static] :  String
ObjectList.find ( String p1 ) :  Object
ObjectList.getDirectory ( String p1 ) :  String
ObjectList.isArchive ( ) :  boolean
ObjectList.issuedWarning ( ) :  boolean
ObjectList.issuedWarning ( boolean p1 ) :  boolean
ObjectList.lookup ( ) :  int
ObjectList.lookupArchive ( File p1 ) :  int
ObjectList.lookupDirectory ( ) :  int
ObjectList.lookupDirectory ( File p1 ) :  int
ObjectList.matchesClassName ( String p1, String p2 ) :  boolean
ObjectList.newSubList ( ) :  Environment.Tools.ClassList.ObjectList
ObjectList.ObjectList ( )
ObjectList.ObjectList ( File p1 )
ObjectList.processDirectoryClasses ( String[ ] p1, String p2, File p3 ) :  Environment.Tools.ClassList.ObjectList
ObjectList.processSubDirectories ( String[ ] p1, File p2 ) :  int
ObjectList.recursive ( ) :  boolean
ObjectList.recursive ( boolean p1 ) :  boolean
ObjectList.refresh ( ) :  boolean
ObjectList.refresh ( boolean p1 ) :  boolean
ObjectList.sourceIsNewer ( ) :  boolean
ObjectList.toClassName ( String p1 ) :  String
ObjectList.warn ( String p1 ) :  void
ObjectList.warnDirectory ( File p1 ) :  void

cdk-1.2.10.jar, ObjectNotFoundException.class
package org.omegahat.Environment.Databases
ObjectNotFoundException.Class ( ) :  Class
ObjectNotFoundException.Class ( Class p1 ) :  Class
ObjectNotFoundException.Class ( String p1 ) :  Class
ObjectNotFoundException.name ( ) :  String
ObjectNotFoundException.name ( String p1 ) :  String
ObjectNotFoundException.ObjectNotFoundException ( Environment.Parser.Parse.Name p1 )
ObjectNotFoundException.ObjectNotFoundException ( String p1 )
ObjectNotFoundException.ObjectNotFoundException ( String p1, Class p2 )
ObjectNotFoundException.ObjectNotFoundException ( String p1, String p2 )
ObjectNotFoundException.ObjectNotFoundException ( String p1, String p2, boolean p3 )
ObjectNotFoundException.ObjectNotFoundException ( String p1, String p2, Class p3 )
ObjectNotFoundException.ObjectNotFoundException ( String p1, String p2, String p3 )
ObjectNotFoundException.toString ( ) :  String

cdk-1.2.10.jar, ObjectReader.class
package org.omegahat.Environment.Tools.DataScanner
ObjectReader.addListener ( Environment.Tools.DataScanner.RecordStreamListener p1 ) [abstract] :  int
ObjectReader.removeListener ( Environment.Tools.DataScanner.RecordStreamListener p1 ) [abstract] :  boolean

cdk-1.2.10.jar, ObjectSearchFilter.class
package org.omegahat.Environment.Databases
ObjectSearchFilter.accept ( String p1, Object p2 ) [abstract] :  boolean

cdk-1.2.10.jar, omega.class
package org.omegahat.Environment.Console
omega.actionPerformed ( ActionEvent p1 ) :  void
omega.args ( ) :  String[ ]
omega.args ( String[ ] p1 ) :  String[ ]
omega.defaultReaderThread ( Environment.Interpreter.Evaluator p1 ) :  Environment.IO.InputReader
omega.init ( ) :  void
omega.main ( String[ ] p1 ) [static] :  void
omega.omega ( )
omega.omega ( String[ ] p1 )
package org.omegahat.Environment.GUI
omega.args ( ) :  String[ ]
omega.args ( String[ ] p1 ) :  String[ ]
omega.closeFrame ( JFrame p1 ) :  boolean
omega.createGUI ( ) :  JFrame
omega.createGUI ( boolean p1 ) :  JFrame
omega.frames ( ) :  Hashtable
omega.getFrame ( ) :  JFrame
omega.getFrame ( int p1 ) :  JFrame
omega.getFrame ( String p1 ) :  JFrame
omega.init ( ) :  void
omega.main ( String[ ] p1 ) [static] :  void
omega.manager ( ) :  Environment.Interpreter.EvaluatorManager
omega.newFrame ( ) :  JFrame
omega.omega ( )
omega.omega ( Environment.Interpreter.EvaluatorManager p1, boolean p2 )
omega.omega ( String[ ] p1 )
omega.quit ( ) :  void
omega.quit ( int p1 ) :  void
omega.setLookAndFeel ( ) :  String

cdk-1.2.10.jar, OmegaField.class
package org.omegahat.Environment.Language.UserClasses
OmegaField.Class ( ) :  Class
OmegaField.Class ( Class p1 ) :  Class
OmegaField.isFinal ( ) :  boolean
OmegaField.isFinal ( boolean p1 ) :  boolean
OmegaField.isStatic ( ) :  boolean
OmegaField.isStatic ( boolean p1 ) :  boolean
OmegaField.name ( ) :  String
OmegaField.name ( String p1 ) :  String
OmegaField.OmegaField ( )
OmegaField.OmegaField ( String p1 )
OmegaField.OmegaField ( String p1, Class p2 )
OmegaField.OmegaField ( String p1, Class p2, boolean p3 )
OmegaField.OmegaField ( String p1, Class p2, boolean p3, boolean p4 )
OmegaField.OmegaField ( String p1, Class p2, Environment.Language.UserClasses.UserClass p3 )
OmegaField.OmegaField ( String p1, String p2, boolean p3 )
OmegaField.OmegaField ( String p1, String p2, boolean p3, boolean p4 )
OmegaField.source ( ) :  Environment.Language.UserClasses.UserClass
OmegaField.source ( Environment.Language.UserClasses.UserClass p1 ) :  Environment.Language.UserClasses.UserClass
OmegaField.toString ( ) :  String
OmegaField.value ( ) :  Object
OmegaField.value ( Object p1 ) :  Object

cdk-1.2.10.jar, OmegaFieldChangeEvent.class
package org.omegahat.Environment.Language.UserClasses
OmegaFieldChangeEvent.OmegaFieldChangeEvent ( Environment.Language.UserClasses.OmegaField p1 )

cdk-1.2.10.jar, OmegaFieldInstance.class
package org.omegahat.Environment.Language.UserClasses
OmegaFieldInstance.link ( ) :  Environment.Language.UserClasses.OmegaField
OmegaFieldInstance.link ( Environment.Language.UserClasses.OmegaField p1 ) :  Environment.Language.UserClasses.OmegaField
OmegaFieldInstance.OmegaFieldInstance ( Environment.Language.UserClasses.OmegaField p1 )

cdk-1.2.10.jar, OmegahatLazySystemFunctions.class
package org.omegahat.Environment.lib.Language
OmegahatLazySystemFunctions.OmegahatLazySystemFunctions ( )
OmegahatLazySystemFunctions.Quote ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) [static] :  Object
OmegahatLazySystemFunctions.time ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) [static] :  Environment.lib.Language.TimedEvaluation

cdk-1.2.10.jar, OmegahatUserClassHelper.class
package org.omegahat.Environment.Language.UserClasses
OmegahatUserClassHelper.loadTables ( Class p1 ) [static] :  void
OmegahatUserClassHelper.OmegahatUserClassHelper ( )

cdk-1.2.10.jar, OmegahatVarArgsSystemFunctions.class
package org.omegahat.Environment.lib.Language
OmegahatVarArgsSystemFunctions.OmegahatVarArgsSystemFunctions ( )
OmegahatVarArgsSystemFunctions.Switch ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) [static] :  Object

cdk-1.2.10.jar, OmegaInterface.class
package org.omegahat.Environment.GUI
OmegaInterface.actionPerformed ( ActionEvent p1 ) :  void
OmegaInterface.createMenu ( String p1, Environment.GUI.MenuDescription p2 ) :  JMenu
OmegaInterface.createMenus ( ) :  JMenuBar
OmegaInterface.evaluator ( ) :  Environment.Interpreter.Evaluator
OmegaInterface.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
OmegaInterface.make ( ) :  boolean
OmegaInterface.menuActionPerformed ( JMenuItem p1, ActionEvent p2 ) :  void
OmegaInterface.OmegaInterface ( )
OmegaInterface.OmegaInterface ( Environment.Interpreter.Evaluator p1 )
OmegaInterface.OmegaInterface ( Environment.Interpreter.EvaluatorManager p1 )
OmegaInterface.OmegaInterface ( String p1, Environment.Interpreter.EvaluatorManager p2, Environment.GUI.omega p3 )
OmegaInterface.output ( ) :  Object

cdk-1.2.10.jar, OmegaInterfaceManager.class
package org.omegahat.Interfaces.NativeInterface
OmegaInterfaceManager.anonymousAssign ( Object p1 ) :  Object
OmegaInterfaceManager.anonymousDatabase ( ) :  Environment.Databases.Database
OmegaInterfaceManager.anonymousDatabase ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
OmegaInterfaceManager.argsToList ( String[ ] p1 ) :  Environment.Parser.Parse.List
OmegaInterfaceManager.arrayLength ( Object p1 ) :  int
OmegaInterfaceManager.assignArguments ( Object[ ] p1, String[ ] p2 ) :  int
OmegaInterfaceManager.assignException ( Throwable p1 ) :  void
OmegaInterfaceManager.assignResult ( String p1, Object p2 ) :  Object
OmegaInterfaceManager.assignResult ( String p1, Object p2, boolean p3 ) :  Object
OmegaInterfaceManager.callConstructor ( String p1, Object[ ] p2, String[ ] p3, String p4, boolean p5 ) :  Object
OmegaInterfaceManager.clearReference ( String p1, boolean p2 ) :  boolean
OmegaInterfaceManager.clearReferences ( boolean p1 ) :  int
OmegaInterfaceManager.convertable ( Class p1 ) :  boolean
OmegaInterfaceManager.convertable ( Object p1 ) :  boolean
OmegaInterfaceManager.createArray ( Class p1, int[ ] p2 ) :  Object
OmegaInterfaceManager.createArray ( String p1, int p2 ) :  Object
OmegaInterfaceManager.createArray ( String p1, int[ ] p2 ) :  Object
OmegaInterfaceManager.createCallFrame ( Object[ ] p1, String[ ] p2 ) :  Environment.Databases.Database
OmegaInterfaceManager.database ( ) :  Environment.Databases.Database
OmegaInterfaceManager.database ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
OmegaInterfaceManager.debug ( ) :  boolean
OmegaInterfaceManager.debug ( boolean p1 ) :  boolean
OmegaInterfaceManager.debug ( int p1 ) :  boolean
OmegaInterfaceManager.displayTask ( Environment.Interpreter.Task p1 ) :  boolean
OmegaInterfaceManager.eval ( String p1, Environment.Parser.Parse.ExpressionInt p2 ) :  String
OmegaInterfaceManager.evalConstructor ( String p1, Object[ ] p2, String[ ] p3, String p4 ) :  String
OmegaInterfaceManager.evalConstructor ( String p1, String[ ] p2, String p3 ) :  String
OmegaInterfaceManager.evalMethod ( String p1, String p2, String[ ] p3, String p4 ) :  String
OmegaInterfaceManager.evaluate ( String p1, Object[ ] p2, String[ ] p3, String p4, boolean p5 ) :  Object
OmegaInterfaceManager.expandClassName ( String p1, boolean p2 ) :  String
OmegaInterfaceManager.genericCallMethod ( Environment.Language.Evaluable p1, String p2, Object[ ] p3, String[ ] p4, String p5, boolean p6 ) :  Object
OmegaInterfaceManager.genericCallMethod ( Environment.Parser.Parse.MethodCall p1, String p2, boolean p3 ) :  Object
OmegaInterfaceManager.genericCallMethod ( Object p1, String p2, Object[ ] p3, String[ ] p4, String p5, boolean p6 ) :  Object
OmegaInterfaceManager.genericCallMethod ( String p1, String p2, Object[ ] p3, String[ ] p4, String p5, boolean p6 ) :  Object
OmegaInterfaceManager.genericCallMethod ( String[ ] p1, Object[ ] p2, String[ ] p3, String p4, boolean p5 ) :  Object
OmegaInterfaceManager.getAllClasses ( ) :  Class[ ][ ]
OmegaInterfaceManager.getArrayClasses ( ) [static] :  Class[ ]
OmegaInterfaceManager.getArrayElement ( Object p1, int p2 ) :  Object
OmegaInterfaceManager.getArrayElement ( Object p1, int[ ] p2 ) :  Object
OmegaInterfaceManager.getArrayElements ( Object p1, int[ ] p2 ) :  Object
OmegaInterfaceManager.getConstructors ( Class p1 ) :  Constructor[ ]
OmegaInterfaceManager.getConstructors ( String p1 ) :  Constructor[ ]
OmegaInterfaceManager.getConvertibleClasses ( ) :  String[ ]
OmegaInterfaceManager.getConvertibleClassifier ( ) :  Interfaces.NativeInterface.ConvertibleClassifierInt
OmegaInterfaceManager.getDatabaseID ( ) :  String
OmegaInterfaceManager.getDataType ( Object p1 ) [static] :  String
OmegaInterfaceManager.getMethod ( Class p1, String p2 ) :  Object
OmegaInterfaceManager.getMethod ( String p1, String p2 ) :  Object
OmegaInterfaceManager.getMethods ( Class p1 ) :  Method[ ]
OmegaInterfaceManager.getMethods ( String p1 ) :  Method[ ]
OmegaInterfaceManager.getPrimitiveClasses ( ) [static] :  Class[ ]
OmegaInterfaceManager.getReferences ( boolean p1 ) :  Interfaces.NativeInterface.InterfaceReference[ ]
OmegaInterfaceManager.getReferences ( Environment.Databases.Database p1, boolean p2 ) :  Interfaces.NativeInterface.InterfaceReference[ ]
OmegaInterfaceManager.getReferenceValue ( Object p1 ) :  Object
OmegaInterfaceManager.getReferenceValue ( String p1, boolean p2 ) :  Object
OmegaInterfaceManager.getWrapperClasses ( ) [static] :  Class[ ]
OmegaInterfaceManager.identity ( Object p1 ) :  Object
OmegaInterfaceManager.identity ( Object p1, boolean p2 ) :  Object
OmegaInterfaceManager.is ( Object p1, Class p2, boolean p3 ) :  boolean
OmegaInterfaceManager.is ( Object p1, String p2, boolean p3 ) :  boolean
OmegaInterfaceManager.isArray ( Object p1 ) :  boolean
OmegaInterfaceManager.nativeSetup ( Interfaces.NativeInterface.OmegaInterfaceManager p1, Object p2 ) [static] :  boolean
OmegaInterfaceManager.objects ( boolean p1 ) :  String[ ]
OmegaInterfaceManager.OmegaInterfaceManager ( )
OmegaInterfaceManager.OmegaInterfaceManager ( boolean p1 )
OmegaInterfaceManager.OmegaInterfaceManager ( File p1 )
OmegaInterfaceManager.OmegaInterfaceManager ( InputStream p1 )
OmegaInterfaceManager.OmegaInterfaceManager ( String p1 )
OmegaInterfaceManager.remove ( Interfaces.NativeInterface.AnonymousReference p1 ) :  boolean
OmegaInterfaceManager.remove ( Interfaces.NativeInterface.NamedReference p1 ) :  boolean
OmegaInterfaceManager.remove ( Object p1 ) :  boolean
OmegaInterfaceManager.remove ( String p1 ) :  boolean
OmegaInterfaceManager.remove ( String p1, Environment.Databases.Database p2 ) :  boolean
OmegaInterfaceManager.setArrayElement ( Object p1, int p2, Object p3 ) :  void
OmegaInterfaceManager.setArrayElement ( Object p1, int[ ] p2, Object p3 ) :  void
OmegaInterfaceManager.setConvertible ( Class p1, int p2, boolean p3 ) :  void
OmegaInterfaceManager.setConvertible ( String p1, int p2, boolean p3 ) :  void
OmegaInterfaceManager.setConvertibleClassifier ( ) :  void
OmegaInterfaceManager.setConvertibleClassifier ( Interfaces.NativeInterface.ConvertibleClassifierInt p1 ) :  void
OmegaInterfaceManager.setDebug ( int p1 ) :  boolean
OmegaInterfaceManager.testBooleanArray ( ) :  boolean[ ][ ]
OmegaInterfaceManager.testBooleanArrays ( ) :  boolean[ ][ ][ ]
OmegaInterfaceManager.testDoubleArray ( ) :  double[ ][ ]
OmegaInterfaceManager.testIntArray ( ) :  int[ ][ ]
OmegaInterfaceManager.testStringArray ( ) :  String[ ]
OmegaInterfaceManager.testStringArray ( String[ ] p1 ) :  String[ ]

cdk-1.2.10.jar, omegaJavaGrammar.class
package org.omegahat.Environment.Parser.AntlrParser
omegaJavaGrammar.aCase ( ) :  void
omegaJavaGrammar.additiveExpression ( ) :  void
omegaJavaGrammar.andExpression ( ) :  void
omegaJavaGrammar.argList ( ) :  void
omegaJavaGrammar.arrayInitializer ( ) :  void
omegaJavaGrammar.assignmentExpression ( ) :  void
omegaJavaGrammar.builtInType ( ) :  void
omegaJavaGrammar.casesGroup ( ) :  void
omegaJavaGrammar.caseSList ( ) :  void
omegaJavaGrammar.castExpression ( ) :  void
omegaJavaGrammar.classBlock ( ) :  void
omegaJavaGrammar.classDefinition ( AST p1 ) :  void
omegaJavaGrammar.comments ( ) :  void
omegaJavaGrammar.compoundStatement ( ) :  void
omegaJavaGrammar.conditionalExpression ( ) :  void
omegaJavaGrammar.constant ( ) :  void
omegaJavaGrammar.createConstructorExpression ( String p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.List p3 ) :  Environment.Parser.Parse.FunctionExpression
omegaJavaGrammar.createConstructorExpression ( String p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.List p3, boolean p4 ) :  Environment.Parser.Parse.FunctionExpression
omegaJavaGrammar.createFieldAccess ( Environment.Parser.Parse.ExpressionInt p1, String p2 ) :  Environment.Parser.Parse.FieldAccess
omegaJavaGrammar.createFieldAccess ( Environment.Parser.Parse.Name p1, String p2 ) :  Environment.Parser.Parse.FieldAccess
omegaJavaGrammar.createFunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 ) :  Environment.Parser.Parse.FunctionExpression
omegaJavaGrammar.createFunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7, boolean p8 ) :  Environment.Parser.Parse.FunctionExpression
omegaJavaGrammar.createMethodCall ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2 ) :  Environment.Parser.Parse.MethodCall
omegaJavaGrammar.createMethodCall ( Environment.Parser.Parse.ExpressionInt p1, String p2, Environment.Parser.Parse.List p3 ) :  Environment.Parser.Parse.MethodCall
omegaJavaGrammar.createMethodCall ( Environment.Parser.Parse.FieldAccess p1, String p2, Environment.Parser.Parse.List p3 ) :  Environment.Parser.Parse.MethodCall
omegaJavaGrammar.createMethodCall ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2 ) :  Environment.Parser.Parse.MethodCall
omegaJavaGrammar.createMethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 ) :  Environment.Parser.Parse.MethodExpression
omegaJavaGrammar.createMethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6, Environment.Parser.Parse.Comment p7 ) :  Environment.Parser.Parse.MethodExpression
omegaJavaGrammar.ctorHead ( ) :  void
omegaJavaGrammar.declaration ( ) :  void
omegaJavaGrammar.declaratorBrackets ( AST p1 ) :  void
omegaJavaGrammar.equalityExpression ( ) :  void
omegaJavaGrammar.evaluationUnit ( ) :  void
omegaJavaGrammar.exclusiveOrExpression ( ) :  void
omegaJavaGrammar.expression ( ) :  void
omegaJavaGrammar.expressionList ( ) :  void
omegaJavaGrammar.field ( ) :  void
omegaJavaGrammar.forInit ( ) :  void
omegaJavaGrammar.forLoop ( ) :  void
omegaJavaGrammar.functionDefinition ( ) :  void
omegaJavaGrammar.functionExpression ( ) :  void
omegaJavaGrammar.functionIdentifier ( ) :  void
omegaJavaGrammar.functionParameter ( ) :  void
omegaJavaGrammar.functionParametersList ( ) :  void
omegaJavaGrammar.handler ( ) :  void
omegaJavaGrammar.honorCharacters ( ) :  boolean
omegaJavaGrammar.honorCharacters ( boolean p1 ) :  boolean
omegaJavaGrammar.identifier ( ) :  void
omegaJavaGrammar.identifierStar ( ) :  void
omegaJavaGrammar.imaginaryTokenDefinitions ( ) :  void
omegaJavaGrammar.implementsClause ( ) :  void
omegaJavaGrammar.importDefinition ( ) :  void
omegaJavaGrammar.inclusiveOrExpression ( ) :  void
omegaJavaGrammar.initializer ( ) :  void
omegaJavaGrammar.interfaceDefinition ( AST p1 ) :  void
omegaJavaGrammar.interfaceExtends ( ) :  void
omegaJavaGrammar.lazyEvaluation ( ) :  void
omegaJavaGrammar.logicalAndExpression ( ) :  void
omegaJavaGrammar.logicalOrExpression ( ) :  void
omegaJavaGrammar.makeComment ( AST p1 ) :  Environment.Parser.Parse.Comment
omegaJavaGrammar.modifier ( ) :  void
omegaJavaGrammar.modifiers ( ) :  void
omegaJavaGrammar.multiplicativeExpression ( ) :  void
omegaJavaGrammar.newArrayDeclarator ( ) :  void
omegaJavaGrammar.newExpression ( ) :  void
omegaJavaGrammar.omegaExpression ( ) :  void
omegaJavaGrammar.omegaJavaGrammar ( TokenBuffer p1 )
omegaJavaGrammar.omegaJavaGrammar ( TokenBuffer p1, int p2 )
omegaJavaGrammar.omegaJavaGrammar ( Tokenizer p1 )
omegaJavaGrammar.omegaJavaGrammar ( Tokenizer p1, int p2 )
omegaJavaGrammar.optionalExpression ( ) :  void
omegaJavaGrammar.parameterDeclaration ( ) :  void
omegaJavaGrammar.parameterDeclarationList ( ) :  void
omegaJavaGrammar.parameterDeclaratorBrackets ( AST p1 ) :  void
omegaJavaGrammar.parameterModifier ( ) :  void
omegaJavaGrammar.postfixExpression ( ) :  void
omegaJavaGrammar.powerExpression ( ) :  void
omegaJavaGrammar.primaryExpression ( ) :  void
omegaJavaGrammar.relationalExpression ( ) :  void
omegaJavaGrammar.returnTypeBrackersOnEndOfMethodHead ( AST p1 ) :  void
omegaJavaGrammar.shiftExpression ( ) :  void
omegaJavaGrammar.statement ( ) :  void
omegaJavaGrammar.superClassClause ( ) :  void
omegaJavaGrammar.throwsClause ( ) :  void
omegaJavaGrammar.tryBlock ( ) :  void
omegaJavaGrammar.type ( ) :  void
omegaJavaGrammar.typeDefinition ( ) :  void
omegaJavaGrammar.typeSpec ( boolean p1 ) :  void
omegaJavaGrammar.typeSpec ( boolean p1, boolean p2 ) :  void
omegaJavaGrammar.variableDeclarator ( AST p1, AST p2 ) :  void
omegaJavaGrammar.variableDefinitions ( AST p1, AST p2 ) :  void
omegaJavaGrammar.varInitializer ( ) :  void

cdk-1.2.10.jar, omegaJavaLexer.class
package org.omegahat.Environment.Parser.AntlrParser
omegaJavaLexer.mASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mBAND ( boolean p1 ) :  void
omegaJavaLexer.mBAND_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mBNOT ( boolean p1 ) :  void
omegaJavaLexer.mBOR ( boolean p1 ) :  void
omegaJavaLexer.mBOR_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mBSR ( boolean p1 ) :  void
omegaJavaLexer.mBSR_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mBXOR ( boolean p1 ) :  void
omegaJavaLexer.mBXOR_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mCHAR_LITERAL ( boolean p1 ) :  void
omegaJavaLexer.mCOLON ( boolean p1 ) :  void
omegaJavaLexer.mCOMMA ( boolean p1 ) :  void
omegaJavaLexer.mDEC ( boolean p1 ) :  void
omegaJavaLexer.mDIV ( boolean p1 ) :  void
omegaJavaLexer.mDIV_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mDOTS ( boolean p1 ) :  void
omegaJavaLexer.mEQUAL ( boolean p1 ) :  void
omegaJavaLexer.mESC ( boolean p1 ) :  void
omegaJavaLexer.mEXPONENT ( boolean p1 ) :  void
omegaJavaLexer.mEXPONENT_OP ( boolean p1 ) :  void
omegaJavaLexer.mFLOAT_SUFFIX ( boolean p1 ) :  void
omegaJavaLexer.mGE ( boolean p1 ) :  void
omegaJavaLexer.mGT ( boolean p1 ) :  void
omegaJavaLexer.mHEX_DIGIT ( boolean p1 ) :  void
omegaJavaLexer.mIDENT ( boolean p1 ) :  void
omegaJavaLexer.mINC ( boolean p1 ) :  void
omegaJavaLexer.mLAND ( boolean p1 ) :  void
omegaJavaLexer.mLBRACK ( boolean p1 ) :  void
omegaJavaLexer.mLCURLY ( boolean p1 ) :  void
omegaJavaLexer.mLE ( boolean p1 ) :  void
omegaJavaLexer.mLNOT ( boolean p1 ) :  void
omegaJavaLexer.mLOR ( boolean p1 ) :  void
omegaJavaLexer.mLPAREN ( boolean p1 ) :  void
omegaJavaLexer.mLT ( boolean p1 ) :  void
omegaJavaLexer.mMINUS ( boolean p1 ) :  void
omegaJavaLexer.mMINUS_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mML_COMMENT ( boolean p1 ) :  void
omegaJavaLexer.mMOD ( boolean p1 ) :  void
omegaJavaLexer.mMOD_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mNOT_EQUAL ( boolean p1 ) :  void
omegaJavaLexer.mNUM_INT ( boolean p1 ) :  void
omegaJavaLexer.mPLUS ( boolean p1 ) :  void
omegaJavaLexer.mPLUS_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mQUESTION ( boolean p1 ) :  void
omegaJavaLexer.mRBRACK ( boolean p1 ) :  void
omegaJavaLexer.mRCURLY ( boolean p1 ) :  void
omegaJavaLexer.mRPAREN ( boolean p1 ) :  void
omegaJavaLexer.mSEMI ( boolean p1 ) :  void
omegaJavaLexer.mSEQUENCE_OP ( boolean p1 ) :  void
omegaJavaLexer.mSL ( boolean p1 ) :  void
omegaJavaLexer.mSL_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mSL_COMMENT ( boolean p1 ) :  void
omegaJavaLexer.mSR ( boolean p1 ) :  void
omegaJavaLexer.mSR_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mSTAR ( boolean p1 ) :  void
omegaJavaLexer.mSTAR_ASSIGN ( boolean p1 ) :  void
omegaJavaLexer.mSTRING_LITERAL ( boolean p1 ) :  void
omegaJavaLexer.mVOCAB ( boolean p1 ) :  void
omegaJavaLexer.mWS ( boolean p1 ) :  void
omegaJavaLexer.nextToken ( ) :  Token
omegaJavaLexer.omegaJavaLexer ( InputBuffer p1 )
omegaJavaLexer.omegaJavaLexer ( InputStream p1 )
omegaJavaLexer.omegaJavaLexer ( Reader p1 )

cdk-1.2.10.jar, OmegaListener.class
package org.omegahat.Environment.GUITools
OmegaListener.callback ( ) :  Environment.Language.Evaluable
OmegaListener.callback ( Environment.Language.Evaluable p1 ) :  Environment.Language.Evaluable
OmegaListener.eval ( ) :  Object
OmegaListener.evaluator ( ) :  Environment.Interpreter.Evaluator
OmegaListener.evaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
OmegaListener.OmegaListener ( )
OmegaListener.OmegaListener ( Environment.Language.Evaluable p1 )
OmegaListener.OmegaListener ( Environment.Language.Evaluable p1, Environment.Interpreter.Evaluator p2 )

cdk-1.2.10.jar, omegaNestedStringLexer.class
package org.omegahat.Environment.Parser.AntlrParser
omegaNestedStringLexer.mASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mBAND ( boolean p1 ) :  void
omegaNestedStringLexer.mBAND_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mBNOT ( boolean p1 ) :  void
omegaNestedStringLexer.mBOR ( boolean p1 ) :  void
omegaNestedStringLexer.mBOR_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mBSR ( boolean p1 ) :  void
omegaNestedStringLexer.mBSR_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mBXOR ( boolean p1 ) :  void
omegaNestedStringLexer.mBXOR_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mCHAR_LITERAL ( boolean p1 ) :  void
omegaNestedStringLexer.mCOLON ( boolean p1 ) :  void
omegaNestedStringLexer.mCOMMA ( boolean p1 ) :  void
omegaNestedStringLexer.mDEC ( boolean p1 ) :  void
omegaNestedStringLexer.mDIV ( boolean p1 ) :  void
omegaNestedStringLexer.mDIV_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mDOTS ( boolean p1 ) :  void
omegaNestedStringLexer.mEQUAL ( boolean p1 ) :  void
omegaNestedStringLexer.mESC ( boolean p1 ) :  void
omegaNestedStringLexer.mEXPONENT ( boolean p1 ) :  void
omegaNestedStringLexer.mEXPONENT_OP ( boolean p1 ) :  void
omegaNestedStringLexer.mFLOAT_SUFFIX ( boolean p1 ) :  void
omegaNestedStringLexer.mGE ( boolean p1 ) :  void
omegaNestedStringLexer.mGT ( boolean p1 ) :  void
omegaNestedStringLexer.mHEX_DIGIT ( boolean p1 ) :  void
omegaNestedStringLexer.mIDENT ( boolean p1 ) :  void
omegaNestedStringLexer.mINC ( boolean p1 ) :  void
omegaNestedStringLexer.mLAND ( boolean p1 ) :  void
omegaNestedStringLexer.mLBRACK ( boolean p1 ) :  void
omegaNestedStringLexer.mLCURLY ( boolean p1 ) :  void
omegaNestedStringLexer.mLE ( boolean p1 ) :  void
omegaNestedStringLexer.mLNOT ( boolean p1 ) :  void
omegaNestedStringLexer.mLOR ( boolean p1 ) :  void
omegaNestedStringLexer.mLPAREN ( boolean p1 ) :  void
omegaNestedStringLexer.mLT ( boolean p1 ) :  void
omegaNestedStringLexer.mMINUS ( boolean p1 ) :  void
omegaNestedStringLexer.mMINUS_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mML_COMMENT ( boolean p1 ) :  void
omegaNestedStringLexer.mMOD ( boolean p1 ) :  void
omegaNestedStringLexer.mMOD_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mNOT_EQUAL ( boolean p1 ) :  void
omegaNestedStringLexer.mNUM_INT ( boolean p1 ) :  void
omegaNestedStringLexer.mPLUS ( boolean p1 ) :  void
omegaNestedStringLexer.mPLUS_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mQUESTION ( boolean p1 ) :  void
omegaNestedStringLexer.mRBRACK ( boolean p1 ) :  void
omegaNestedStringLexer.mRCURLY ( boolean p1 ) :  void
omegaNestedStringLexer.mRPAREN ( boolean p1 ) :  void
omegaNestedStringLexer.mSEMI ( boolean p1 ) :  void
omegaNestedStringLexer.mSEQUENCE_OP ( boolean p1 ) :  void
omegaNestedStringLexer.mSL ( boolean p1 ) :  void
omegaNestedStringLexer.mSL_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mSL_COMMENT ( boolean p1 ) :  void
omegaNestedStringLexer.mSR ( boolean p1 ) :  void
omegaNestedStringLexer.mSR_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mSTAR ( boolean p1 ) :  void
omegaNestedStringLexer.mSTAR_ASSIGN ( boolean p1 ) :  void
omegaNestedStringLexer.mSTRING_LITERAL ( boolean p1 ) :  void
omegaNestedStringLexer.mVOCAB ( boolean p1 ) :  void
omegaNestedStringLexer.mWS ( boolean p1 ) :  void
omegaNestedStringLexer.nextToken ( ) :  Token
omegaNestedStringLexer.omegaNestedStringLexer ( InputBuffer p1 )
omegaNestedStringLexer.omegaNestedStringLexer ( InputStream p1 )
omegaNestedStringLexer.omegaNestedStringLexer ( Reader p1 )

cdk-1.2.10.jar, OperatorExpression.class
package org.omegahat.Environment.Parser.Parse
OperatorExpression.operator ( ) :  int
OperatorExpression.operator ( int p1 ) :  int
OperatorExpression.OperatorExpression ( )
OperatorExpression.OperatorExpression ( Object p1, int p2 )
OperatorExpression.OperatorExpression ( Object p1, Object p2, int p3 )
OperatorExpression.separator ( ) :  String

cdk-1.2.10.jar, OptionalLazyArgument.class
package org.omegahat.Environment.Language
OptionalLazyArgument.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
OptionalLazyArgument.optionalArgument ( ) :  String
OptionalLazyArgument.optionalArgument ( String p1 ) :  String
OptionalLazyArgument.OptionalLazyArgument ( )
OptionalLazyArgument.OptionalLazyArgument ( String p1 )
OptionalLazyArgument.OptionalLazyArgument ( String p1, String p2, Environment.Parser.Parse.ExpressionInt p3 )
OptionalLazyArgument.toString ( ) :  String

cdk-1.2.10.jar, Options.class
package org.omegahat.Environment.Interpreter
Options.getProperty ( String p1 ) :  String
Options.getProperty ( String p1, boolean p2 ) :  String
Options.getProperty ( String p1, String p2, boolean p3 ) :  String
Options.load ( InputStream p1 ) :  void
Options.Options ( )
Options.Options ( File p1 )
Options.Options ( InputStream p1 )
Options.Options ( String p1 )
Options.parserDebug ( ) :  boolean
Options.parserDebug ( boolean p1 ) :  boolean
Options.processProperties ( ) :  int
Options.prompt ( ) :  String
Options.prompt ( int p1 ) :  String

cdk-1.2.10.jar, OptionsEditor.class
package org.omegahat.Environment.GUI
OptionsEditor.make ( ) :  boolean
OptionsEditor.OptionsEditor ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, OrderedListEvent.class
package org.omegahat.Environment.Utils
OrderedListEvent.index ( ) :  int
OrderedListEvent.OrderedListEvent ( Object p1, int p2, int p3, Object p4 )
OrderedListEvent.value ( ) :  Object

cdk-1.2.10.jar, OrderedTable.class
package org.omegahat.Environment.Utils
OrderedTable.add ( Object p1 ) :  Object
OrderedTable.add ( Object p1, Object p2 ) :  Object
OrderedTable.addListListener ( Environment.Utils.ListListener p1 ) :  void
OrderedTable.assign ( String p1, Object p2 ) :  boolean
OrderedTable.assignSubset ( Object p1, Object p2 ) :  Object
OrderedTable.attach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
OrderedTable.clear ( ) :  void
OrderedTable.copy ( ) :  Environment.Utils.OrderedTable
OrderedTable.copy ( Environment.Utils.OrderedTable p1 ) :  Environment.Utils.OrderedTable
OrderedTable.detach ( Environment.Databases.DatabaseCustomer p1 ) :  boolean
OrderedTable.elementAt ( int p1 ) :  Object
OrderedTable.exists ( String p1 ) :  boolean
OrderedTable.get ( String p1 ) :  Object
OrderedTable.getName ( ) :  String
OrderedTable.getOrderedKeys ( ) :  Vector
OrderedTable.getState ( ) :  int
OrderedTable.keys ( ) :  Enumeration
OrderedTable.listeners ( ) :  Vector
OrderedTable.listeners ( Vector p1 ) :  Vector
OrderedTable.notifyListeners ( Object p1, Object p2, int p3, int p4 ) :  void
OrderedTable.objects ( ) :  String[ ]
OrderedTable.ordered ( ) :  Vector
OrderedTable.orderedKeys ( ) :  Vector
OrderedTable.OrderedTable ( )
OrderedTable.OrderedTable ( Environment.Utils.OrderedTable p1 )
OrderedTable.OrderedTable ( int p1 )
OrderedTable.OrderedTable ( int p1, float p2 )
OrderedTable.OrderedTable ( Vector p1 )
OrderedTable.put ( Object p1, Object p2 ) :  Object
OrderedTable.put ( Object p1, Object p2, boolean p3 ) :  Object
OrderedTable.put ( Object p1, Object p2, boolean p3, boolean p4 ) :  Object
OrderedTable.remove ( Object p1 ) :  Object
OrderedTable.remove ( String p1 ) :  Object
OrderedTable.removeElement ( Object p1 ) :  Object
OrderedTable.removeElement ( Object p1, boolean p2 ) :  Object
OrderedTable.removeElementAt ( int p1 ) :  Object
OrderedTable.removeElementAt ( int p1, boolean p2 ) :  Object
OrderedTable.removeListListener ( Environment.Utils.ListListener p1 ) :  void
OrderedTable.setElementAt ( Object p1, int p2 ) :  void
OrderedTable.setName ( String p1 ) :  String
OrderedTable.setState ( int p1 ) :  int
OrderedTable.subset ( Environment.Parser.Parse.List p1, boolean p2 ) :  Object
OrderedTable.subset ( int p1 ) :  Object
OrderedTable.subset ( Object p1, boolean p2 ) :  Object

cdk-1.2.10.jar, PackageClassList.class
package org.omegahat.Environment.Tools.ClassList
PackageClassList.lookupDirectory ( ) :  int
PackageClassList.newSubList ( ) :  Environment.Tools.ClassList.ObjectList
PackageClassList.PackageClassList ( )
PackageClassList.PackageClassList ( String p1 )
PackageClassList.PackageClassList ( String p1, String p2 )
PackageClassList.packageDirectories ( String p1 ) :  String[ ]
PackageClassList.realDirectory ( ) :  File
PackageClassList.realDirectory ( File p1 ) :  File

cdk-1.2.10.jar, PartialFilledStructureMerger.class
package org.openscience.cdk.structgen.stochastic
PartialFilledStructureMerger.generate ( ) :  IAtomContainer
PartialFilledStructureMerger.getAtomContainer ( ) :  IAtomContainer
PartialFilledStructureMerger.setAtomContainer ( IAtomContainer gc ) :  void

cdk-1.2.10.jar, PeriodicTable.class
package org.openscience.cdk.tools
PeriodicTable.getAtomicNumber ( String symbol ) [static] :  Integer
PeriodicTable.getCASId ( String symbol ) [static] :  String
PeriodicTable.getChemicalSeries ( String symbol ) [static] :  String
PeriodicTable.getCovalentRadius ( String symbol ) [static] :  Double
PeriodicTable.getGroup ( String symbol ) [static] :  Integer
PeriodicTable.getName ( String symbol ) [static] :  String
PeriodicTable.getPaulingElectronegativity ( String symbol ) [static] :  Double
PeriodicTable.getPeriod ( String symbol ) [static] :  Integer
PeriodicTable.getPhase ( String symbol ) [static] :  String
PeriodicTable.getVdwRadius ( String symbol ) [static] :  Double
PeriodicTable.PeriodicTable ( )

cdk-1.2.10.jar, PeriodicTableElement.class
package org.openscience.cdk
PeriodicTableElement.clone ( ) :  Object
PeriodicTableElement.getCASid ( ) :  String
PeriodicTableElement.getChemicalSerie ( ) :  String
PeriodicTableElement.getCovalentRadius ( ) :  Double
PeriodicTableElement.getGroup ( ) :  Integer
PeriodicTableElement.getName ( ) :  String
PeriodicTableElement.getPaulingEneg ( ) :  Double
PeriodicTableElement.getPeriod ( ) :  Integer
PeriodicTableElement.getPhase ( ) :  String
PeriodicTableElement.getVdwRadius ( ) :  Double
PeriodicTableElement.PeriodicTableElement ( String symbol )
PeriodicTableElement.setCASid ( String casId ) :  void
PeriodicTableElement.setChemicalSerie ( String chemicalSerie ) :  void
PeriodicTableElement.setCovalentRadius ( Double covalentRadius ) :  void
PeriodicTableElement.setGroup ( Integer group ) :  void
PeriodicTableElement.setName ( String name ) :  void
PeriodicTableElement.setPaulingEneg ( Double paulingEneg ) :  void
PeriodicTableElement.setPeriod ( Integer period ) :  void
PeriodicTableElement.setPhase ( String phase ) :  void
PeriodicTableElement.setVdwRadius ( Double vdwRadius ) :  void
PeriodicTableElement.toString ( ) :  String

cdk-1.2.10.jar, PersistentObjectDatabase.class
package org.omegahat.Environment.Databases
PersistentObjectDatabase.asFile ( String p1 ) :  File
PersistentObjectDatabase.assign ( String p1, Object p2 ) :  boolean
PersistentObjectDatabase.directory ( ) :  File
PersistentObjectDatabase.directory ( File p1 ) :  File
PersistentObjectDatabase.directory ( File p1, boolean p2 ) :  File
PersistentObjectDatabase.filter ( ) :  FilenameFilter
PersistentObjectDatabase.filter ( FilenameFilter p1 ) :  FilenameFilter
PersistentObjectDatabase.get ( String p1 ) :  Object
PersistentObjectDatabase.objects ( ) :  String[ ]
PersistentObjectDatabase.objects ( boolean p1 ) :  String[ ]
PersistentObjectDatabase.PersistentObjectDatabase ( File p1 )
PersistentObjectDatabase.PersistentObjectDatabase ( File p1, boolean p2 )
PersistentObjectDatabase.PersistentObjectDatabase ( File p1, boolean p2, boolean p3 )
PersistentObjectDatabase.PersistentObjectDatabase ( String p1 )
PersistentObjectDatabase.read ( String p1 ) :  Object
PersistentObjectDatabase.readEntries ( File p1 ) :  int
PersistentObjectDatabase.readEntries ( File p1, FilenameFilter p2 ) :  int
PersistentObjectDatabase.remove ( String p1 ) :  Object
PersistentObjectDatabase.synchronize ( ) :  int
PersistentObjectDatabase.synchronize ( boolean p1 ) :  int
PersistentObjectDatabase.write ( String p1, Object p2 ) :  Object

cdk-1.2.10.jar, PharmacophoreMatcher.class
package org.openscience.cdk.pharmacophore
PharmacophoreMatcher.getPharmacophoreQuery ( ) :  IQueryAtomContainer
PharmacophoreMatcher.PharmacophoreMatcher ( IQueryAtomContainer pharmacophoreQuery )
PharmacophoreMatcher.setPharmacophoreQuery ( IQueryAtomContainer query ) :  void

cdk-1.2.10.jar, PharmacophoreUtils.class
package org.openscience.cdk.pharmacophore
PharmacophoreUtils.writePharmacophoreDefinition ( IQueryAtomContainer query, OutputStream out ) [static] :  void
PharmacophoreUtils.writePharmacophoreDefinition ( IQueryAtomContainer[ ] queries, OutputStream out ) [static] :  void

cdk-1.2.10.jar, PLSRegressionModel.class
package org.openscience.cdk.qsar.model.R
PLSRegressionModel.build ( ) :  void
PLSRegressionModel.finalize ( ) :  void
PLSRegressionModel.getFitB ( ) :  double[ ][ ][ ]
PLSRegressionModel.getFitMethod ( ) :  String
PLSRegressionModel.getFitNComp ( ) :  int[ ]
PLSRegressionModel.getFitRMS ( ) :  double[ ][ ]
PLSRegressionModel.getFitWasValidated ( ) :  boolean
PLSRegressionModel.getFitXLoading ( ) :  double[ ][ ]
PLSRegressionModel.getFitXScores ( ) :  double[ ][ ]
PLSRegressionModel.getFitYLoading ( ) :  double[ ][ ]
PLSRegressionModel.getFitYPred ( ) :  double[ ][ ][ ]
PLSRegressionModel.getFitYScores ( ) :  double[ ][ ]
PLSRegressionModel.getPredictPredicted ( ) :  double[ ][ ]
PLSRegressionModel.getValidationIter ( ) :  int
PLSRegressionModel.getValidationLV ( ) :  int
PLSRegressionModel.getValidationR2 ( ) :  double[ ][ ]
PLSRegressionModel.getValidationRMS ( ) :  double[ ][ ]
PLSRegressionModel.getValidationRMSsd ( ) :  double[ ][ ]
PLSRegressionModel.getValidationYPred ( ) :  double[ ][ ][ ]
PLSRegressionModel.loadModel ( String fileName ) :  void
PLSRegressionModel.loadModel ( String serializedModel, String modelName ) :  void
PLSRegressionModel.PLSRegressionModel ( )
PLSRegressionModel.PLSRegressionModel ( double[ ][ ] xx, double[ ] yy )
PLSRegressionModel.PLSRegressionModel ( double[ ][ ] xx, double[ ][ ] yy )
PLSRegressionModel.predict ( ) :  void
PLSRegressionModel.setParameters ( String key, Object obj ) :  void

cdk-1.2.10.jar, PLSRegressionModelFit.class
package org.openscience.cdk.qsar.model.R
PLSRegressionModelFit.getB ( ) :  double[ ][ ][ ]
PLSRegressionModelFit.getMethod ( ) :  String
PLSRegressionModelFit.getNComp ( ) :  int[ ]
PLSRegressionModelFit.getTrainingRMS ( ) :  double[ ][ ]
PLSRegressionModelFit.getTrainingYPred ( ) :  double[ ][ ][ ]
PLSRegressionModelFit.getValidationIter ( ) :  int
PLSRegressionModelFit.getValidationLV ( ) :  int
PLSRegressionModelFit.getValidationR2 ( ) :  double[ ][ ]
PLSRegressionModelFit.getValidationRMS ( ) :  double[ ][ ]
PLSRegressionModelFit.getValidationRMSSD ( ) :  double[ ][ ]
PLSRegressionModelFit.getValidationYPred ( ) :  double[ ][ ][ ]
PLSRegressionModelFit.getXLoading ( ) :  double[ ][ ]
PLSRegressionModelFit.getXScores ( ) :  double[ ][ ]
PLSRegressionModelFit.getYLoading ( ) :  double[ ][ ]
PLSRegressionModelFit.getYScores ( ) :  double[ ][ ]
PLSRegressionModelFit.PLSRegressionModelFit ( int nobs, int nvar, int npred, int[ ] ncomp, String method )
PLSRegressionModelFit.setTrainingData ( double[ ] B, double[ ] ypred, double[ ] rms, double[ ] xscores, double[ ] yscores, double[ ] xload, double[ ] yload ) :  void
PLSRegressionModelFit.setValidationData ( int niter, int nlv, double[ ] ypred, double[ ] rms, double[ ] rmssd, double[ ] r2 ) :  void
PLSRegressionModelFit.wasValidated ( ) :  boolean

cdk-1.2.10.jar, PLSRegressionModelPredict.class
package org.openscience.cdk.qsar.model.R
PLSRegressionModelPredict.getPredictions ( ) :  double[ ][ ]
PLSRegressionModelPredict.PLSRegressionModelPredict ( int ncol, double[ ] preds )

cdk-1.2.10.jar, PrefixClassList.class
package org.omegahat.Environment.Tools.ClassList
PrefixClassList.add ( String p1 ) :  String
PrefixClassList.prefix ( ) :  String
PrefixClassList.prefix ( String p1 ) :  String
PrefixClassList.PrefixClassList ( File p1 )
PrefixClassList.PrefixClassList ( File p1, String p2 )

cdk-1.2.10.jar, PromptSource.class
package org.omegahat.Environment.IO
PromptSource.prompt ( ) [abstract] :  String

cdk-1.2.10.jar, QSARModelException.class
package org.openscience.cdk.qsar.model
QSARModelException.QSARModelException ( String message )

cdk-1.2.10.jar, RBool.class
package org.rosuda.JRI
RBool.isFALSE ( ) :  boolean
RBool.isNA ( ) :  boolean
RBool.isTRUE ( ) :  boolean
RBool.RBool ( boolean p1 )
RBool.RBool ( int p1 )
RBool.RBool ( JRI.RBool p1 )
RBool.toString ( ) :  String

cdk-1.2.10.jar, RConsoleOutputStream.class
package org.rosuda.JRI
RConsoleOutputStream.close ( ) :  void
RConsoleOutputStream.RConsoleOutputStream ( JRI.Rengine p1, int p2 )
RConsoleOutputStream.write ( byte[ ] p1 ) :  void
RConsoleOutputStream.write ( byte[ ] p1, int p2, int p3 ) :  void
RConsoleOutputStream.write ( int p1 ) :  void

cdk-1.2.10.jar, ReadWriteDatabase.class
package org.omegahat.Environment.Databases
ReadWriteDatabase.assign ( String p1, Object p2 ) :  boolean
ReadWriteDatabase.permissions ( ) :  Vector
ReadWriteDatabase.permissions ( Vector p1 ) :  Vector
ReadWriteDatabase.readOnly ( String p1 ) :  boolean
ReadWriteDatabase.readOnly ( String p1, boolean p2 ) :  boolean
ReadWriteDatabase.ReadWriteDatabase ( )
ReadWriteDatabase.ReadWriteDatabase ( int p1 )
ReadWriteDatabase.ReadWriteDatabase ( String p1 )
ReadWriteDatabase.remove ( String p1 ) :  Object

cdk-1.2.10.jar, ReadWriteDatabaseInt.class
package org.omegahat.Environment.Databases
ReadWriteDatabaseInt.readOnly ( String p1 ) [abstract] :  boolean
ReadWriteDatabaseInt.readOnly ( String p1, boolean p2 ) [abstract] :  boolean

cdk-1.2.10.jar, RecordLexer.class
package org.omegahat.Environment.Tools.DataScanner
RecordLexer.currentRecord ( ) [abstract] :  Object
RecordLexer.endRecord ( ) [abstract] :  Object
RecordLexer.nextRecord ( ) [abstract] :  Object
RecordLexer.nextRecord ( boolean p1 ) [abstract] :  Object
RecordLexer.readRecords ( ) [abstract] :  long

cdk-1.2.10.jar, RecordStreamListener.class
package org.omegahat.Environment.Tools.DataScanner
RecordStreamListener.newRecord ( Object p1, Environment.Tools.DataScanner.ObjectReader p2 ) [abstract] :  boolean

cdk-1.2.10.jar, RelationalOperator.class
package org.omegahat.Environment.DataStructures
RelationalOperator.compare ( Object p1, int p2 ) [abstract] :  Object

cdk-1.2.10.jar, Rengine.class
package org.rosuda.JRI
Rengine.addMainLoopCallbacks ( JRI.RMainLoopCallbacks p1 ) :  void
Rengine.assign ( String p1, boolean[ ] p2 ) :  void
Rengine.assign ( String p1, double[ ] p2 ) :  void
Rengine.assign ( String p1, int[ ] p2 ) :  void
Rengine.assign ( String p1, JRI.REXP p2 ) :  void
Rengine.assign ( String p1, String p2 ) :  void
Rengine.assign ( String p1, String[ ] p2 ) :  void
Rengine.createRJavaRef ( Object p1 ) :  JRI.REXP
Rengine.end ( ) :  void
Rengine.eval ( String p1 ) :  JRI.REXP
Rengine.eval ( String p1, boolean p2 ) :  JRI.REXP
Rengine.getMainEngine ( ) [static] :  JRI.Rengine
Rengine.getRsync ( ) :  JRI.Mutex
Rengine.getVersion ( ) [static] :  long
Rengine.idleEval ( String p1 ) :  JRI.REXP
Rengine.idleEval ( String p1, boolean p2 ) :  JRI.REXP
Rengine.inMainRThread ( ) [static] :  boolean
Rengine.isStandAlone ( ) :  boolean
Rengine.jriBusy ( int p1 ) :  void
Rengine.jriChooseFile ( int p1 ) :  String
Rengine.jriFlushConsole ( ) :  void
Rengine.jriLoadHistory ( String p1 ) :  void
Rengine.jriReadConsole ( String p1, int p2 ) :  String
Rengine.jriSaveHistory ( String p1 ) :  void
Rengine.jriShowMessage ( String p1 ) :  void
Rengine.jriWriteConsole ( String p1, int p2 ) :  void
Rengine.Rengine ( )
Rengine.Rengine ( String[ ] p1, boolean p2, JRI.RMainLoopCallbacks p3 )
Rengine.rniAssign ( String p1, long p2, long p3 ) :  void
Rengine.rniCAR ( long p1 ) :  long
Rengine.rniCDR ( long p1 ) :  long
Rengine.rniCons ( long p1, long p2 ) :  long
Rengine.rniCons ( long p1, long p2, long p3, boolean p4 ) :  long
Rengine.rniEval ( long p1, long p2 ) :  long
Rengine.rniExpType ( long p1 ) :  int
Rengine.rniGetAttr ( long p1, String p2 ) :  long
Rengine.rniGetBoolArrayI ( long p1 ) :  int[ ]
Rengine.rniGetDoubleArray ( long p1 ) :  double[ ]
Rengine.rniGetIntArray ( long p1 ) :  int[ ]
Rengine.rniGetList ( long p1 ) :  long[ ]
Rengine.rniGetString ( long p1 ) :  String
Rengine.rniGetStringArray ( long p1 ) :  String[ ]
Rengine.rniGetSymbolName ( long p1 ) :  String
Rengine.rniGetVector ( long p1 ) :  long[ ]
Rengine.rniGetVersion ( ) [static] :  long
Rengine.rniIdle ( ) :  void
Rengine.rniInherits ( long p1, String p2 ) :  boolean
Rengine.rniInstallSymbol ( String p1 ) :  long
Rengine.rniLCons ( long p1, long p2 ) :  long
Rengine.rniParse ( String p1, int p2 ) :  long
Rengine.rniPrint ( String p1, int p2 ) :  void
Rengine.rniProtect ( long p1 ) :  void
Rengine.rniPutBoolArray ( boolean[ ] p1 ) :  long
Rengine.rniPutBoolArrayI ( int[ ] p1 ) :  long
Rengine.rniPutDoubleArray ( double[ ] p1 ) :  long
Rengine.rniPutIntArray ( int[ ] p1 ) :  long
Rengine.rniPutList ( long[ ] p1 ) :  long
Rengine.rniPutString ( String p1 ) :  long
Rengine.rniPutStringArray ( String[ ] p1 ) :  long
Rengine.rniPutVector ( long[ ] p1 ) :  long
Rengine.rniRJavaLock ( ) :  int
Rengine.rniRJavaUnlock ( ) :  int
Rengine.rniRunMainLoop ( ) :  void
Rengine.rniSetAttr ( long p1, String p2, long p3 ) :  void
Rengine.rniSetupRJava ( int p1, int p2 ) :  int
Rengine.rniStop ( int p1 ) :  int
Rengine.rniTAG ( long p1 ) :  long
Rengine.rniUnprotect ( int p1 ) :  void
Rengine.run ( ) :  void
Rengine.startMainLoop ( ) :  void
Rengine.versionCheck ( ) [static] :  boolean
Rengine.waitForR ( ) :  boolean

cdk-1.2.10.jar, ResettableLexer.class
package org.omegahat.Environment.Parser.AntlrParser
ResettableLexer.setInput ( Reader p1 ) [abstract] :  InputBuffer

cdk-1.2.10.jar, ResolvingProperties.class
package sea36.util.config
ResolvingProperties.get ( Object key ) :  Object
ResolvingProperties.getProperty ( String key ) :  String
ResolvingProperties.put ( Object key, Object value ) :  Object
ResolvingProperties.ResolvingProperties ( )
ResolvingProperties.ResolvingProperties ( Map params )
ResolvingProperties.ResolvingProperties ( ResolvingProperties defaults )
ResolvingProperties.ResolvingProperties ( ResolvingProperties defaults, Map params )

cdk-1.2.10.jar, REvaluator.class
package org.omegahat.R.Java
REvaluator.call ( String p1 ) :  Object
REvaluator.call ( String p1, Environment.Utils.OrderedTable p2 ) :  Object
REvaluator.call ( String p1, Environment.Utils.OrderedTable p2, Class p3 ) :  Object
REvaluator.call ( String p1, Environment.Utils.OrderedTable p2, Class p3, boolean p4 ) :  Object
REvaluator.call ( String p1, Hashtable p2 ) :  Object
REvaluator.call ( String p1, Object[ ] p2 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, boolean p3 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, Hashtable p3 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, String[ ] p3 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, String[ ] p3, boolean p4 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, String[ ] p3, Class p4 ) :  Object
REvaluator.call ( String p1, Object[ ] p2, String[ ] p3, Class p4, boolean p5 ) :  Object
REvaluator.createArgs ( Hashtable p1, String[ ] p2 ) :  Object[ ]
REvaluator.createArgs ( Hashtable p1, String[ ] p2, Object[ ] p3, int p4 ) :  Object[ ]
REvaluator.eval ( String p1 ) :  Object
REvaluator.eval ( String p1, boolean p2 ) :  Object
REvaluator.eval ( String p1, boolean p2, Class p3, boolean p4 ) :  Object
REvaluator.eval ( String p1, Class p2 ) :  Object
REvaluator.eval ( String p1, Class p2, boolean p3 ) :  Object
REvaluator.lockEvaluator ( boolean p1 ) [static] :  boolean
REvaluator.REvaluator ( )
REvaluator.voidEval ( String p1 ) :  Object
REvaluator.yieldThread ( ) [static] :  void

cdk-1.2.10.jar, RException.class
package org.omegahat.R.Java
RException.RException ( String p1 )

cdk-1.2.10.jar, REXP.class
package org.rosuda.JRI
REXP.asBool ( ) :  JRI.RBool
REXP.asDouble ( ) :  double
REXP.asDoubleArray ( ) :  double[ ]
REXP.asDoubleMatrix ( ) :  double[ ][ ]
REXP.asFactor ( ) :  JRI.RFactor
REXP.asInt ( ) :  int
REXP.asIntArray ( ) :  int[ ]
REXP.asList ( ) :  JRI.RList
REXP.asMatrix ( ) :  double[ ][ ]
REXP.asString ( ) :  String
REXP.asStringArray ( ) :  String[ ]
REXP.asSymbolName ( ) :  String
REXP.asVector ( ) :  JRI.RVector
REXP.getAttribute ( String p1 ) :  JRI.REXP
REXP.getAttributes ( ) :  JRI.REXP
REXP.getContent ( ) :  Object
REXP.getType ( ) :  int
REXP.quoteString ( String p1 ) [static] :  String
REXP.REXP ( )
REXP.REXP ( boolean[ ] p1 )
REXP.REXP ( double[ ] p1 )
REXP.REXP ( int p1, Object p2 )
REXP.REXP ( int p1, Object p2, JRI.REXP p3 )
REXP.REXP ( int[ ] p1 )
REXP.REXP ( JRI.Rengine p1, long p2 )
REXP.REXP ( JRI.Rengine p1, long p2, boolean p3 )
REXP.REXP ( String[ ] p1 )
REXP.toString ( ) :  String
REXP.xtName ( int p1 ) [static] :  String

cdk-1.2.10.jar, RFactor.class
package org.rosuda.JRI
RFactor.add ( String p1 ) :  void
RFactor.at ( int p1 ) :  String
RFactor.RFactor ( )
RFactor.RFactor ( int[ ] p1, String[ ] p2 )
RFactor.size ( ) :  int
RFactor.toString ( ) :  String

cdk-1.2.10.jar, RForeignReference.class
package org.omegahat.R.Java
RForeignReference.localEval ( Environment.Parser.Parse.List p1, String p2, String p3, String[ ] p4 ) :  Object
RForeignReference.reval ( String p1, Object[ ] p2, String p3, String p4, String[ ] p5 ) :  Object
RForeignReference.RForeignReference ( Interfaces.NativeInterface.ForeignReference p1 )
RForeignReference.RForeignReference ( Interfaces.NativeInterface.ForeignReference p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
RForeignReference.RForeignReference ( String p1 )
RForeignReference.RForeignReference ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )

cdk-1.2.10.jar, RJavaInstance.class
package org.omegahat.R.Java
RJavaInstance.getSkipOmittedMethods ( ) :  boolean
RJavaInstance.RJavaInstance ( Interfaces.NativeInterface.ForeignReference p1 )
RJavaInstance.RJavaInstance ( String p1 )
RJavaInstance.setSkipOmittedMethods ( boolean p1 ) :  boolean

cdk-1.2.10.jar, RList.class
package org.rosuda.JRI
RList.at ( int p1 ) :  JRI.REXP
RList.at ( String p1 ) :  JRI.REXP
RList.getBody ( ) :  JRI.REXP
RList.getHead ( ) :  JRI.REXP
RList.getTag ( ) :  JRI.REXP
RList.keys ( ) :  String[ ]
RList.RList ( )
RList.RList ( JRI.REXP p1, JRI.REXP p2 )
RList.RList ( JRI.REXP p1, JRI.REXP p2, JRI.REXP p3 )
RList.RList ( JRI.RVector p1 )

cdk-1.2.10.jar, RMainLoopCallbacks.class
package org.rosuda.JRI
RMainLoopCallbacks.rBusy ( JRI.Rengine p1, int p2 ) [abstract] :  void
RMainLoopCallbacks.rChooseFile ( JRI.Rengine p1, int p2 ) [abstract] :  String
RMainLoopCallbacks.rFlushConsole ( JRI.Rengine p1 ) [abstract] :  void
RMainLoopCallbacks.rLoadHistory ( JRI.Rengine p1, String p2 ) [abstract] :  void
RMainLoopCallbacks.rReadConsole ( JRI.Rengine p1, String p2, int p3 ) [abstract] :  String
RMainLoopCallbacks.rSaveHistory ( JRI.Rengine p1, String p2 ) [abstract] :  void
RMainLoopCallbacks.rShowMessage ( JRI.Rengine p1, String p2 ) [abstract] :  void
RMainLoopCallbacks.rWriteConsole ( JRI.Rengine p1, String p2, int p3 ) [abstract] :  void

cdk-1.2.10.jar, RManualFunctionActionListener.class
package org.omegahat.R.Java
RManualFunctionActionListener.actionPerformed ( ActionEvent p1 ) :  void
RManualFunctionActionListener.RManualFunctionActionListener ( Interfaces.NativeInterface.ForeignReference p1 )
RManualFunctionActionListener.RManualFunctionActionListener ( Interfaces.NativeInterface.ForeignReference p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )
RManualFunctionActionListener.RManualFunctionActionListener ( String p1 )
RManualFunctionActionListener.RManualFunctionActionListener ( String p1, Interfaces.NativeInterface.OmegaInterfaceManager p2 )

cdk-1.2.10.jar, RModel.class
package org.openscience.cdk.qsar.model.R
RModel.build ( ) [abstract] :  void
RModel.getModelName ( ) :  String
RModel.loadModel ( String p1 ) [abstract] :  void
RModel.loadModel ( String p1, String p2 ) [abstract] :  void
RModel.predict ( ) [abstract] :  void
RModel.RModel ( )
RModel.RModel ( String[ ] args )
RModel.saveModel ( String modelname, String filename ) [static] :  void
RModel.setModelName ( String newName ) :  void
RModel.setParameters ( String p1, Object p2 ) [abstract] :  void
package org.openscience.cdk.qsar.model.R2
RModel.build ( ) [abstract] :  void
RModel.finalize ( ) :  void
RModel.getModelName ( ) :  String
RModel.getModelObject ( ) :  JRI.RList
RModel.getRengine ( ) [static] :  JRI.Rengine
RModel.getUniqueVariableName ( String prefix ) :  String
RModel.isOfClass ( String objectName, String objectClass ) :  boolean
RModel.loadModel ( String p1 ) [abstract] :  void
RModel.loadModel ( String p1, String p2 ) [abstract] :  void
RModel.loadParametersIntoRSession ( ) :  String
RModel.predict ( ) [abstract] :  void
RModel.removeObject ( String objectName ) :  void
RModel.RModel ( )
RModel.saveModel ( String modelName, String fileName ) :  void
RModel.setModelName ( String newName ) :  void
RModel.setParameters ( String p1, Object p2 ) [abstract] :  void

cdk-1.2.10.jar, ROmegahatInterpreter.class
package org.omegahat.R.Java
ROmegahatInterpreter.fixArgs ( String[ ] p1 ) [static] :  String[ ]
ROmegahatInterpreter.initR ( String[ ] p1 ) :  boolean
ROmegahatInterpreter.main ( String[ ] p1 ) [static] :  void
ROmegahatInterpreter.registerNativeConverters ( ) :  boolean
ROmegahatInterpreter.ROmegahatInterpreter ( String[ ] p1 )
ROmegahatInterpreter.ROmegahatInterpreter ( String[ ] p1, boolean p2 )
ROmegahatInterpreter.run ( ) :  void

cdk-1.2.10.jar, RSplash.class
package org.omegahat.R.Java
RSplash.init ( ) :  void
RSplash.RSplash ( )

cdk-1.2.10.jar, RVector.class
package org.rosuda.JRI
RVector.at ( int p1 ) :  JRI.REXP
RVector.at ( String p1 ) :  JRI.REXP
RVector.getNames ( ) :  Vector
RVector.RVector ( )
RVector.setNames ( String[ ] p1 ) :  void

cdk-1.2.10.jar, SearchPath.class
package org.omegahat.Environment.Databases
SearchPath.addAssignListener ( Environment.Databases.DatabaseAssignListener p1 ) :  int
SearchPath.addPathListener ( Environment.Databases.SearchPathListener p1 ) :  int
SearchPath.assign ( String p1, Object p2 ) :  boolean
SearchPath.attach ( Environment.Databases.Database p1 ) :  Environment.Databases.AttachedDatabase
SearchPath.attach ( Environment.Databases.Database p1, int p2 ) :  Environment.Databases.AttachedDatabase
SearchPath.attach ( Environment.Databases.Database p1, String p2 ) :  Environment.Databases.AttachedDatabase
SearchPath.attach ( Environment.Databases.Database p1, String p2, int p3 ) :  Environment.Databases.AttachedDatabase
SearchPath.detach ( Environment.Databases.Database p1 ) :  int
SearchPath.detach ( int p1 ) :  int
SearchPath.elementAt ( int p1 ) :  Object
SearchPath.exists ( String p1 ) :  boolean
SearchPath.find ( String p1, boolean p2 ) :  Environment.Databases.Database[ ]
SearchPath.get ( String p1 ) :  Object
SearchPath.getDatabase ( String p1 ) :  Environment.Databases.Database
SearchPath.notifyListeners ( Environment.Databases.SearchPathEvent p1 ) :  void
SearchPath.objects ( ) :  String[ ]
SearchPath.pathListeners ( ) :  Vector
SearchPath.pathListeners ( Vector p1 ) :  Vector
SearchPath.remove ( String p1 ) :  Object
SearchPath.removePathListener ( Environment.Databases.SearchPathListener p1 ) :  void
SearchPath.SearchPath ( )
SearchPath.SearchPath ( Environment.Databases.Database p1 )
SearchPath.SearchPath ( Environment.Databases.SearchPath p1 )
SearchPath.SearchPath ( int p1 )
SearchPath.SearchPath ( Vector p1 )

cdk-1.2.10.jar, SearchPathEvent.class
package org.omegahat.Environment.Databases
SearchPathEvent.searchPath ( ) :  Environment.Databases.SearchPath
SearchPathEvent.searchPath ( Environment.Databases.SearchPath p1 ) :  Environment.Databases.SearchPath
SearchPathEvent.SearchPathEvent ( )
SearchPathEvent.SearchPathEvent ( Environment.Databases.Database p1, Environment.Databases.SearchPath p2 )

cdk-1.2.10.jar, SearchPathListener.class
package org.omegahat.Environment.Databases
SearchPathListener.searchPathAction ( Environment.Databases.SearchPathEvent p1 ) [abstract] :  void

cdk-1.2.10.jar, SearchPathView.class
package org.omegahat.Environment.GUI
SearchPathView.getName ( Object p1 ) :  String
SearchPathView.make ( ) :  boolean
SearchPathView.make ( Environment.Databases.SearchPath p1 ) :  boolean
SearchPathView.makeElement ( Object p1 ) :  Component
SearchPathView.searchPathAction ( Environment.Databases.SearchPathEvent p1 ) :  void
SearchPathView.SearchPathView ( Environment.Databases.SearchPath p1 )
SearchPathView.SearchPathView ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, SearchPathViewerFrame.class
package org.omegahat.Environment.GUI
SearchPathViewerFrame.SearchPathViewerFrame ( )
SearchPathViewerFrame.SearchPathViewerFrame ( Environment.Databases.SearchPath p1 )
SearchPathViewerFrame.SearchPathViewerFrame ( Environment.GUI.SearchPathView p1 )
SearchPathViewerFrame.SearchPathViewerFrame ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, SelfDisplaying.class
package org.omegahat.Environment.IO
SelfDisplaying.display ( Environment.IO.ObjectDisplayFilter p1, long p2 ) [abstract] :  boolean

cdk-1.2.10.jar, SequenceExpression.class
package org.omegahat.Environment.Parser.Parse
SequenceExpression.end ( ) :  Object
SequenceExpression.end ( Object p1 ) :  Object
SequenceExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
SequenceExpression.separator ( ) :  String
SequenceExpression.SequenceExpression ( Object p1, Object p2 )
SequenceExpression.start ( ) :  Object
SequenceExpression.start ( Object p1 ) :  Object

cdk-1.2.10.jar, SequenceFunctions.class
package org.omegahat.Environment.lib.Language
SequenceFunctions.c ( Object[ ] p1, Object[ ] p2 ) [static] :  Object[ ]
SequenceFunctions.cycle ( Object[ ] p1, int p2 ) [static] :  Object
SequenceFunctions.cycle ( Vector p1, int p2 ) [static] :  Object
SequenceFunctions.rep ( Object p1, int p2 ) [static] :  Object[ ]
SequenceFunctions.rep ( Object p1, int p2, boolean p3 ) [static] :  Object[ ]
SequenceFunctions.SequenceFunctions ( )

cdk-1.2.10.jar, ServerPool.class
package org.omegahat.Environment.TaskManagement
ServerPool.addElement ( Object p1 ) [abstract] :  void
ServerPool.clear ( ) [abstract] :  void
ServerPool.elementAt ( int p1 ) [abstract] :  Object
ServerPool.remove ( Object p1 ) [abstract] :  boolean
ServerPool.removeElement ( Object p1 ) [abstract] :  boolean
ServerPool.size ( ) [abstract] :  int

cdk-1.2.10.jar, ShiftExpression.class
package org.omegahat.Environment.Parser.Parse
ShiftExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
ShiftExpression.operate ( int[ ] p1 ) :  int
ShiftExpression.ShiftExpression ( Object p1, int p2 )
ShiftExpression.ShiftExpression ( Object p1, Object p2, int p3 )

cdk-1.2.10.jar, Signature.class
package org.omegahat.Environment.GUITools
Signature.addType ( String p1 ) :  Vector
Signature.addTypes ( String[ ] p1 ) :  Vector
Signature.argsToString ( ) :  String
Signature.createCode ( ) :  CodeAttr
Signature.separator ( ) :  String
Signature.Signature ( )
Signature.Signature ( String p1 )
Signature.Signature ( String[ ] p1 )
Signature.size ( ) :  int
Signature.types ( ) :  Vector
package org.omegahat.Environment.Language
Signature.equals ( Environment.Language.Signature p1 ) :  boolean
Signature.hashCode ( ) :  int
Signature.parameterTypes ( ) :  Environment.Databases.Database
Signature.parameterTypes ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
Signature.returnType ( ) :  Class
Signature.returnType ( Class p1 ) :  Class
Signature.Signature ( Class p1 )
Signature.Signature ( Environment.Language.Function p1 )

cdk-1.2.10.jar, SimpleEvaluationMonitor.class
package org.omegahat.Environment.Debugger
SimpleEvaluationMonitor.nextEvaluation ( Environment.Interpreter.EvaluationEvent p1 ) :  void
SimpleEvaluationMonitor.out ( ) :  PrintStream
SimpleEvaluationMonitor.out ( PrintStream p1 ) :  PrintStream
SimpleEvaluationMonitor.SimpleEvaluationMonitor ( )
SimpleEvaluationMonitor.SimpleEvaluationMonitor ( PrintStream p1 )

cdk-1.2.10.jar, SimpleParameterModifier.class
package org.omegahat.Environment.Parser.Parse
SimpleParameterModifier.isFinal ( ) :  boolean
SimpleParameterModifier.isFinal ( boolean p1 ) :  boolean
SimpleParameterModifier.SimpleParameterModifier ( )
SimpleParameterModifier.SimpleParameterModifier ( boolean p1 )

cdk-1.2.10.jar, SimulationManager.class
package org.omegahat.Environment.TaskManagement
SimulationManager.addVariable ( String p1, Object[ ] p2 ) :  void
SimulationManager.ensureTaskQueue ( int p1 ) :  void
SimulationManager.getTask ( ) :  Environment.TaskManagement.Task
SimulationManager.setExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
SimulationManager.SimulationManager ( )
SimulationManager.SimulationManager ( int p1 )

cdk-1.2.10.jar, SimulationTask.class
package org.omegahat.Environment.TaskManagement
SimulationTask.eval ( ) :  Object
SimulationTask.eval ( Object[ ] p1 ) :  Object
SimulationTask.getDatabase ( ) :  Environment.Databases.Database
SimulationTask.getEvaluator ( ) :  Environment.Interpreter.Evaluator
SimulationTask.getExpression ( ) :  Environment.Parser.Parse.ExpressionInt
SimulationTask.getGlobalEvaluator ( ) :  Environment.Interpreter.Evaluator
SimulationTask.setDatabase ( Environment.Databases.Database p1 ) :  Environment.Databases.Database
SimulationTask.setDatabase ( String p1 ) :  Environment.Databases.Database
SimulationTask.setEvaluator ( Environment.Interpreter.Evaluator p1 ) :  Environment.Interpreter.Evaluator
SimulationTask.setExpression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
SimulationTask.SimulationTask ( )

cdk-1.2.10.jar, single.class
package org.omegahat.Environment.DataStructures
single.data ( float p1 ) :  Object
single.data ( float[ ] p1 ) :  Object
single.data ( int p1 ) :  Object
single.getElement ( int p1 ) :  float
single.setData ( float[ ] p1 ) :  int
single.single ( )
single.single ( float p1 )
single.single ( float[ ] p1 )
single.single ( int p1 )
single.valueOf ( String p1 ) [static] :  float
package org.omegahat.Environment.ObjectDataStructures
single.convertElement ( Object p1 ) :  Object
single.data ( float p1 ) :  Environment.ObjectDataStructures.single
single.data ( float[ ] p1 ) :  Environment.ObjectDataStructures.single
single.setData ( float[ ] p1 ) :  int
single.single ( )
single.single ( float p1 )
single.single ( float[ ] p1 )
single.single ( int p1 )
single.targetClass ( ) :  Class
single.valueOf ( String p1 ) [static] :  float

cdk-1.2.10.jar, SingleLineComment.class
package org.omegahat.Environment.Parser.Parse
SingleLineComment.SingleLineComment ( String p1 )
SingleLineComment.toString ( ) :  String

cdk-1.2.10.jar, SmilesGenerator.class
package org.openscience.cdk.smiles
SmilesGenerator.createChiralSMILES ( IMolecule molecule, boolean[ ] doubleBondConfiguration ) :  String
SmilesGenerator.createSMILES ( IMolecule molecule ) :  String
SmilesGenerator.createSMILES ( IMolecule molecule, boolean chiral, boolean[ ] doubleBondConfiguration ) :  String

cdk-1.2.10.jar, SmoothingFunctions.class
package org.openscience.cdk.modeling.forcefield
SmoothingFunctions.getSmoothingFunction ( ) :  double[ ]
SmoothingFunctions.setSmoothingFunction ( double[ ] atomDistances ) :  void
SmoothingFunctions.SmoothingFunctions ( )

cdk-1.2.10.jar, SourceAttr.class
package jas
SourceAttr.SourceAttr ( CP name )
SourceAttr.SourceAttr ( String name )

cdk-1.2.10.jar, StatementList.class
package org.omegahat.Environment.Parser.Parse
StatementList.close ( Environment.Interpreter.Evaluator p1 ) :  boolean
StatementList.definesLocalVariables ( Environment.Interpreter.Evaluator p1 ) :  boolean
StatementList.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
StatementList.getComments ( ) :  Environment.Parser.Parse.List
StatementList.getComments ( boolean p1 ) :  Environment.Parser.Parse.List
StatementList.getFirstChild ( ) :  AST
StatementList.handleLocalFrame ( ) :  boolean
StatementList.handleLocalFrame ( boolean p1 ) :  boolean
StatementList.separator ( ) :  String
StatementList.StatementList ( )
StatementList.StatementList ( AST p1, boolean p2 )
StatementList.StatementList ( Object p1 )
StatementList.toString ( ) :  String

cdk-1.2.10.jar, StaticMethodAlias.class
package org.omegahat.Environment.Language
StaticMethodAlias.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
StaticMethodAlias.eval ( Object[ ] p1, Environment.Interpreter.Evaluator p2 ) :  Object
StaticMethodAlias.Method ( ) :  Method
StaticMethodAlias.Method ( Method p1 ) :  Method
StaticMethodAlias.StaticMethodAlias ( )
StaticMethodAlias.StaticMethodAlias ( Method p1 )
StaticMethodAlias.This ( ) :  Object
StaticMethodAlias.toString ( ) :  String

cdk-1.2.10.jar, SteepestDescentsMethod.class
package org.openscience.cdk.modeling.forcefield
SteepestDescentsMethod.setSk ( GVector gk ) :  void
SteepestDescentsMethod.SteepestDescentsMethod ( )
SteepestDescentsMethod.SteepestDescentsMethod ( GVector coords3d )

cdk-1.2.10.jar, StretchBendInteractions.class
package org.openscience.cdk.modeling.forcefield
StretchBendInteractions.get2ndOrderErrorApproximateGradientMMFF94SumEBA ( ) :  GVector
StretchBendInteractions.get5thOrderErrorApproximateGradientMMFF94SumEBA ( ) :  GVector
StretchBendInteractions.getFunctionMMFF94SumEBA ( ) :  double
StretchBendInteractions.getGradientMMFF94SumEBA ( ) :  GVector
StretchBendInteractions.getHessianMMFF94SumEBA ( ) :  GMatrix
StretchBendInteractions.set2ndOrderErrorApproximateGradientMMFF94SumEBA ( GVector coord3d ) :  void
StretchBendInteractions.set5thOrderErrorApproximateGradientMMFF94SumEBA ( GVector coord3d ) :  void
StretchBendInteractions.setDeltarijAndDeltarkj ( GVector coords3d ) :  void
StretchBendInteractions.setFunctionMMFF94SumEBA ( GVector coords3d ) :  void
StretchBendInteractions.setGradientMMFF94SumEBA ( GVector coords3d ) :  void
StretchBendInteractions.setHessianMMFF94SumEBA ( GVector coords3d ) :  void
StretchBendInteractions.setMMFF94StretchBendParameters ( IAtomContainer molecule, Map parameterSet, boolean angleBendingFlag ) :  void
StretchBendInteractions.StretchBendInteractions ( )

cdk-1.2.10.jar, StringCP.class
package jas
StringCP.StringCP ( String s )

cdk-1.2.10.jar, StringUtils.class
package org.omegahat.Environment.Utils
StringUtils.join ( String[ ] p1, String p2 ) [static] :  String
StringUtils.stringList ( String p1 ) [static] :  String[ ]
StringUtils.stringList ( String p1, char p2 ) [static] :  String[ ]
StringUtils.StringUtils ( )

cdk-1.2.10.jar, SubArchiveClassList.class
package org.omegahat.Environment.Tools.ClassList
SubArchiveClassList.add ( ZipEntry p1 ) :  Object
SubArchiveClassList.getSubDirectory ( ) :  String
SubArchiveClassList.setSubDirectory ( String p1 ) :  String
SubArchiveClassList.SubArchiveClassList ( )
SubArchiveClassList.SubArchiveClassList ( File p1 )
SubArchiveClassList.SubArchiveClassList ( File p1, String p2 )

cdk-1.2.10.jar, SubsetFunctions.class
package org.omegahat.Environment.lib.Language
SubsetFunctions.subset ( AST p1, Environment.Parser.Parse.List p2, boolean p3 ) [static] :  Object
SubsetFunctions.SubsetFunctions ( )

cdk-1.2.10.jar, Subsettable.class
package org.omegahat.Environment.DataStructures
Subsettable.subset ( Object p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, SubstitutedTrimmedProperties.class
package org.omegahat.Environment.Utils
SubstitutedTrimmedProperties.load ( InputStream p1 ) :  void
SubstitutedTrimmedProperties.substitute ( Reader p1, Properties p2 ) :  String
SubstitutedTrimmedProperties.substitute ( String p1, Properties p2 ) :  String
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( File p1 )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( File p1, Properties p2 )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( Properties p1 )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( Reader p1, Properties p2 )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( String p1 )
SubstitutedTrimmedProperties.SubstitutedTrimmedProperties ( String p1, Properties p2 )
SubstitutedTrimmedProperties.variables ( ) :  Properties

cdk-1.2.10.jar, Subtractable.class
package org.omegahat.Environment.DataStructures
Subtractable.subtractValue ( Object p1, boolean p2 ) [abstract] :  Object

cdk-1.2.10.jar, SuperName.class
package org.omegahat.Environment.Parser.Parse
SuperName.SuperName ( )

cdk-1.2.10.jar, SwitchCase.class
package org.omegahat.Environment.Parser.Parse
SwitchCase.addElement ( Object p1 ) :  void
SwitchCase.asString ( ) :  String
SwitchCase.body ( ) :  Object
SwitchCase.body ( Object p1 ) :  Object
SwitchCase.evalBody ( Environment.Interpreter.Evaluator p1 ) :  Object
SwitchCase.getFirstChild ( ) :  AST
SwitchCase.isDefault ( ) :  boolean
SwitchCase.isDefault ( boolean p1 ) :  boolean
SwitchCase.separator ( ) :  String
SwitchCase.SwitchCase ( )
SwitchCase.SwitchCase ( Object p1 )
SwitchCase.toString ( ) :  String

cdk-1.2.10.jar, SwitchStatement.class
package org.omegahat.Environment.Parser.Parse
SwitchStatement.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
SwitchStatement.evalDefault ( Environment.Interpreter.Evaluator p1 ) :  Object
SwitchStatement.match ( Object p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.List p3 ) :  int
SwitchStatement.SwitchStatement ( Object p1, Object p2 )

cdk-1.2.10.jar, Symbols.class
package org.openscience.cdk.config
Symbols.getAtomicNumber ( String symbol ) [static] :  Integer
Symbols.Symbols ( )

cdk-1.2.10.jar, SynchronizedExpression.class
package org.omegahat.Environment.Parser.Parse
SynchronizedExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
SynchronizedExpression.SynchronizedExpression ( )
SynchronizedExpression.SynchronizedExpression ( Object p1, Object p2 )

cdk-1.2.10.jar, SyntaxErrorException.class
package org.omegahat.Environment.Parser.Parse
SyntaxErrorException.column ( ) :  int
SyntaxErrorException.line ( ) :  int
SyntaxErrorException.SyntaxErrorException ( )
SyntaxErrorException.SyntaxErrorException ( Object p1 )
SyntaxErrorException.SyntaxErrorException ( Object p1, String p2 )
SyntaxErrorException.toString ( ) :  String

cdk-1.2.10.jar, SystemErrorHandler.class
package org.omegahat.Environment.Debugger
SystemErrorHandler.error ( Throwable p1, String p2, Environment.Parser.Parse.ExpressionInt p3 ) :  Object
SystemErrorHandler.SystemErrorHandler ( )
SystemErrorHandler.SystemErrorHandler ( Environment.Interpreter.Evaluator p1 )
SystemErrorHandler.SystemErrorHandler ( Throwable p1, String p2, Environment.Interpreter.Evaluator p3 )

cdk-1.2.10.jar, SystemTool.class
package net.sf.jnati
SystemTool.getArchitecture ( ) [static] :  String
SystemTool.getPlatform ( ) [static] :  String
SystemTool.main ( String[ ] args ) [static] :  void
SystemTool.SystemTool ( )

cdk-1.2.10.jar, SystemViewer.class
package org.omegahat.Environment.System
SystemViewer.SystemViewer ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, TabbedElementContainer.class
package org.omegahat.Environment.GUI
TabbedElementContainer.add ( Enumeration p1 ) :  int
TabbedElementContainer.addElement ( Object p1 ) :  Object
TabbedElementContainer.addElement ( Object p1, int p2 ) :  Object
TabbedElementContainer.elementCount ( ) :  int
TabbedElementContainer.getElement ( int p1 ) :  Component
TabbedElementContainer.getElement ( Object p1 ) :  Component
TabbedElementContainer.getIndex ( Object p1 ) :  int
TabbedElementContainer.getName ( Object p1 ) [abstract] :  String
TabbedElementContainer.make ( ) [abstract] :  boolean
TabbedElementContainer.make ( Enumeration p1 ) :  boolean
TabbedElementContainer.makeElement ( Object p1 ) [abstract] :  Component
TabbedElementContainer.removeElement ( Object p1 ) :  boolean
TabbedElementContainer.TabbedElementContainer ( )
TabbedElementContainer.TabbedElementContainer ( Environment.Interpreter.Evaluator p1 )
TabbedElementContainer.TabbedElementContainer ( Environment.Interpreter.Evaluator p1, boolean p2 )

cdk-1.2.10.jar, TableswitchInsn.class
package jas
TableswitchInsn.TableswitchInsn ( int min, int max, Label def, Label[ ] j )

cdk-1.2.10.jar, TailRecursiveClosure.class
package org.omegahat.Environment.Language
TailRecursiveClosure.evalBody ( Environment.Interpreter.Evaluator p1 ) :  Object
TailRecursiveClosure.processBody ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveClosure.tail ( ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveClosure.tail ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveClosure.TailRecursiveClosure ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Interpreter.Evaluator p6 )

cdk-1.2.10.jar, TailRecursiveFunction.class
package org.omegahat.Environment.Language
TailRecursiveFunction.evalBody ( Environment.Interpreter.Evaluator p1 ) :  Object
TailRecursiveFunction.processBody ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveFunction.tail ( ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveFunction.tail ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
TailRecursiveFunction.TailRecursiveFunction ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, String p5, Environment.Interpreter.Evaluator p6 )

cdk-1.2.10.jar, Task.class
package org.omegahat.Environment.Interpreter
Task.error ( ) :  Throwable
Task.error ( Throwable p1 ) :  Throwable
Task.evaluate ( Environment.Interpreter.Evaluator p1 ) :  Object
Task.expression ( ) :  Environment.Parser.Parse.ExpressionInt
Task.expression ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Parser.Parse.ExpressionInt
Task.lexer ( ) :  Environment.Parser.AntlrParser.omegaJavaLexer
Task.lexer ( String p1 ) :  Environment.Parser.AntlrParser.omegaJavaLexer
Task.parse ( ) :  Environment.Parser.Parse.ExpressionInt
Task.Task ( )
Task.Task ( Environment.Parser.Parse.ExpressionInt p1 )
Task.Task ( String p1 )
Task.Task ( String p1, Environment.Parser.Parse.ExpressionInt p2 )
Task.taskString ( ) :  String
Task.taskString ( String p1 ) :  String
Task.value ( ) :  Object
Task.value ( Object p1 ) :  Object
package org.omegahat.Environment.TaskManagement
Task.eval ( ) [abstract] :  Object
Task.eval ( Object[ ] p1 ) [abstract] :  Object

cdk-1.2.10.jar, TaskDisplayFilter.class
package org.omegahat.Environment.IO
TaskDisplayFilter.display ( Environment.Interpreter.Task p1 ) [abstract] :  boolean

cdk-1.2.10.jar, TaskManager.class
package org.omegahat.Environment.TaskManagement
TaskManager.addListener ( Environment.TaskManagement.DistributedTaskListener p1 ) :  int
TaskManager.addTask ( Environment.TaskManagement.Task p1 ) :  int
TaskManager.createQueue ( int p1 ) :  Environment.TaskManagement.TaskQueue
TaskManager.dispatchTask ( Environment.TaskManagement.Task p1 ) :  Object
TaskManager.getTask ( ) :  Environment.TaskManagement.Task
TaskManager.getTask ( boolean p1 ) :  Environment.TaskManagement.Task
TaskManager.isComplete ( ) :  boolean
TaskManager.listeners ( ) :  Vector
TaskManager.listeners ( Vector p1 ) :  Vector
TaskManager.notify ( Environment.TaskManagement.DistributedTaskEvent p1 ) :  boolean
TaskManager.notify ( Environment.TaskManagement.DistributedTaskEvent p1, int p2 ) :  boolean
TaskManager.notify ( Environment.TaskManagement.Task p1, Object p2, int p3 ) :  boolean
TaskManager.removeListener ( Environment.TaskManagement.DistributedTaskListener p1 ) :  boolean
TaskManager.run ( ) :  void
TaskManager.TaskManager ( )
TaskManager.TaskManager ( Environment.TaskManagement.TaskQueue p1 )
TaskManager.TaskManager ( Environment.TaskManagement.TaskQueue p1, boolean p2 )
TaskManager.TaskManager ( int p1 )
TaskManager.TaskManager ( int p1, boolean p2 )
TaskManager.tasks ( ) :  Environment.TaskManagement.TaskQueue
TaskManager.tasks ( Environment.TaskManagement.TaskQueue p1 ) :  Environment.TaskManagement.TaskQueue
TaskManager.warn ( Environment.TaskManagement.Task p1, Exception p2 ) :  boolean

cdk-1.2.10.jar, TaskQueue.class
package org.omegahat.Environment.Interpreter
TaskQueue.TaskQueue ( )
TaskQueue.TaskQueue ( int p1 )
package org.omegahat.Environment.TaskManagement
TaskQueue.addTask ( Environment.TaskManagement.Task p1 ) :  int
TaskQueue.addTask ( Environment.TaskManagement.Task p1, boolean p2 ) :  int
TaskQueue.getTask ( ) :  Environment.TaskManagement.Task
TaskQueue.getTask ( boolean p1, boolean p2 ) :  Environment.TaskManagement.Task
TaskQueue.TaskQueue ( )
TaskQueue.TaskQueue ( Environment.TaskManagement.Task p1 )
TaskQueue.TaskQueue ( Environment.TaskManagement.Task[ ] p1 )
TaskQueue.TaskQueue ( int p1 )
TaskQueue.TaskQueue ( Vector p1 )
TaskQueue.tasks ( ) :  Environment.TaskManagement.TaskQueue
TaskQueue.tasks ( Environment.TaskManagement.Task[ ] p1 ) :  Environment.TaskManagement.TaskQueue
TaskQueue.tasks ( Vector p1 ) :  Environment.TaskManagement.TaskQueue

cdk-1.2.10.jar, TaskQueueEvaluator.class
package org.omegahat.Environment.Interpreter
TaskQueueEvaluator.addTask ( Environment.Interpreter.Task p1 ) :  Environment.Interpreter.Task
TaskQueueEvaluator.addTask ( Environment.Parser.Parse.ExpressionInt p1 ) :  Environment.Interpreter.Task
TaskQueueEvaluator.run ( ) :  void
TaskQueueEvaluator.TaskQueueEvaluator ( )
TaskQueueEvaluator.TaskQueueEvaluator ( Environment.Interpreter.Evaluator p1 )
TaskQueueEvaluator.TaskQueueEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
TaskQueueEvaluator.TaskQueueEvaluator ( Environment.Interpreter.Options p1 )
TaskQueueEvaluator.terminate ( ) :  boolean
TaskQueueEvaluator.terminate ( boolean p1 ) :  boolean

cdk-1.2.10.jar, TextFile.class
package org.omegahat.Environment.IO
TextFile.getContents ( ) :  String
TextFile.getContents ( int p1 ) :  String
TextFile.getContentsBuffer ( ) :  StringBuffer
TextFile.getContentsBuffer ( int p1 ) :  StringBuffer
TextFile.TextFile ( File p1 )
TextFile.TextFile ( String p1 )

cdk-1.2.10.jar, ThreadSuspendButton.class
package org.omegahat.Environment.GUITools
ThreadSuspendButton.actionPerformed ( ActionEvent p1 ) :  void
ThreadSuspendButton.ThreadSuspendButton ( Thread p1 )

cdk-1.2.10.jar, TimedEvaluation.class
package org.omegahat.Environment.lib.Language
TimedEvaluation.duration ( ) :  long
TimedEvaluation.eval ( Environment.Language.Evaluable p1, Environment.Interpreter.Evaluator p2 ) :  Object
TimedEvaluation.getStart ( ) :  long
TimedEvaluation.getStop ( ) :  long
TimedEvaluation.start ( ) :  long
TimedEvaluation.stop ( ) :  long
TimedEvaluation.TimedEvaluation ( )
TimedEvaluation.times ( ) :  long[ ]
TimedEvaluation.times ( long[ ] p1 ) :  long[ ]

cdk-1.2.10.jar, TimedExpressionEvaluation.class
package org.omegahat.Environment.lib.Language
TimedExpressionEvaluation.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
TimedExpressionEvaluation.eval ( Environment.Language.Evaluable p1 ) :  Object
TimedExpressionEvaluation.eval ( Environment.Language.Evaluable p1, Environment.Interpreter.Evaluator p2 ) :  Object
TimedExpressionEvaluation.expression ( ) :  Environment.Language.Evaluable
TimedExpressionEvaluation.expression ( Environment.Language.Evaluable p1 ) :  Environment.Language.Evaluable
TimedExpressionEvaluation.TimedExpressionEvaluation ( Environment.Language.Evaluable p1, Environment.Interpreter.Evaluator p2 )
TimedExpressionEvaluation.TimedExpressionEvaluation ( Environment.Language.Evaluable p1, Environment.Interpreter.Evaluator p2, boolean p3 )
TimedExpressionEvaluation.value ( ) :  Object
TimedExpressionEvaluation.value ( Object p1 ) :  Object

cdk-1.2.10.jar, tool.class
tool.init ( ) :  void
tool.main ( String[ ] p1 ) [static] :  void
tool.tool ( )

cdk-1.2.10.jar, ToolsPanel.class
package org.omegahat.Environment.GUI
ToolsPanel.make ( ) :  boolean
ToolsPanel.ToolsPanel ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, Torsions.class
package org.openscience.cdk.modeling.forcefield
Torsions.functionMMFF94SumET ( GVector coords3d ) :  double
Torsions.get2ndOrderErrorApproximateGradientMMFF94SumET ( ) :  GVector
Torsions.get2ndOrderErrorApproximateHessianMMFF94SumET ( ) :  GMatrix
Torsions.get5thOrderErrorApproximateGradientMMFF94SumET ( ) :  GVector
Torsions.getGradientMMFF94SumET ( ) :  GVector
Torsions.getHessianMMFF94SumET ( ) :  GMatrix
Torsions.set2ndOrderErrorApproximateGradientMMFF94SumET ( GVector coord3d ) :  void
Torsions.set2ndOrderErrorApproximateHessianMMFF94SumET ( GVector coord3d ) :  void
Torsions.set5thOrderApproximateGradientMMFF94SumET ( GVector coord3d ) :  void
Torsions.setGradientMMFF94SumET ( GVector coords3d ) :  void
Torsions.setHessianMMFF94SumET ( GVector coords3d ) :  void
Torsions.setMMFF94TorsionsParameters ( IAtomContainer molecule, Map parameterSet ) :  void
Torsions.setPhi ( GVector coords3d ) :  void
Torsions.Torsions ( )

cdk-1.2.10.jar, TracingEvaluator.class
package org.omegahat.Environment.Interpreter
TracingEvaluator.evaluate ( Environment.Parser.Parse.ExpressionInt p1 ) :  Object
TracingEvaluator.make ( ) :  boolean
TracingEvaluator.parserViewer ( ) :  Environment.Debugger.ParserViewer.ExpressionTreeWindow
TracingEvaluator.parserViewer ( Environment.Debugger.ParserViewer.ExpressionTreeWindow p1 ) :  Environment.Debugger.ParserViewer.ExpressionTreeWindow
TracingEvaluator.TracingEvaluator ( )
TracingEvaluator.TracingEvaluator ( Environment.Interpreter.Evaluator p1 )
TracingEvaluator.TracingEvaluator ( Environment.Interpreter.EvaluatorManager p1 )

cdk-1.2.10.jar, TreeNodeInt.class
package org.omegahat.Environment.Parser.Parse
TreeNodeInt.addChild ( Environment.Parser.Parse.TreeNodeInt p1 ) [abstract] :  Environment.Parser.Parse.TreeNodeInt
TreeNodeInt.children ( ) [abstract] :  Vector
TreeNodeInt.depth ( ) [abstract] :  int
TreeNodeInt.parent ( ) [abstract] :  Environment.Parser.Parse.TreeNodeInt
TreeNodeInt.parent ( Environment.Parser.Parse.TreeNodeInt p1 ) [abstract] :  Environment.Parser.Parse.TreeNodeInt
TreeNodeInt.replaceChild ( Environment.Parser.Parse.TreeNodeInt p1, Environment.Parser.Parse.TreeNodeInt p2 ) [abstract] :  int

cdk-1.2.10.jar, TrimmedProperties.class
package org.omegahat.Environment.Utils
TrimmedProperties.asBoolean ( String p1 ) :  boolean
TrimmedProperties.isBoolean ( String p1 ) :  boolean
TrimmedProperties.load ( File p1 ) :  void
TrimmedProperties.load ( InputStream p1 ) :  void
TrimmedProperties.merge ( Properties p1 ) :  int
TrimmedProperties.merge ( Properties p1, boolean p2 ) :  int
TrimmedProperties.parse ( String p1 ) :  boolean
TrimmedProperties.processElement ( String p1, String p2 ) :  boolean
TrimmedProperties.processElements ( ) :  int
TrimmedProperties.stringList ( String p1 ) :  String[ ]
TrimmedProperties.stringList ( String p1, char p2 ) :  String[ ]
TrimmedProperties.stripQuotes ( ) :  boolean
TrimmedProperties.stripQuotes ( boolean p1 ) :  boolean
TrimmedProperties.trim ( ) :  void
TrimmedProperties.TrimmedProperties ( )
TrimmedProperties.TrimmedProperties ( boolean p1 )
TrimmedProperties.TrimmedProperties ( Environment.IO.InputFileInt p1 )
TrimmedProperties.TrimmedProperties ( Environment.IO.InputFileInt p1, boolean p2 )
TrimmedProperties.TrimmedProperties ( File p1 )
TrimmedProperties.TrimmedProperties ( File p1, boolean p2 )
TrimmedProperties.TrimmedProperties ( InputStream p1 )
TrimmedProperties.TrimmedProperties ( Properties p1 )
TrimmedProperties.TrimmedProperties ( Properties p1, boolean p2 )
TrimmedProperties.TrimmedProperties ( String p1 )
TrimmedProperties.TrimmedProperties ( String p1, boolean p2 )

cdk-1.2.10.jar, TruncatedObjectDisplay.class
package org.omegahat.Environment.IO
TruncatedObjectDisplay.above ( ) :  int
TruncatedObjectDisplay.above ( int p1 ) :  int
TruncatedObjectDisplay.below ( ) :  int
TruncatedObjectDisplay.below ( int p1 ) :  int
TruncatedObjectDisplay.defaultDisplay ( Object p1 ) :  boolean
TruncatedObjectDisplay.display ( Class p1 ) :  boolean
TruncatedObjectDisplay.display ( Enumeration p1 ) :  boolean
TruncatedObjectDisplay.display ( Hashtable p1 ) :  boolean
TruncatedObjectDisplay.display ( Object p1, int p2 ) :  boolean
TruncatedObjectDisplay.display ( Object p1, int p2, int p3 ) :  boolean
TruncatedObjectDisplay.display ( Vector p1 ) :  boolean
TruncatedObjectDisplay.displayArray ( Object p1 ) :  boolean
TruncatedObjectDisplay.TruncatedObjectDisplay ( )
TruncatedObjectDisplay.TruncatedObjectDisplay ( PrintWriter p1 )
TruncatedObjectDisplay.TruncatedObjectDisplay ( PrintWriter p1, int p2, int p3 )

cdk-1.2.10.jar, TryCatch.class
package org.omegahat.Environment.Parser.Parse
TryCatch.asString ( ) :  String
TryCatch.body ( ) :  Environment.Parser.Parse.StatementList
TryCatch.body ( Environment.Parser.Parse.StatementList p1 ) :  Environment.Parser.Parse.StatementList
TryCatch.catches ( ) :  Environment.Parser.Parse.List
TryCatch.catches ( Environment.Parser.Parse.List p1 ) :  Environment.Parser.Parse.List
TryCatch.catchThrowable ( Throwable p1, Environment.Interpreter.Evaluator p2 ) :  Object
TryCatch.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
TryCatch.getCatchBody ( Throwable p1 ) :  Environment.Parser.Parse.Catch
TryCatch.getFirstChild ( ) :  AST
TryCatch.makeExceptionTable ( Environment.Interpreter.Evaluator p1 ) :  int
TryCatch.TryCatch ( Environment.Parser.Parse.StatementList p1, Environment.Parser.Parse.List p2 )
TryCatch.TryCatch ( Environment.Parser.Parse.StatementList p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Catch p3 )
TryCatch.TryCatch ( Environment.Parser.Parse.StatementList p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.StatementList p3 )

cdk-1.2.10.jar, Type.class
package org.omegahat.Environment.Parser.Parse
Type.isFinal ( ) :  boolean
Type.isFinal ( boolean p1 ) :  boolean
Type.toString ( ) :  String
Type.Type ( )
Type.type ( ) :  Environment.Parser.Parse.Name
Type.Type ( Environment.Parser.Parse.Name p1 )
Type.type ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
Type.Type ( String p1 )
Type.type ( String p1 ) :  Environment.Parser.Parse.Name

cdk-1.2.10.jar, TypedDatabase.class
package org.omegahat.Environment.Databases
TypedDatabase.assign ( String p1, Object p2 ) :  boolean
TypedDatabase.checkType ( String p1, Object p2 ) :  boolean
TypedDatabase.remove ( String p1 ) :  Object
TypedDatabase.setType ( Environment.Parser.Parse.Name p1, Class p2 ) :  Class
TypedDatabase.setType ( String p1, Class p2 ) :  Class
TypedDatabase.setType ( String p1, Environment.Parser.Parse.Name p2 ) :  Class
TypedDatabase.setType ( String p1, Environment.Parser.Parse.Type p2 ) :  Class
TypedDatabase.type ( String p1 ) :  Class
TypedDatabase.TypedDatabase ( )
TypedDatabase.TypedDatabase ( int p1 )
TypedDatabase.TypedDatabase ( String p1 )

cdk-1.2.10.jar, TypedDatabaseInt.class
package org.omegahat.Environment.Databases
TypedDatabaseInt.setType ( String p1, Class p2 ) [abstract] :  Class

cdk-1.2.10.jar, TypeTaskDisplay.class
package org.omegahat.Environment.IO
TypeTaskDisplay.display ( Environment.Interpreter.Task p1 ) :  boolean
TypeTaskDisplay.TypeTaskDisplay ( )
TypeTaskDisplay.TypeTaskDisplay ( PrintWriter p1 )
TypeTaskDisplay.TypeTaskDisplay ( PrintWriter p1, int p2, int p3 )

cdk-1.2.10.jar, UnaryExpression.class
package org.omegahat.Environment.Parser.Parse
UnaryExpression.asBoolean ( Object p1 ) :  boolean
UnaryExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
UnaryExpression.expression ( ) :  Object
UnaryExpression.expression ( Object p1 ) :  Object
UnaryExpression.getFirstChild ( ) :  AST
UnaryExpression.isReassignment ( ) :  boolean
UnaryExpression.op ( ) :  int
UnaryExpression.op ( int p1 ) :  int
UnaryExpression.operate ( Object p1 ) :  Object
UnaryExpression.opString ( ) :  String
UnaryExpression.toString ( ) :  String
UnaryExpression.UnaryExpression ( Object p1, int p2 )

cdk-1.2.10.jar, UnavailableClassNode.class
package org.omegahat.Environment.Tools.ClassHierarchy
UnavailableClassNode.findInterfaces ( ) :  int
UnavailableClassNode.findParents ( ) :  int
UnavailableClassNode.name ( ) :  String
UnavailableClassNode.name ( String p1 ) :  String
UnavailableClassNode.UnavailableClassNode ( String p1 )

cdk-1.2.10.jar, UpdateUnaryExpression.class
package org.omegahat.Environment.Parser.Parse
UpdateUnaryExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
UpdateUnaryExpression.isPrefix ( ) :  boolean
UpdateUnaryExpression.isPrefix ( boolean p1 ) :  boolean
UpdateUnaryExpression.operate ( Object p1 ) :  Object
UpdateUnaryExpression.toNumber ( double p1, Object p2 ) [static] :  Object
UpdateUnaryExpression.toString ( ) :  String
UpdateUnaryExpression.UpdateUnaryExpression ( Object p1, int p2 )
UpdateUnaryExpression.UpdateUnaryExpression ( Object p1, int p2, boolean p3 )

cdk-1.2.10.jar, URLClassList.class
package org.omegahat.Environment.Tools.ClassList
URLClassList.base ( ) :  URL
URLClassList.base ( URL p1 ) :  URL
URLClassList.lookup ( ) :  int
URLClassList.lookup ( ZipInputStream p1 ) :  int
URLClassList.sourceIsNewer ( ) :  boolean
URLClassList.URLClassList ( URL p1 )

cdk-1.2.10.jar, URLClassLoader.class
package org.omegahat.Environment.System
URLClassLoader.base ( ) :  URL
URLClassLoader.base ( URL p1 ) :  URL
URLClassLoader.getInputStream ( String p1 ) :  InputStream
URLClassLoader.URLClassLoader ( URL p1 )

cdk-1.2.10.jar, UserArea.class
package org.omegahat.Environment.GUI
UserArea.make ( ) :  boolean
UserArea.output ( ) :  Object
UserArea.UserArea ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, UserClass.class
package org.omegahat.Environment.Language.UserClasses
UserClass.createInstance ( ) :  Environment.Language.UserClasses.UserClassInstance
UserClass.UserClass ( )
UserClass.UserClass ( int p1 )
UserClass.UserClass ( String p1 )
UserClass.UserClass ( String p1, Environment.Language.UserClasses.UserClass p2 )
UserClass.UserClass ( String p1, Environment.Language.UserClasses.UserClass[ ] p2 )
UserClass.UserClass ( String p1, Vector p2 )

cdk-1.2.10.jar, UserClassChangeEvent.class
package org.omegahat.Environment.Language.UserClasses
UserClassChangeEvent.UserClassChangeEvent ( Object p1 )

cdk-1.2.10.jar, UserClassChangeListener.class
package org.omegahat.Environment.Language.UserClasses
UserClassChangeListener.classRepresentationChanged ( Environment.Language.UserClasses.UserClassChangeEvent p1, boolean p2 ) [abstract] :  boolean

cdk-1.2.10.jar, UserClassEvaluator.class
package org.omegahat.Environment.Interpreter
UserClassEvaluator.addMethod ( Environment.Language.Method p1, Environment.Parser.Parse.Name p2 ) :  boolean
UserClassEvaluator.classManager ( ) :  Environment.Language.UserClasses.UserClassManager
UserClassEvaluator.classManager ( Environment.Language.UserClasses.UserClassManager p1 ) :  Environment.Language.UserClasses.UserClassManager
UserClassEvaluator.createInstance ( Environment.Language.UserClasses.UserClass p1 ) :  Environment.Language.UserClasses.UserClassInstance
UserClassEvaluator.createInstance ( Environment.Parser.Parse.Name p1 ) :  Environment.Language.UserClasses.UserClassInstance
UserClassEvaluator.createInstance ( String p1 ) :  Environment.Language.UserClasses.UserClassInstance
UserClassEvaluator.defineClass ( Environment.Language.UserClasses.AbstractUserClass p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.defineClass ( String p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.defineClass ( String p1, boolean p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.defineClass ( String p1, String p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.defineClass ( String p1, Vector p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.defineClass ( String p1, Vector p2, boolean p3 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.DefineUserClass ( String p1 ) :  Object
UserClassEvaluator.DefineUserClass ( String p1, boolean p2 ) :  Object
UserClassEvaluator.DefineUserClass ( String p1, boolean p2, boolean p3 ) :  Object
UserClassEvaluator.findUserClass ( Environment.Parser.Parse.Name p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.findUserClass ( String p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassEvaluator.parseClass ( String p1 ) :  Object
UserClassEvaluator.parser ( Tokenizer p1 ) :  Environment.Parser.AntlrParser.omegaJavaGrammar
UserClassEvaluator.UserClassEvaluator ( )
UserClassEvaluator.UserClassEvaluator ( Environment.Interpreter.Evaluator p1 )
UserClassEvaluator.UserClassEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
UserClassEvaluator.UserClassEvaluator ( Environment.Interpreter.Options p1 )

cdk-1.2.10.jar, UserClassFieldAccess.class
package org.omegahat.Environment.Parser.Parse
UserClassFieldAccess.getFieldValue ( Object p1, Class p2, Environment.Interpreter.Evaluator p3 ) :  Object
UserClassFieldAccess.UserClassFieldAccess ( Environment.Parser.Parse.ExpressionInt p1, String p2 )
UserClassFieldAccess.UserClassFieldAccess ( Environment.Parser.Parse.Name p1, String p2 )

cdk-1.2.10.jar, UserClassFunctionExpression.class
package org.omegahat.Environment.Parser.Parse
UserClassFunctionExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
UserClassFunctionExpression.name ( ) :  Environment.Parser.Parse.Name
UserClassFunctionExpression.name ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
UserClassFunctionExpression.UserClassFunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 )

cdk-1.2.10.jar, UserClassGenerator.class
package org.omegahat.Environment.Language.UserClasses
UserClassGenerator.addClassMethod ( String p1, String p2, Environment.Language.Function p3 ) :  boolean
UserClassGenerator.addConstructor ( Constructor p1 ) :  CodeAttr
UserClassGenerator.addConstructor ( String p1, Environment.Language.Function p2 ) :  CodeAttr
UserClassGenerator.addConstructors ( ) :  boolean
UserClassGenerator.addEvaluatorField ( ) :  boolean
UserClassGenerator.addEvaluatorGetMethod ( String p1, String p2 ) :  boolean
UserClassGenerator.addEvaluatorGetMethod ( String p1, String p2, int p3 ) :  boolean
UserClassGenerator.addLocalField ( Environment.Parser.Parse.LocalVariable p1 ) :  boolean
UserClassGenerator.addStaticFields ( ) :  boolean
UserClassGenerator.addStaticInitializer ( ) :  boolean
UserClassGenerator.createFields ( Environment.Parser.Parse.List p1 ) :  int
UserClassGenerator.createMethods ( Environment.Language.UserClasses.MethodsCollection p1 ) :  int
UserClassGenerator.createMethods ( String p1, Environment.Language.Method p2 ) :  boolean
UserClassGenerator.make ( ) :  boolean
UserClassGenerator.make ( boolean p1 ) :  boolean
UserClassGenerator.make ( Environment.Parser.Parse.ClassDefinition p1, boolean p2 ) :  boolean
UserClassGenerator.matchOverriddenMethod ( Environment.Language.Function p1 ) :  Method
UserClassGenerator.modifier ( Environment.Parser.Parse.Modifier p1 ) :  short
UserClassGenerator.modifier ( Environment.Parser.Parse.Modifier p1, short p2 ) :  short
UserClassGenerator.omegaClassDef ( ) :  Environment.Parser.Parse.ClassDefinition
UserClassGenerator.omegaClassDef ( Environment.Parser.Parse.ClassDefinition p1 ) :  Environment.Parser.Parse.ClassDefinition
UserClassGenerator.overrides ( Constructor p1 ) :  boolean
UserClassGenerator.returnType ( Environment.Language.Function p1 ) :  Class
UserClassGenerator.superClassName ( ) :  String
UserClassGenerator.UserClassGenerator ( )
UserClassGenerator.UserClassGenerator ( Environment.Parser.Parse.ClassDefinition p1 )
UserClassGenerator.UserClassGenerator ( Environment.Parser.Parse.ClassDefinition p1, boolean p2 )
UserClassGenerator.UserClassGenerator ( String p1, String p2, String[ ] p3 )

cdk-1.2.10.jar, UserClassInstance.class
package org.omegahat.Environment.Language.UserClasses
UserClassInstance.UserClassInstance ( )
UserClassInstance.UserClassInstance ( Environment.Language.UserClasses.UserClass p1 )
UserClassInstance.UserClassInstance ( Environment.Language.UserClasses.UserClass p1, Environment.Parser.Parse.List p2 )
UserClassInstance.UserClassInstance ( Environment.Language.UserClasses.UserClass p1, Object[ ] p2 )
UserClassInstance.UserClassInstance ( int p1 )

cdk-1.2.10.jar, UserClassLoader.class
package org.omegahat.Environment.System
UserClassLoader.add ( File p1 ) :  Object
UserClassLoader.add ( String p1 ) :  Object
UserClassLoader.classes ( ) :  Hashtable
UserClassLoader.classes ( Hashtable p1 ) :  Hashtable
UserClassLoader.containers ( ) :  Environment.Utils.OrderedTable
UserClassLoader.containers ( Environment.Utils.OrderedTable p1 ) :  Environment.Utils.OrderedTable
UserClassLoader.defineClass ( String p1 ) :  Class
UserClassLoader.defineClass ( String p1, byte[ ] p2 ) :  Class
UserClassLoader.Import ( String p1 ) :  Object
UserClassLoader.loadClass ( String p1 ) :  Class
UserClassLoader.loadClass ( String p1, boolean p2 ) :  Class
UserClassLoader.parent ( ) :  ClassLoader
UserClassLoader.parent ( ClassLoader p1 ) :  ClassLoader
UserClassLoader.readBytes ( InputStream p1 ) :  byte[ ]
UserClassLoader.UserClassLoader ( )
UserClassLoader.UserClassLoader ( ClassLoader p1 )
UserClassLoader.UserClassLoader ( File p1 )

cdk-1.2.10.jar, UserClassManager.class
package org.omegahat.Environment.Language.UserClasses
UserClassManager.defineClass ( Environment.Language.UserClasses.AbstractUserClass p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassManager.defineClass ( Environment.Language.UserClasses.UserClassPackage p1, Environment.Language.UserClasses.AbstractUserClass p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassManager.defineClass ( Environment.Parser.Parse.Name p1, Environment.Language.UserClasses.AbstractUserClass p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassManager.defineClass ( String p1, Environment.Language.UserClasses.AbstractUserClass p2 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassManager.getClass ( Environment.Parser.Parse.Name p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassManager.getPackage ( Environment.Parser.Parse.Name p1 ) :  Environment.Language.UserClasses.UserClassPackage
UserClassManager.getPackage ( String p1 ) :  Environment.Language.UserClasses.UserClassPackage
UserClassManager.getPackage ( String p1, boolean p2 ) :  Environment.Language.UserClasses.UserClassPackage
UserClassManager.UserClassManager ( )
UserClassManager.UserClassManager ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, UserClassMethod.class
package org.omegahat.Environment.Language.UserClasses
UserClassMethod.source ( ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassMethod.source ( Environment.Language.UserClasses.AbstractUserClass p1 ) :  Environment.Language.UserClasses.AbstractUserClass
UserClassMethod.UserClassMethod ( )
UserClassMethod.UserClassMethod ( Environment.Language.Function p1, Environment.Language.UserClasses.AbstractUserClass p2 )
UserClassMethod.UserClassMethod ( Environment.Language.Method p1 )
UserClassMethod.UserClassMethod ( Environment.Language.Method p1, Environment.Language.UserClasses.AbstractUserClass p2 )
UserClassMethod.UserClassMethod ( String p1 )
UserClassMethod.UserClassMethod ( String p1, Environment.Language.Function p2, Environment.Language.UserClasses.AbstractUserClass p3 )

cdk-1.2.10.jar, UserClassMethodCall.class
package org.omegahat.Environment.Parser.Parse
UserClassMethodCall.findEvalMethod ( Object p1, Environment.Interpreter.Evaluator p2 ) :  Object
UserClassMethodCall.UserClassMethodCall ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2 )
UserClassMethodCall.UserClassMethodCall ( Environment.Parser.Parse.ExpressionInt p1, String p2, Environment.Parser.Parse.List p3 )
UserClassMethodCall.UserClassMethodCall ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2 )
UserClassMethodCall.UserClassMethodCall ( String p1, Environment.Parser.Parse.List p2 )
UserClassMethodCall.UserClassMethodCall ( String p1, String[ ] p2 )

cdk-1.2.10.jar, UserClassMethodExpression.class
package org.omegahat.Environment.Parser.Parse
UserClassMethodExpression.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
UserClassMethodExpression.fullName ( ) :  Environment.Parser.Parse.Name
UserClassMethodExpression.fullName ( Environment.Parser.Parse.Name p1 ) :  Environment.Parser.Parse.Name
UserClassMethodExpression.UserClassMethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 )

cdk-1.2.10.jar, UserClassOmegaParser.class
package org.omegahat.Environment.Parser.AntlrParser
UserClassOmegaParser.createFieldAcces ( Environment.Parser.Parse.ExpressionInt p1, String p2 ) :  Environment.Parser.Parse.FieldAccess
UserClassOmegaParser.createFieldAcces ( Environment.Parser.Parse.Name p1, String p2 ) :  Environment.Parser.Parse.FieldAccess
UserClassOmegaParser.createFunctionExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 ) :  Environment.Parser.Parse.FunctionExpression
UserClassOmegaParser.createMethodCall ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2 ) :  Environment.Parser.Parse.MethodCall
UserClassOmegaParser.createMethodCall ( Environment.Parser.Parse.FieldAccess p1, String p2, Environment.Parser.Parse.List p3 ) :  Environment.Parser.Parse.MethodCall
UserClassOmegaParser.createMethodCall ( Environment.Parser.Parse.Name p1, Environment.Parser.Parse.List p2 ) :  Environment.Parser.Parse.MethodCall
UserClassOmegaParser.createMethodExpression ( Environment.Parser.Parse.ExpressionInt p1, Environment.Parser.Parse.List p2, Environment.Parser.Parse.Name p3, Environment.Parser.Parse.List p4, Environment.Parser.Parse.Name p5, Environment.Parser.Parse.FunctionParameterModifier p6 ) :  Environment.Parser.Parse.MethodExpression
UserClassOmegaParser.UserClassOmegaParser ( Tokenizer p1 )

cdk-1.2.10.jar, UserClassPackage.class
package org.omegahat.Environment.Language.UserClasses
UserClassPackage.parent ( ) :  Environment.Language.UserClasses.UserClassPackage
UserClassPackage.parent ( Environment.Language.UserClasses.UserClassPackage p1 ) :  Environment.Language.UserClasses.UserClassPackage
UserClassPackage.UserClassPackage ( )
UserClassPackage.UserClassPackage ( String p1 )
UserClassPackage.UserClassPackage ( String p1, Environment.Language.UserClasses.UserClassPackage p2 )

cdk-1.2.10.jar, UserInput.class
package org.omegahat.Environment.GUI
UserInput.actionPerformed ( ActionEvent p1 ) :  void
UserInput.addListener ( ) :  void
UserInput.createDisplayAttributes ( ) :  boolean
UserInput.getValue ( String p1 ) :  Object
UserInput.make ( ) :  boolean
UserInput.prompt ( ) :  boolean
UserInput.putValue ( String p1, Object p2 ) :  void
UserInput.UserInput ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, UtilityEvaluator.class
package org.omegahat.Environment.Interpreter
UtilityEvaluator.evaluator ( ) :  Environment.Interpreter.Evaluator
UtilityEvaluator.exec ( String p1 ) :  Object
UtilityEvaluator.exec ( String p1, boolean p2 ) :  Object
UtilityEvaluator.findFile ( String p1 ) :  Object
UtilityEvaluator.getEvaluator ( ) :  Environment.Interpreter.Evaluator
UtilityEvaluator.setProperty ( String p1, String p2 ) :  String
UtilityEvaluator.setProperty ( String p1, String p2, boolean p3 ) :  String
UtilityEvaluator.UtilityEvaluator ( )
UtilityEvaluator.UtilityEvaluator ( Environment.Interpreter.Evaluator p1 )
UtilityEvaluator.UtilityEvaluator ( Environment.Interpreter.EvaluatorManager p1 )
UtilityEvaluator.UtilityEvaluator ( Environment.Interpreter.Options p1 )

cdk-1.2.10.jar, VanDerWaalsInteractions.class
package org.openscience.cdk.modeling.forcefield
VanDerWaalsInteractions.functionCCGSumEvdWAv ( GVector coords3d, double[ ] s ) :  double
VanDerWaalsInteractions.functionCCGSumEvdWSK ( GVector coords3d, double[ ] s ) :  double
VanDerWaalsInteractions.get2ndOrderErrorApproximateGradientMMFF94SumEvdW ( ) :  GVector
VanDerWaalsInteractions.get5OrderApproximateGradientMMFF94SumEvdW ( ) :  GVector
VanDerWaalsInteractions.getAtomDistance ( ) :  double[ ]
VanDerWaalsInteractions.getAtomsDistancesFirstDerivative ( ) :  double[ ][ ]
VanDerWaalsInteractions.getBondLengthsSecondDerivative ( ) :  double[ ][ ][ ]
VanDerWaalsInteractions.getForHessianMMFF94SumEvdW ( ) :  double[ ]
VanDerWaalsInteractions.getFunctionMMFF94SumEvdW ( ) :  double
VanDerWaalsInteractions.getGradientMMFF94SumEvdW ( ) :  GVector
VanDerWaalsInteractions.getHessianMMFF94SumEvdW ( ) :  GMatrix
VanDerWaalsInteractions.set2ndOrderErrorApproximateGradientMMFF94SumEvdW ( GVector coord3d ) :  void
VanDerWaalsInteractions.set5thOrderErrorApproximateGradientMMFF94SumEvdW ( GVector coord3d ) :  void
VanDerWaalsInteractions.setAtomDistance ( GVector coords3d ) :  void
VanDerWaalsInteractions.setAtomsDistancesFirstOrderDerivative ( GVector coord3d ) :  void
VanDerWaalsInteractions.setBondLengthsSecondDerivative ( GVector coord3d ) :  void
VanDerWaalsInteractions.setFunctionMMFF94SumEvdW ( GVector coords3d ) :  void
VanDerWaalsInteractions.setGradientMMFF94SumEvdW ( GVector coords3d ) :  void
VanDerWaalsInteractions.setHessianMMFF94SumEvdW ( GVector coord3d ) :  void
VanDerWaalsInteractions.setMMFF94VanDerWaalsParameters ( IAtomContainer molecule, Map parameterSet ) :  void
VanDerWaalsInteractions.VanDerWaalsInteractions ( )

cdk-1.2.10.jar, Var.class
package jas
Var.Var ( short vacc, CP name, CP sig, ConstAttr cattr )

cdk-1.2.10.jar, VariableExpansion.class
package org.omegahat.Environment.Tools.VariableExpansion
VariableExpansion.expandString ( ) :  String
VariableExpansion.expandString ( boolean p1 ) :  String
VariableExpansion.getUseSelfAsResolved ( ) :  boolean
VariableExpansion.isBashCompliant ( ) :  boolean
VariableExpansion.isSet ( String p1 ) :  boolean
VariableExpansion.mAlternative ( boolean p1 ) :  void
VariableExpansion.mEscapedDollar ( boolean p1 ) :  void
VariableExpansion.mId ( boolean p1 ) :  void
VariableExpansion.mOmegahat ( boolean p1 ) :  void
VariableExpansion.mOther ( boolean p1 ) :  void
VariableExpansion.mSimpleVar ( boolean p1 ) :  void
VariableExpansion.mTilde ( boolean p1 ) :  void
VariableExpansion.mVarRef ( boolean p1 ) :  void
VariableExpansion.mWS ( boolean p1 ) :  void
VariableExpansion.nextToken ( ) :  Token
VariableExpansion.properties ( ) :  Properties
VariableExpansion.properties ( Properties p1 ) :  Properties
VariableExpansion.resolve ( String p1 ) :  String
VariableExpansion.resolve ( String p1, String p2 ) :  String
VariableExpansion.result ( ) :  String
VariableExpansion.setBashCompliant ( ) :  boolean
VariableExpansion.setUseSelfAsResolved ( boolean p1 ) :  boolean
VariableExpansion.VariableExpansion ( InputBuffer p1 )
VariableExpansion.VariableExpansion ( InputStream p1 )
VariableExpansion.VariableExpansion ( InputStream p1, Properties p2 )
VariableExpansion.VariableExpansion ( Reader p1 )
VariableExpansion.VariableExpansion ( Reader p1, Properties p2 )
VariableExpansion.VariableExpansion ( String p1, Properties p2 )

cdk-1.2.10.jar, VarSequenceFunctions.class
package org.omegahat.Environment.lib.Language
VarSequenceFunctions.append ( Object[ ] p1, Object p2, int p3, boolean p4, Environment.Interpreter.Evaluator p5 ) [static] :  Object[ ]
VarSequenceFunctions.append ( Object[ ] p1, Object[ ] p2, int p3 ) [static] :  Object[ ]
VarSequenceFunctions.c ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2 ) [static] :  Object
VarSequenceFunctions.c ( Environment.Parser.Parse.List p1, Environment.Interpreter.Evaluator p2, boolean p3 ) [static] :  Object
VarSequenceFunctions.c ( Hashtable p1, Environment.Interpreter.Evaluator p2 ) [static] :  Object
VarSequenceFunctions.getLength ( Object p1, Environment.Interpreter.Evaluator p2 ) [static] :  int
VarSequenceFunctions.VarSequenceFunctions ( )

cdk-1.2.10.jar, vector.class
package org.omegahat.Environment.DataStructures
vector.asArray ( ) :  Object[ ]
vector.data ( ) :  Object
vector.data ( int p1 ) :  Object
vector.data ( int p1, Object p2 ) :  Object
vector.data ( Object p1 ) :  Object
vector.data ( Object[ ] p1 ) :  Object
vector.element ( int p1 ) :  Object
vector.exp ( Environment.DataStructures.vector p1 ) :  Object
vector.isNA ( ) :  Environment.DataStructures.logical
vector.isNA ( int p1 ) :  Environment.DataStructures.logical
vector.length ( ) :  int
vector.minus ( Environment.DataStructures.vector p1 ) :  Object
vector.multiply ( Environment.DataStructures.vector p1 ) :  Object
vector.plus ( Environment.DataStructures.vector p1 ) :  Object
vector.vector ( )
package org.omegahat.Environment.ObjectDataStructures
vector.add ( double p1, int p2 ) :  void
vector.add ( Object p1, int p2 ) :  void
vector.addElement ( Object p1 ) :  int
vector.addValue ( Object p1, boolean p2 ) :  Object
vector.apply ( Environment.Language.Function p1 ) :  Environment.ObjectDataStructures.vector
vector.apply ( String p1 ) :  Environment.ObjectDataStructures.vector
vector.asArray ( ) :  Object[ ]
vector.assignElement ( int p1, Object p2 ) :  Object
vector.assignSubset ( Object p1, Object p2 ) :  Object
vector.convertElement ( Object p1 ) [abstract] :  Object
vector.copy ( boolean p1 ) :  Environment.ObjectDataStructures.vector
vector.createElement ( double p1 ) :  Object
vector.createElement ( double p1, Object p2 ) :  Object
vector.createVariable ( ) :  DataStructures.Data.VariableInt
vector.data ( ) :  Vector
vector.data ( int p1 ) :  Vector
vector.data ( int p1, Object p2 ) :  Vector
vector.data ( Object p1 ) :  Vector
vector.data ( Object[ ] p1 ) :  Vector
vector.divide ( Environment.ObjectDataStructures.vector p1 ) :  Object
vector.divide ( Number p1 ) :  Object
vector.divideValue ( Object p1, boolean p2 ) :  Object
vector.element ( int p1 ) :  Object
vector.elementMathOp ( Object p1, double p2, int p3 ) :  Object
vector.elementToString ( Object p1 ) :  String
vector.exp ( Environment.ObjectDataStructures.vector p1 ) :  Object
vector.findMethod ( String p1, Object p2 ) :  Method
vector.getDataFrame ( ) :  DataStructures.Data.DataFrameInt
vector.getName ( ) :  String
vector.isNA ( ) :  Environment.ObjectDataStructures.logical
vector.isNA ( int p1 ) :  Environment.ObjectDataStructures.logical
vector.length ( ) :  int
vector.length ( int p1 ) :  int
vector.length ( int p1, boolean p2 ) :  int
vector.mathOperation ( double p1, int p2 ) :  Environment.ObjectDataStructures.vector
vector.mathOperation ( Environment.ObjectDataStructures.vector p1, int p2 ) :  Object
vector.mathOperation ( Object p1, boolean p2, int p3 ) :  Object
vector.metaData ( ) :  Hashtable
vector.minus ( Environment.ObjectDataStructures.vector p1 ) :  Object
vector.minus ( Number p1 ) :  Object
vector.multiply ( Environment.ObjectDataStructures.vector p1 ) :  Object
vector.multiply ( Number p1 ) :  Object
vector.multiplyValue ( Object p1, boolean p2 ) :  Object
vector.numObservations ( ) :  long
vector.plus ( Environment.ObjectDataStructures.vector p1 ) :  Object
vector.plus ( Number p1 ) :  Object
vector.read ( InputStream p1 ) :  int
vector.read ( Reader p1 ) :  int
vector.separator ( ) :  String
vector.setDataFrame ( DataStructures.Data.DataFrameInt p1 ) :  DataStructures.Data.DataFrameInt
vector.setName ( String p1 ) :  String
vector.subset ( Object p1, boolean p2 ) :  Object
vector.subtractValue ( Object p1, boolean p2 ) :  Object
vector.targetClass ( ) [abstract] :  Class
vector.toString ( ) :  String
vector.value ( long p1 ) :  Object
vector.values ( DataStructures.Data.SelectorInt p1 ) :  DataStructures.Data.VariableInt
vector.values ( int[ ] p1 ) :  DataStructures.Data.VariableInt
vector.vector ( )
vector.vector ( Environment.ObjectDataStructures.vector p1, boolean p2 )
vector.vector ( int p1 )
vector.vector ( long p1 )
vector.vector ( long p1, boolean p2 )

cdk-1.2.10.jar, ViewerFrame.class
package org.omegahat.Environment.GUI
ViewerFrame.make ( Component p1, String p2 ) :  void
ViewerFrame.ViewerFrame ( )
ViewerFrame.ViewerFrame ( Component p1, String p2 )

cdk-1.2.10.jar, While.class
package org.omegahat.Environment.Parser.Parse
While.doLoop ( ) :  boolean
While.doLoop ( boolean p1 ) :  boolean
While.eval ( Environment.Interpreter.Evaluator p1 ) :  Object
While.getFirstChild ( ) :  AST
While.prefix ( ) :  String
While.suffix ( ) :  String
While.toString ( ) :  String
While.While ( Object p1, Object p2 )
While.While ( Object p1, Object p2, boolean p3 )

cdk-1.2.10.jar, WorkArea.class
package org.omegahat.Environment.GUI
WorkArea.addToolbarElements ( JToolBar p1 ) :  int
WorkArea.createToolbar ( ) :  JToolBar
WorkArea.getPreferredSize ( ) :  Dimension
WorkArea.make ( ) :  boolean
WorkArea.output ( ) :  Object
WorkArea.WorkArea ( Environment.Interpreter.Evaluator p1 )

cdk-1.2.10.jar, ZipClassLoader.class
package org.omegahat.Environment.System
ZipClassLoader.defineClass ( String p1 ) :  Class
ZipClassLoader.getInputStream ( String p1 ) :  InputStream
ZipClassLoader.ZipClassLoader ( )
ZipClassLoader.ZipClassLoader ( File p1 )
ZipClassLoader.ZipClassLoader ( File p1, ZipFile p2 )
ZipClassLoader.zipFile ( ) :  ZipFile
ZipClassLoader.zipFile ( File p1 ) :  ZipFile
ZipClassLoader.zipFile ( ZipFile p1 ) :  ZipFile

cdk-1.2.10.jar, ZipInputFile.class
package org.omegahat.Environment.IO
ZipInputFile.archive ( ) :  ZipFile
ZipInputFile.archive ( ZipFile p1 ) :  ZipFile
ZipInputFile.asURL ( ) :  URL
ZipInputFile.canRead ( ) :  boolean
ZipInputFile.getContents ( ) :  String
ZipInputFile.getInputStream ( ) :  InputStream
ZipInputFile.ZipInputFile ( String p1, ZipFile p2 )
ZipInputFile.ZipInputFile ( ZipEntry p1, ZipFile p2 )

cdk-1.2.10.jar, ZipNameFilter.class
package org.omegahat.Environment.Databases
ZipNameFilter.accept ( File p1, String p2 ) :  boolean
ZipNameFilter.ZipNameFilter ( )
ZipNameFilter.ZipNameFilter ( String p1 )

to the top

Problems with Data Types, High Severity (584)

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class DatabaseListModel.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class DatabaseObjectRenderer.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class tool.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class AsciiCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class CatchEntry.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Catchtable.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class ClassCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class ClassEnv.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class CodeAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class ConstAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class CP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class DoubleCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class ExceptAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class FieldCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class FloatCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class GenericAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class IincInsn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Insn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class IntegerCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class InterfaceCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class InvokeinterfaceInsn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class jasError.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Label.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class LineTableAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class LocalVarEntry.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class LocalVarTableAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class LongCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class LookupswitchInsn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Method.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class MethodCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class MultiarrayInsn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class NameTypeCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class SourceAttr.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class StringCP.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class TableswitchInsn.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Var.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class ArtefactLocation.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class SystemTool.

	Change	Effect
1	This interface has been removed.	Recompilation of a client program may be terminated with the message: cannot find class IInchiGenerator.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_BOND_STEREO.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_BOND_TYPE.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_KEY.
2	Field NOT_INCHI_INPUT of type INCHI_KEY has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable NOT_INCHI_INPUT in INCHI_KEY.
3	Field ERROR_IN_FLAG_CHAR has been renamed to INVALID_STD_INCHI.	Recompilation of a client program may be terminated with the message: cannot find variable ERROR_IN_FLAG_CHAR in INCHI_KEY.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_KEY_STATUS.
2	Field INVALID_CHECKSUM has been renamed to INVALID_VERSION.	Recompilation of a client program may be terminated with the message: cannot find variable INVALID_CHECKSUM in INCHI_KEY_STATUS.
3	Field VALID has been renamed to VALID_NON_STANDARD.	Recompilation of a client program may be terminated with the message: cannot find variable VALID in INCHI_KEY_STATUS.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_PARITY.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_RADICAL.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_RET.

	Change	Effect
1	This class became final.	Recompilation of a client program may be terminated with the message: cannot inherit from final INCHI_STEREOTYPE.

cdk-1.2.10.jar
[+] DatabaseListModel (1)
[+] DatabaseObjectRenderer (1)
[+] tool (1)

package jas
[+] AsciiCP (1)
[+] CatchEntry (1)
[+] Catchtable (1)
[+] ClassCP (1)
[+] ClassEnv (1)
[+] CodeAttr (1)
[+] ConstAttr (1)
[+] CP (1)
[+] DoubleCP (1)
[+] ExceptAttr (1)
[+] FieldCP (1)
[+] FloatCP (1)
[+] GenericAttr (1)
[+] IincInsn (1)
[+] Insn (1)
[+] IntegerCP (1)
[+] InterfaceCP (1)
[+] InvokeinterfaceInsn (1)
[+] jasError (1)
[+] Label (1)
[+] LineTableAttr (1)
[+] LocalVarEntry (1)
[+] LocalVarTableAttr (1)
[+] LongCP (1)
[+] LookupswitchInsn (1)
[+] Method (1)
[+] MethodCP (1)
[+] MultiarrayInsn (1)
[+] NameTypeCP (1)
[+] SourceAttr (1)
[+] StringCP (1)
[+] TableswitchInsn (1)
[+] Var (1)

package net.sf.jnati
[+] ArtefactLocation (1)
[+] SystemTool (1)

package net.sf.jniinchi
[+] IInchiGenerator (1)
[+] INCHI_BOND_STEREO (1)
[+] INCHI_BOND_TYPE (1)
[+] INCHI_KEY (3)
[+] INCHI_KEY_STATUS (3)
[+] INCHI_PARITY (1)
[+] INCHI_RADICAL (1)
[+] INCHI_RET (1)
[+] INCHI_STEREOTYPE (1)

package org.omegahat.Environment.Compile
[+] DynamicCompiler (1)

package org.omegahat.Environment.Console
[+] omega (1)

package org.omegahat.Environment.DataStructures
[+] Addable (1)
[+] AssignableSubset (1)
[+] character (1)
[+] Copyable (1)
[+] Decrementable (1)
[+] Divisable (1)
[+] ElementAssignableSubset (1)
[+] ElementSubsettable (1)
[+] EqualityOperator (1)
[+] Incrementable (1)
[+] integer (1)
[+] list (1)
[+] logical (1)
[+] Multiplicable (1)
[+] numeric (1)
[+] ObjectIncrementable (1)
[+] RelationalOperator (1)
[+] single (1)
[+] Subsettable (1)
[+] Subtractable (1)
[+] vector (1)

package org.omegahat.Environment.Databases
[+] Activable (1)
[+] AttachableSearchPath (1)
[+] AttachedDatabase (1)
[+] ClosureDatabase (1)
[+] Database (1)
[+] DatabaseAssignEvent (1)
[+] DatabaseAssignListener (1)
[+] DatabaseAttachEvent (1)
[+] DatabaseAttachListener (1)
[+] DatabaseDetachEvent (1)
[+] DatabaseDetachListener (1)
[+] DatabaseEvent (1)
[+] DatabaseNotifier (1)
[+] DatabaseObjectEvent (1)
[+] DatabaseRemoveEvent (1)
[+] DatabaseRemoveListener (1)
[+] EvaluationFrame (1)
[+] HomogeneousTypedDatabase (1)
[+] IncorrectTypeException (1)
[+] LazyFunctionDatabase (1)
[+] MergableInt (1)
[+] NameTypeSearchFilter (1)
[+] ObjectDatabase (1)
[+] ObjectNotFoundException (1)
[+] ObjectSearchFilter (1)
[+] PersistentObjectDatabase (1)
[+] ReadWriteDatabase (1)
[+] ReadWriteDatabaseInt (1)
[+] SearchPath (1)
[+] SearchPathEvent (1)
[+] SearchPathListener (1)
[+] TypedDatabase (1)
[+] TypedDatabaseInt (1)
[+] ZipNameFilter (1)

package org.omegahat.Environment.Debugger
[+] BasicErrorHandler (1)
[+] BugReportData (1)
[+] Debugger (1)
[+] DefaultErrorHandler (1)
[+] ErrorHandler (1)
[+] EvaluatorDebugger (1)
[+] SimpleEvaluationMonitor (1)
[+] SystemErrorHandler (1)

package org.omegahat.Environment.Debugger.ParserViewer
[+] ASTFrame (1)
[+] ExpressionList (1)
[+] ExpressionTraceTree (1)
[+] ExpressionTreeRenderer (1)
[+] ExpressionTreeWindow (1)
[+] JTreeASTModel (1)
[+] JTreeASTPanel (1)

package org.omegahat.Environment.GUI
[+] BasicDatabaseRenderer (1)
[+] ClassNameListCellRenderer (1)
[+] ClassPathViewer (1)
[+] ClassPathViewerFrame (1)
[+] ClassTreeViewer (1)
[+] ClassViewer (1)
[+] ClassViewerTreeModel (1)
[+] DatabaseViewer (1)
[+] DatabaseViewerFrame (1)
[+] EvaluatorJPanel (1)
[+] EvaluatorOutput (1)
[+] EvaluatorStatusBar (1)
[+] MenuDescription (1)
[+] omega (1)
[+] OmegaInterface (1)
[+] OptionsEditor (1)
[+] SearchPathView (1)
[+] SearchPathViewerFrame (1)
[+] TabbedElementContainer (1)
[+] ToolsPanel (1)
[+] UserArea (1)
[+] UserInput (1)
[+] ViewerFrame (1)
[+] WorkArea (1)

package org.omegahat.Environment.GUITools
[+] ClassTreeRenderer (1)
[+] EvaluableInterfaceGenerator (1)
[+] FunctionListener (1)
[+] GenericFrame (1)
[+] OmegaListener (1)
[+] Signature (1)
[+] ThreadSuspendButton (1)

package org.omegahat.Environment.GUITools.MethodViewer
[+] MethodTreeModel (1)
[+] MethodTreeRenderer (1)
[+] MethodViewer (1)
[+] MethodViewerFrame (1)

package org.omegahat.Environment.IO
[+] ArchiveEntry (1)
[+] BasicObjectDisplay (1)
[+] BasicTaskDisplay (1)
[+] DefaultPromptSource (1)
[+] DirectoryFilter (1)
[+] DirectoryNameFilter (1)
[+] EvaluatorInputConsumer (1)
[+] ExtensionFilenameFilter (1)
[+] IncompleteInputException (1)
[+] InputConsumer (1)
[+] InputFile (1)
[+] InputFileInt (1)
[+] InputReader (1)
[+] InputSupplier (1)
[+] NumberedInputReader (1)
[+] ObjectDisplayFilter (1)
[+] PromptSource (1)
[+] SelfDisplaying (1)
[+] TaskDisplayFilter (1)
[+] TextFile (1)
[+] TruncatedObjectDisplay (1)
[+] TypeTaskDisplay (1)
[+] ZipInputFile (1)

package org.omegahat.Environment.Interpreter
[+] BasicEvaluator (1)
[+] CastFunctionCall (1)
[+] DynamicFieldAccessInt (1)
[+] DynamicMethodAccessInt (1)
[+] EndSourceInputException (1)
[+] EvaluationEvent (1)
[+] EvaluationException (1)
[+] EvaluationListener (1)
[+] Evaluator (1)
[+] EvaluatorManager (1)
[+] GUIHelpEvaluator (1)
[+] InteractiveEvaluator (1)
[+] InterruptButton (1)
[+] ManagedEvaluatorInt (1)
[+] Options (1)
[+] Task (1)
[+] TaskQueue (1)
[+] TaskQueueEvaluator (1)
[+] TracingEvaluator (1)
[+] UserClassEvaluator (1)
[+] UtilityEvaluator (1)

package org.omegahat.Environment.Language
[+] Closure (1)
[+] Evaluable (1)
[+] Function (1)
[+] FunctionCallArguments (1)
[+] LazyArgument (1)
[+] LazyFunction (1)
[+] Method (1)
[+] MethodAlias (1)
[+] MethodAliasException (1)
[+] MultiMethodAliasException (1)
[+] OptionalLazyArgument (1)
[+] Signature (1)
[+] StaticMethodAlias (1)
[+] TailRecursiveClosure (1)
[+] TailRecursiveFunction (1)

package org.omegahat.Environment.Language.UserClasses
[+] AbstractUserClass (1)
[+] MethodsCollection (1)
[+] OmegaField (1)
[+] OmegaFieldChangeEvent (1)
[+] OmegaFieldInstance (1)
[+] OmegahatUserClassHelper (1)
[+] UserClass (1)
[+] UserClassChangeEvent (1)
[+] UserClassChangeListener (1)
[+] UserClassGenerator (1)
[+] UserClassInstance (1)
[+] UserClassManager (1)
[+] UserClassMethod (1)
[+] UserClassPackage (1)

package org.omegahat.Environment.ObjectDataStructures
[+] character (1)
[+] integer (1)
[+] list (1)
[+] logical (1)
[+] numeric (1)
[+] single (1)
[+] vector (1)

package org.omegahat.Environment.Parser.AntlrParser
[+] IncompleteExpression (1)
[+] omegaJavaGrammar (1)
[+] omegaJavaLexer (1)
[+] omegaNestedStringLexer (1)
[+] ResettableLexer (1)
[+] UserClassOmegaParser (1)

package org.omegahat.Environment.Parser.Parse
[+] ArgList (1)
[+] ArrayAccess (1)
[+] ArrayAccessAssignExpression (1)
[+] ArrayAccessInfix (1)
[+] ArrayConstructorExpression (1)
[+] ArrayDimensionExpression (1)
[+] ArrayType (1)
[+] AssignExpression (1)
[+] BasicExpression (1)
[+] BinaryExpression (1)
[+] CastExpression (1)
[+] Catch (1)
[+] ClassDefinition (1)
[+] ClassList (1)
[+] ClassName (1)
[+] ClassReference (1)
[+] Comment (1)
[+] ConditionalExpressionStatement (1)
[+] ConstantExpression (1)
[+] ConstantSymbol (1)
[+] ConstructorDefinitionExpression (1)
[+] ConstructorExpression (1)
[+] ControlFlowException (1)
[+] DynamicFieldAccess (1)
[+] ElementAccess (1)
[+] EnumeratedForLoop (1)
[+] ExpressionInt (1)
[+] FieldAccess (1)
[+] FlowControl (1)
[+] ForLoop (1)
[+] FormalComment (1)
[+] FunctionCall (1)
[+] FunctionExpression (1)
[+] FunctionParameterModifier (1)
[+] FunctionType (1)
[+] GlobalName (1)
[+] IfElseExpression (1)
[+] ImportExpression (1)
[+] InstanceOfExpression (1)
[+] List (1)
[+] LocalVariable (1)
[+] LogicalExpression (1)
[+] MathExpression (1)
[+] MethodCall (1)
[+] MethodDefinition (1)
[+] MethodExpression (1)
[+] MethodHeader (1)
[+] MethodLocator (1)
[+] MethodParameter (1)
[+] Modifier (1)
[+] MultiLineComment (1)
[+] Name (1)
[+] NumberExpression (1)
[+] OperatorExpression (1)
[+] SequenceExpression (1)
[+] ShiftExpression (1)
[+] SimpleParameterModifier (1)
[+] SingleLineComment (1)
[+] StatementList (1)
[+] SuperName (1)
[+] SwitchCase (1)
[+] SwitchStatement (1)
[+] SynchronizedExpression (1)
[+] SyntaxErrorException (1)
[+] TreeNodeInt (1)
[+] TryCatch (1)
[+] Type (1)
[+] UnaryExpression (1)
[+] UpdateUnaryExpression (1)
[+] UserClassFieldAccess (1)
[+] UserClassFunctionExpression (1)
[+] UserClassMethodCall (1)
[+] UserClassMethodExpression (1)
[+] While (1)

package org.omegahat.Environment.System
[+] DeferredEagerURLClassLoader (1)
[+] DynamicClassLoader (1)
[+] EagerURLClassLoader (1)
[+] Globals (1)
[+] JarClassLoader (1)
[+] NotImplementedException (1)
[+] SystemViewer (1)
[+] URLClassLoader (1)
[+] UserClassLoader (1)
[+] ZipClassLoader (1)

package org.omegahat.Environment.System.Functions
[+] BasicHelpSystem (1)
[+] HelpSystem (1)
[+] HelpTOC (1)

package org.omegahat.Environment.TaskManagement
[+] BasicServerPool (1)
[+] DistributedTaskEvent (1)
[+] DistributedTaskListener (1)
[+] NamedServerPool (1)
[+] ServerPool (1)
[+] SimulationManager (1)
[+] SimulationTask (1)
[+] Task (1)
[+] TaskManager (1)
[+] TaskQueue (1)

package org.omegahat.Environment.Tools.ClassHierarchy
[+] ClassNode (1)
[+] ClassNodeAgent (1)
[+] HierarchyGenerator (1)
[+] InterfaceNode (1)
[+] UnavailableClassNode (1)

package org.omegahat.Environment.Tools.ClassList
[+] ArchiveClassList (1)
[+] ClassFileFilter (1)
[+] ClassList (1)
[+] ClassLocator (1)
[+] ClassLocatorInt (1)
[+] GroupedClassLocator (1)
[+] LocalClassList (1)
[+] LocalClassLocator (1)
[+] LocalURLClassList (1)
[+] ObjectList (1)
[+] PackageClassList (1)
[+] PrefixClassList (1)
[+] SubArchiveClassList (1)
[+] URLClassList (1)

package org.omegahat.Environment.Tools.DataScanner
[+] DataLexer (1)
[+] DataScanner (1)
[+] DataTokenizer (1)
[+] EOFException (1)
[+] EventDataScanner (1)
[+] ObjectReader (1)
[+] RecordLexer (1)
[+] RecordStreamListener (1)

package org.omegahat.Environment.Tools.Factory
[+] FactoryTable (1)

package org.omegahat.Environment.Tools.FileLocator
[+] DynamicFileFilter (1)
[+] FileLocator (1)
[+] FileLocatorInt (1)

package org.omegahat.Environment.Tools.VariableExpansion
[+] VariableExpansion (1)

package org.omegahat.Environment.Utils
[+] ListListener (1)
[+] MergableHashtable (1)
[+] Named (1)
[+] OrderedListEvent (1)
[+] OrderedTable (1)
[+] StringUtils (1)
[+] SubstitutedTrimmedProperties (1)
[+] TrimmedProperties (1)

package org.omegahat.Environment.lib.Language
[+] OmegahatLazySystemFunctions (1)
[+] OmegahatVarArgsSystemFunctions (1)
[+] SequenceFunctions (1)
[+] SubsetFunctions (1)
[+] TimedEvaluation (1)
[+] TimedExpressionEvaluation (1)
[+] VarSequenceFunctions (1)

package org.omegahat.Interfaces.NativeInterface
[+] AnonymousReference (1)
[+] BasicConvertibleClassifier (1)
[+] ConvertibleClassifier (1)
[+] ConvertibleClassifierInt (1)
[+] ForeignReference (1)
[+] ForeignReferenceClassGenerator (1)
[+] ForeignReferenceInt (1)
[+] InterfaceDatabase (1)
[+] InterfaceReference (1)
[+] MetaForeignReference (1)
[+] NamedReference (1)
[+] OmegaInterfaceManager (1)

package org.omegahat.R.Java
[+] MissingMethodException (1)
[+] REvaluator (1)
[+] RException (1)
[+] RForeignReference (1)
[+] RJavaInstance (1)
[+] RManualFunctionActionListener (1)
[+] ROmegahatInterpreter (1)
[+] RSplash (1)

package org.openscience.cdk
[+] AtomContainer (1)
[+] AtomParity (1)
[+] Bond (1)
[+] CDKConstants (6)
[+] PeriodicTableElement (1)

package org.openscience.cdk.config
[+] ElementPTFactory (1)
[+] Elements (1)
[+] Symbols (1)

package org.openscience.cdk.config.elements
[+] ElementPTHandler (1)
[+] ElementPTReader (1)

package org.openscience.cdk.formula
[+] MolecularFormula (1)

package org.openscience.cdk.interfaces
[+] IAtom (4)
[+] IAtomContainer (6)
[+] IAtomContainerSet (1)
[+] IAtomParity (1)
[+] IBond (4)
[+] IChemObject (2)
[+] IChemObjectBuilder (76)
[+] IMolecularFormula (1)
[+] IMolecularFormulaSet (1)
[+] IPDBStructure (1)

package org.openscience.cdk.io
[+] IChemObjectReader (5)
[+] MDLWriter (1)

package org.openscience.cdk.io.cml
[+] CMLCoreModule (1)

package org.openscience.cdk.io.iterator.event
[+] EventCMLHandler (1)

package org.openscience.cdk.io.random
[+] RandomAccessReader (1)

package org.openscience.cdk.isomorphism
[+] UniversalIsomorphismTester (1)

package org.openscience.cdk.modeling.forcefield
[+] AngleBending (1)
[+] BondStretching (1)
[+] ConjugateGradientMethod (1)
[+] ElectrostaticInteractions (1)
[+] ForceField (1)
[+] ForceFieldTools (1)
[+] GeometricMinimizer (1)
[+] IPotentialFunction (1)
[+] LineSearch (1)
[+] LineSearchForTheWolfeConditions (1)
[+] MMFF94EnergyFunction (1)
[+] NewtonRaphsonMethod (1)
[+] SmoothingFunctions (1)
[+] SteepestDescentsMethod (1)
[+] StretchBendInteractions (1)
[+] Torsions (1)
[+] VanDerWaalsInteractions (1)

package org.openscience.cdk.qsar.model
[+] IModel (1)
[+] QSARModelException (1)

package org.openscience.cdk.qsar.model.R
[+] CNNClassificationModel (1)
[+] CNNClassificationModelFit (1)
[+] CNNClassificationModelPredict (1)
[+] CNNRegressionModel (1)
[+] CNNRegressionModelFit (1)
[+] CNNRegressionModelPredict (1)
[+] CNNRegressionModelSummary (1)
[+] LinearRegressionModel (1)
[+] LinearRegressionModelFit (1)
[+] LinearRegressionModelPredict (1)
[+] LinearRegressionModelSummary (1)
[+] PLSRegressionModel (1)
[+] PLSRegressionModelFit (1)
[+] PLSRegressionModelPredict (1)
[+] RModel (1)

package org.openscience.cdk.qsar.model.R2
[+] CNNRegressionModel (1)
[+] LinearRegressionModel (1)
[+] RModel (1)

package org.openscience.cdk.qsar.result
[+] IDescriptorResult (1)

package org.openscience.cdk.tools
[+] GenerateFragments (1)
[+] Normalizer (1)
[+] PeriodicTable (1)
[+] SmilesValencyChecker (1)

package org.rosuda.JRI
[+] Mutex (1)
[+] RBool (1)
[+] RConsoleOutputStream (1)
[+] Rengine (1)
[+] REXP (1)
[+] RFactor (1)
[+] RList (1)
[+] RMainLoopCallbacks (1)
[+] RVector (1)

package sea36.util.config
[+] Configuration (1)
[+] ResolvingProperties (1)

to the top

Problems with Methods, High Severity (15)

cdk-1.2.10.jar, AtomContainerDiff
package org.openscience.cdk.tools.diff
[+] AtomContainerDiff.AtomContainerDiff ( ) (1)

cdk-1.2.10.jar, AtomDiff
package org.openscience.cdk.tools.diff
[+] AtomDiff.AtomDiff ( ) (1)

cdk-1.2.10.jar, AtomTypeDiff
package org.openscience.cdk.tools.diff
[+] AtomTypeDiff.AtomTypeDiff ( ) (1)

cdk-1.2.10.jar, BondDiff
package org.openscience.cdk.tools.diff
[+] BondDiff.BondDiff ( ) (1)

cdk-1.2.10.jar, CDKSourceCodeWriter
package org.openscience.cdk.io
[+] CDKSourceCodeWriter.writeAtom ( IAtom atom ) :  void (1)
[+] CDKSourceCodeWriter.writeAtomContainer ( IAtomContainer molecule ) :  void (1)
[+] CDKSourceCodeWriter.writeBond ( IBond bond ) :  void (1)
[+] CDKSourceCodeWriter.writeMolecule ( IMolecule molecule ) :  void (1)

cdk-1.2.10.jar, ChemObjectDiff
package org.openscience.cdk.tools.diff
[+] ChemObjectDiff.ChemObjectDiff ( ) (1)

cdk-1.2.10.jar, ElectronContainerDiff
package org.openscience.cdk.tools.diff
[+] ElectronContainerDiff.ElectronContainerDiff ( ) (1)

cdk-1.2.10.jar, ElementDiff
package org.openscience.cdk.tools.diff
[+] ElementDiff.ElementDiff ( ) (1)

cdk-1.2.10.jar, InChIGeneratorFactory
package org.openscience.cdk.inchi
[+] InChIGeneratorFactory.InChIGeneratorFactory ( ) (1)

cdk-1.2.10.jar, IsotopeDiff
package org.openscience.cdk.tools.diff
[+] IsotopeDiff.IsotopeDiff ( ) (1)

cdk-1.2.10.jar, LonePairDiff
package org.openscience.cdk.tools.diff
[+] LonePairDiff.LonePairDiff ( ) (1)

cdk-1.2.10.jar, SingleElectronDiff
package org.openscience.cdk.tools.diff
[+] SingleElectronDiff.SingleElectronDiff ( ) (1)

to the top

Problems with Methods, Medium Severity (10)

cdk-1.2.10.jar, PartialFilledStructureMerger
package org.openscience.cdk.structgen.stochastic
[+] PartialFilledStructureMerger.PartialFilledStructureMerger ( ) (1)

cdk-1.2.10.jar, StructureDiagramGenerator
package org.openscience.cdk.layout
[+] StructureDiagramGenerator.generateCoordinates ( ) :  void (2)
[+] StructureDiagramGenerator.generateCoordinates ( Vector2d firstBondVector ) :  void (2)
[+] StructureDiagramGenerator.generateExperimentalCoordinates ( ) :  void (2)
[+] StructureDiagramGenerator.generateExperimentalCoordinates ( Vector2d firstBondVector ) :  void (2)

cdk-1.2.10.jar, StructureResonanceGenerator
package org.openscience.cdk.tools
[+] StructureResonanceGenerator.setReactions ( List newReactionsList ) :  void (1)

to the top

Problems with Data Types, Low Severity (8)

cdk-1.2.10.jar
package net.sf.jniinchi
[+] INCHI_BOND_STEREO (1)
[+] INCHI_BOND_TYPE (1)
[+] INCHI_KEY (1)
[+] INCHI_KEY_STATUS (1)
[+] INCHI_PARITY (1)
[+] INCHI_RADICAL (1)
[+] INCHI_RET (1)
[+] INCHI_STEREOTYPE (1)

to the top

Other Changes in Data Types (14)

cdk-1.2.10.jar
package net.sf.jniinchi
[+] INCHI_KEY (2)
[+] INCHI_KEY_STATUS (1)

package org.openscience.cdk
[+] AtomContainer (1)
[+] CDKConstants (3)

package org.openscience.cdk.io
[+] DefaultChemObjectReader (1)
[+] PDBWriter (1)

package org.openscience.cdk.io.iterator
[+] DefaultIteratingChemObjectReader (1)

package org.openscience.cdk.io.pubchemxml
[+] PubChemXMLHelper (2)

package org.openscience.cdk.layout
[+] RingPlacer (2)

to the top

Java ARchives (1)

cdk-1.2.10.jar

to the top

	Change	Effect
1	Field STEREO_BOND_DOWN (int) with the compile-time constant value -1 has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_DOWN in CDKConstants.
2	Field STEREO_BOND_DOWN_INV (int) with the compile-time constant value -2 has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_DOWN_INV in CDKConstants.
3	Field STEREO_BOND_UNDEFINED (int) with the compile-time constant value 4 has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_UNDEFINED in CDKConstants.
4	Field STEREO_BOND_UP (int) with the compile-time constant value 1 has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_UP in CDKConstants.
5	Field STEREO_BOND_UP_INV (int) with the compile-time constant value 2 has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_UP_INV in CDKConstants.
6	Field STEREO_BOND_NONE of type int has been removed from this class.	Recompilation of a client program may be terminated with the message: cannot find variable STEREO_BOND_NONE in CDKConstants.

	Change	Effect
1	Abstract method getImplicitHydrogenCount ( ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method getImplicitHydrogenCount() in IAtom.
2	Abstract method setImplicitHydrogenCount ( Integer ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method setImplicitHydrogenCount(Integer) in IAtom.
3	Abstract method getHydrogenCount ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method getHydrogenCount() in interface IAtom.
4	Abstract method setHydrogenCount ( Integer ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method setHydrogenCount(Integer) in interface IAtom.

	Change	Effect
1	Abstract method addBond ( int, int, IBond.Order, IBond.Stereo ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method addBond(int, int, IBond.Order, IBond.Stereo) in IAtomContainer.
2	Abstract method addStereoElement ( IStereoElement ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method addStereoElement(IStereoElement) in IAtomContainer.
3	Abstract method stereoElements ( ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method stereoElements() in IAtomContainer.
4	Abstract method addAtomParity ( IAtomParity ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method addAtomParity(IAtomParity) in interface IAtomContainer.
5	Abstract method addBond ( int, int, IBond.Order, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method addBond(int, int, IBond.Order, int) in interface IAtomContainer.
6	Abstract method getAtomParity ( IAtom ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method getAtomParity(IAtom) in interface IAtomContainer.

	Change	Effect
1	Abstract method getStereo ( ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method getStereo() in IBond.
2	Abstract method setStereo ( IBond.Stereo ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method setStereo(IBond.Stereo) in IBond.
3	Abstract method getStereo ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method getStereo() in interface IBond.
4	Abstract method setStereo ( int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method setStereo(int) in interface IBond.

	Change	Effect
1	Added super-interface ICDKObject.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method in ICDKObject.
2	Removed super-interface java.lang.Cloneable.	Recompilation of a client program may be terminated with the message: cannot find method in interface IChemObject.

	Change	Effect
1	Abstract method newInstance ( Class, Object[ ] ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method newInstance(Class, Object[]) in IChemObjectBuilder.
2	Abstract method newAdductFormula ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAdductFormula() in interface IChemObjectBuilder.
3	Abstract method newAdductFormula ( IMolecularFormula ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAdductFormula(IMolecularFormula) in interface IChemObjectBuilder.
4	Abstract method newAminoAcid ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAminoAcid() in interface IChemObjectBuilder.
5	Abstract method newAtom ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtom() in interface IChemObjectBuilder.
6	Abstract method newAtom ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtom(String) in interface IChemObjectBuilder.
7	Abstract method newAtom ( String, Point2d ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtom(String, Point2d) in interface IChemObjectBuilder.
8	Abstract method newAtom ( String, Point3d ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtom(String, Point3d) in interface IChemObjectBuilder.
9	Abstract method newAtom ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtom(IElement) in interface IChemObjectBuilder.
10	Abstract method newAtomContainer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomContainer() in interface IChemObjectBuilder.
11	Abstract method newAtomContainer ( int, int, int, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomContainer(int, int, int, int) in interface IChemObjectBuilder.
12	Abstract method newAtomContainer ( IAtomContainer ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomContainer(IAtomContainer) in interface IChemObjectBuilder.
13	Abstract method newAtomContainerSet ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomContainerSet() in interface IChemObjectBuilder.
14	Abstract method newAtomParity ( IAtom, IAtom, IAtom, IAtom, IAtom, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) in interface IChemObjectBuilder.
15	Abstract method newAtomType ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomType(String) in interface IChemObjectBuilder.
16	Abstract method newAtomType ( String, String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomType(String, String) in interface IChemObjectBuilder.
17	Abstract method newAtomType ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newAtomType(IElement) in interface IChemObjectBuilder.
18	Abstract method newBioPolymer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBioPolymer() in interface IChemObjectBuilder.
19	Abstract method newBond ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond() in interface IChemObjectBuilder.
20	Abstract method newBond ( IAtom, IAtom ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond(IAtom, IAtom) in interface IChemObjectBuilder.
21	Abstract method newBond ( IAtom, IAtom, IBond.Order ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond(IAtom, IAtom, IBond.Order) in interface IChemObjectBuilder.
22	Abstract method newBond ( IAtom, IAtom, IBond.Order, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond(IAtom, IAtom, IBond.Order, int) in interface IChemObjectBuilder.
23	Abstract method newBond ( IAtom[ ] ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond(IAtom[]) in interface IChemObjectBuilder.
24	Abstract method newBond ( IAtom[ ], IBond.Order ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newBond(IAtom[], IBond.Order) in interface IChemObjectBuilder.
25	Abstract method newChemFile ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newChemFile() in interface IChemObjectBuilder.
26	Abstract method newChemModel ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newChemModel() in interface IChemObjectBuilder.
27	Abstract method newChemObject ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newChemObject() in interface IChemObjectBuilder.
28	Abstract method newChemObject ( IChemObject ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newChemObject(IChemObject) in interface IChemObjectBuilder.
29	Abstract method newChemSequence ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newChemSequence() in interface IChemObjectBuilder.
30	Abstract method newCrystal ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newCrystal() in interface IChemObjectBuilder.
31	Abstract method newCrystal ( IAtomContainer ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newCrystal(IAtomContainer) in interface IChemObjectBuilder.
32	Abstract method newElectronContainer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newElectronContainer() in interface IChemObjectBuilder.
33	Abstract method newElement ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newElement() in interface IChemObjectBuilder.
34	Abstract method newElement ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newElement(String) in interface IChemObjectBuilder.
35	Abstract method newElement ( String, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newElement(String, int) in interface IChemObjectBuilder.
36	Abstract method newElement ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newElement(IElement) in interface IChemObjectBuilder.
37	Abstract method newFragmentAtom ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newFragmentAtom() in interface IChemObjectBuilder.
38	Abstract method newIsotope ( int, String, double, double ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newIsotope(int, String, double, double) in interface IChemObjectBuilder.
39	Abstract method newIsotope ( int, String, int, double, double ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newIsotope(int, String, int, double, double) in interface IChemObjectBuilder.
40	Abstract method newIsotope ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newIsotope(String) in interface IChemObjectBuilder.
41	Abstract method newIsotope ( String, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newIsotope(String, int) in interface IChemObjectBuilder.
42	Abstract method newIsotope ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newIsotope(IElement) in interface IChemObjectBuilder.
43	Abstract method newLonePair ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newLonePair() in interface IChemObjectBuilder.
44	Abstract method newLonePair ( IAtom ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newLonePair(IAtom) in interface IChemObjectBuilder.
45	Abstract method newMapping ( IChemObject, IChemObject ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMapping(IChemObject, IChemObject) in interface IChemObjectBuilder.
46	Abstract method newMolecularFormula ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecularFormula() in interface IChemObjectBuilder.
47	Abstract method newMolecularFormulaSet ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecularFormulaSet() in interface IChemObjectBuilder.
48	Abstract method newMolecularFormulaSet ( IMolecularFormula ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecularFormulaSet(IMolecularFormula) in interface IChemObjectBuilder.
49	Abstract method newMolecule ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecule() in interface IChemObjectBuilder.
50	Abstract method newMolecule ( int, int, int, int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecule(int, int, int, int) in interface IChemObjectBuilder.
51	Abstract method newMolecule ( IAtomContainer ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMolecule(IAtomContainer) in interface IChemObjectBuilder.
52	Abstract method newMoleculeSet ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMoleculeSet() in interface IChemObjectBuilder.
53	Abstract method newMonomer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newMonomer() in interface IChemObjectBuilder.
54	Abstract method newPDBAtom ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBAtom(String) in interface IChemObjectBuilder.
55	Abstract method newPDBAtom ( String, Point3d ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBAtom(String, Point3d) in interface IChemObjectBuilder.
56	Abstract method newPDBAtom ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBAtom(IElement) in interface IChemObjectBuilder.
57	Abstract method newPDBMonomer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBMonomer() in interface IChemObjectBuilder.
58	Abstract method newPDBPolymer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBPolymer() in interface IChemObjectBuilder.
59	Abstract method newPDBStructure ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPDBStructure() in interface IChemObjectBuilder.
60	Abstract method newPolymer ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPolymer() in interface IChemObjectBuilder.
61	Abstract method newPseudoAtom ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPseudoAtom() in interface IChemObjectBuilder.
62	Abstract method newPseudoAtom ( String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPseudoAtom(String) in interface IChemObjectBuilder.
63	Abstract method newPseudoAtom ( String, Point2d ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPseudoAtom(String, Point2d) in interface IChemObjectBuilder.
64	Abstract method newPseudoAtom ( String, Point3d ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPseudoAtom(String, Point3d) in interface IChemObjectBuilder.
65	Abstract method newPseudoAtom ( IElement ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newPseudoAtom(IElement) in interface IChemObjectBuilder.
66	Abstract method newReaction ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newReaction() in interface IChemObjectBuilder.
67	Abstract method newReactionScheme ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newReactionScheme() in interface IChemObjectBuilder.
68	Abstract method newReactionSet ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newReactionSet() in interface IChemObjectBuilder.
69	Abstract method newRing ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newRing() in interface IChemObjectBuilder.
70	Abstract method newRing ( int ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newRing(int) in interface IChemObjectBuilder.
71	Abstract method newRing ( int, String ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newRing(int, String) in interface IChemObjectBuilder.
72	Abstract method newRing ( IAtomContainer ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newRing(IAtomContainer) in interface IChemObjectBuilder.
73	Abstract method newRingSet ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newRingSet() in interface IChemObjectBuilder.
74	Abstract method newSingleElectron ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newSingleElectron() in interface IChemObjectBuilder.
75	Abstract method newSingleElectron ( IAtom ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newSingleElectron(IAtom) in interface IChemObjectBuilder.
76	Abstract method newStrand ( ) has been removed from this interface.	Recompilation of a client program may be terminated with the message: cannot find method newStrand() in interface IChemObjectBuilder.

	Change	Effect
1	Abstract method handleError ( String ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method handleError(String) in IChemObjectReader.
2	Abstract method handleError ( String, int, int, int ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method handleError(String, int, int, int) in IChemObjectReader.
3	Abstract method handleError ( String, int, int, int, Exception ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method handleError(String, int, int, int, Exception) in IChemObjectReader.
4	Abstract method handleError ( String, Exception ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method handleError(String, Exception) in IChemObjectReader.
5	Abstract method setErrorHandler ( IChemObjectReaderErrorHandler ) has been added to this interface.	Recompilation of a client program may be terminated with the message: a client class C is not abstract and does not override abstract method setErrorHandler(IChemObjectReaderErrorHandler) in IChemObjectReader.

	Change	Effect
1	Removed java.lang.Exception exception thrown.	Recompilation of a client program may be terminated with the message: cannot override generateCoordinates() in StructureDiagramGenerator; overridden method does not throw java.lang.Exception.
2	Added org.openscience.cdk.exception.CDKException exception thrown.	Recompilation of a client program may be terminated with the message: unreported exception org.openscience.cdk.exception.CDKException must be caught or declared to be thrown.

	Change	Effect
1	Field INVALID_INCHI has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to INVALID_INCHI is ambiguous.
2	Field INVALID_INCHI_PREFIX has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to INVALID_INCHI_PREFIX is ambiguous.

	Change	Effect
1	Field ATOM_ATOM_MAPPING has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to ATOM_ATOM_MAPPING is ambiguous.
2	Field IS_TYPEABLE has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to IS_TYPEABLE is ambiguous.
3	Field REST_H has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to REST_H is ambiguous.

	Change	Effect
1	Field EL_PROPS_BVAL has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to EL_PROPS_BVAL is ambiguous.
2	Field EL_PROPS_FVAL has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to EL_PROPS_FVAL is ambiguous.

	Change	Effect
1	Field defaultAngles has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to defaultAngles is ambiguous.
2	Field jcpAngles has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class. Recompilation of a client class may be terminated with the message: reference to jcpAngles is ambiguous.