Source compatibility report for the CDK library between 1.0.3 and 1.0.4 versions

Test Info

Library Name	CDK
Version #1	1.0.3
Version #2	1.0.4

Test Results

Total Java ARchives	1
Total Methods / Classes	32683 / 3385
Verdict	Incompatible (0.1%)

Problem Summary

	Severity	Count
Added Methods	-	15
Removed Methods	High	46
Problems with Data Types	High	3
	Medium	0
	Low	0
Problems with Methods	High	0
	Medium	3
	Low	0
Other Changes in Data Types	-	4

Added Methods (15)

cdk-1.0.4.jar, AtomEditor.class
package org.openscience.cdk.applications.swing.editor
AtomEditor.AtomEditor ( IChemModel chemModel, UndoableEditSupport undoSupport )

cdk-1.0.4.jar, ChemFileManipulator.class
package org.openscience.cdk.tools.manipulator
ChemFileManipulator.getAllReactions ( IChemFile file ) [static] :  List

cdk-1.0.4.jar, ChemObjectEditor.class
package org.openscience.cdk.applications.swing.editor
ChemObjectEditor.getMayclose ( ) :  boolean

cdk-1.0.4.jar, ConvertToAtomEdit.class
package org.openscience.cdk.applications.undoredo
ConvertToAtomEdit.canRedo ( ) :  boolean
ConvertToAtomEdit.canUndo ( ) :  boolean
ConvertToAtomEdit.ConvertToAtomEdit ( IAtomContainer relevantContainer, IPseudoAtom pseudo, IAtom atom )
ConvertToAtomEdit.getPresentationName ( ) :  String
ConvertToAtomEdit.redo ( ) :  void
ConvertToAtomEdit.undo ( ) :  void

cdk-1.0.4.jar, GeometryTools.class
package org.openscience.cdk.geometry
GeometryTools.center ( IReaction reaction, Dimension areaDim, HashMap renderingCoordinates ) [static] :  void
GeometryTools.translate2D ( IReaction reaction, double transX, double transY, HashMap renderingCoordinates ) [static] :  void
GeometryTools.translate2D ( IReaction reaction, Vector2d vector, HashMap renderingCoordinates ) [static] :  void
GeometryTools.translateAllPositive ( IReaction reaction, HashMap renderingCoordinates ) [static] :  void

cdk-1.0.4.jar, IDCreator.class
package org.openscience.cdk.tools
IDCreator.setIDPolicy ( int policy ) [static] :  void

cdk-1.0.4.jar, MDLRXNWriter.class
package org.openscience.cdk.io
MDLRXNWriter.setRdFields ( Map map ) :  void

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Removed Methods (46)

cdk-1.0.3.jar, AtomEditor.class
package org.openscience.cdk.applications.swing.editor
AtomEditor.AtomEditor ( )

cdk-1.0.3.jar, EquivalentClassesDeterministicGenerator.class
package org.openscience.cdk.structgen.deterministic
EquivalentClassesDeterministicGenerator.EquivalentClassesDeterministicGenerator ( )
EquivalentClassesDeterministicGenerator.setAtomContainer ( IAtomContainer ac ) :  void

cdk-1.0.3.jar, GENMDeterministicGenerator.class
package org.openscience.cdk.structgen.deterministic
GENMDeterministicGenerator.addListener ( IStructureGenerationListener x ) :  void
GENMDeterministicGenerator.analyseMolecularFormula ( MFAnalyser mfa ) :  void
GENMDeterministicGenerator.checkAdmissibility ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix ) :  boolean
GENMDeterministicGenerator.checkConstraint ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix, IAtomContainer ac ) :  boolean
GENMDeterministicGenerator.convertToMol ( List set, int[ ][ ] matrix, List structures ) :  void
GENMDeterministicGenerator.DFSM ( int[ ][ ] adjacency, int number, boolean[ ] isVisited ) :  void
GENMDeterministicGenerator.fireChange ( ) :  void
GENMDeterministicGenerator.forceFilling ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix, int[ ][ ] previousMatrix ) :  int
GENMDeterministicGenerator.generate ( ) :  void
GENMDeterministicGenerator.generateBasicFragments ( ) :  void
GENMDeterministicGenerator.generateBasicUnits ( ) :  void
GENMDeterministicGenerator.generateIsomers ( ) :  void
GENMDeterministicGenerator.GENMDeterministicGenerator ( String mf, String path )
GENMDeterministicGenerator.getAtomContainer ( ) :  IAtomContainer
GENMDeterministicGenerator.getBasicUnit ( List basicUnits ) :  void
GENMDeterministicGenerator.getEquivalentClass ( List setOfBasicFragment, int[ ] setOfStability ) :  int
GENMDeterministicGenerator.getFinalStructure ( List setOfBasicFragment, int[ ][ ] adjacencyMatrix, GENMDeterministicGenerator.IntArray storedSymbolOfStructure, int[ ] totalNumberOfThisSet, int totalNumberOfAtomAndBond ) :  void
GENMDeterministicGenerator.getMaximumWCF ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacency, int[ ][ ] previousMatrix, int[ ] parentID ) :  boolean
GENMDeterministicGenerator.getNextWCF ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacencyMatrix, int[ ][ ] previousMatrix, int[ ] parentID ) :  boolean
GENMDeterministicGenerator.getNumberOfStructures ( ) :  int
GENMDeterministicGenerator.getOrderOfBasicFragmentSet ( List setOfBasicFragment, int[ ] parentID ) :  List
GENMDeterministicGenerator.getReturnedStructureCount ( ) :  long
GENMDeterministicGenerator.getSetOfStability ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacency, int[ ] setOfStability, int[ ] parentID ) :  void
GENMDeterministicGenerator.getStructures ( ) :  List
GENMDeterministicGenerator.getStructuresAtATime ( ) :  int
GENMDeterministicGenerator.getSymmetryFromAllPath ( int size, int[ ][ ] connectivity, int[ ] classID ) :  int
GENMDeterministicGenerator.getSymmetryFromNeighbour ( int size, int number, int[ ][ ] connectivity, int[ ] classID ) :  int
GENMDeterministicGenerator.hasMoreStructures ( ) :  boolean
GENMDeterministicGenerator.initializeMatrix ( List setOfBasicFragment, int[ ] bondAttribute, int[ ][ ] adjacency, int[ ][ ] previousMatrix ) :  void
GENMDeterministicGenerator.initializeParameters ( ) :  void
GENMDeterministicGenerator.isForceFilling ( int step, int[ ][ ] previousMatrix, int[ ][ ] adjacency ) :  boolean
GENMDeterministicGenerator.normalization ( List setOfBasicFragment, int[ ][ ] adjacencyMatrix ) :  int[ ][ ]
GENMDeterministicGenerator.removeChangeListener ( IStructureGenerationListener x ) :  void
GENMDeterministicGenerator.restoreMatrix ( int step, int[ ] freeValence, int[ ][ ] sourceMatrix, int[ ][ ] destMatrix ) :  void
GENMDeterministicGenerator.setAtomContainer ( IAtomContainer atomContainer ) :  void
GENMDeterministicGenerator.setBasicUnits ( List basicUnits ) :  void
GENMDeterministicGenerator.setReturnedStructureCount ( long returnedStructureCount ) :  void
GENMDeterministicGenerator.setStructuresAtATime ( int structuresAtATime ) :  void
GENMDeterministicGenerator.testBasicFragment ( ) :  boolean
GENMDeterministicGenerator.writeToFile ( List setOfBasicFragment, int number, int[ ][ ] adjacency ) :  void

cdk-1.0.3.jar, Graph.class
package org.openscience.cdk.structgen.deterministic
Graph.getNumberOfClasses ( ) :  int
Graph.Graph ( )
Graph.partition ( ) :  void

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Problems with Data Types, High Severity (3)

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class EquivalentClassesDeterministicGenerator.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class GENMDeterministicGenerator.

	Change	Effect
1	This class has been removed.	Recompilation of a client program may be terminated with the message: cannot find class Graph.

cdk-1.0.3.jar
package org.openscience.cdk.structgen.deterministic
[+] EquivalentClassesDeterministicGenerator (1)
[+] GENMDeterministicGenerator (1)
[+] Graph (1)

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Problems with Methods, Medium Severity (3)

	Change	Effect
1	Removed java.lang.Exception exception thrown.	Recompilation of a client program may be terminated with the message: cannot override MDLRXNWriter() in MDLRXNWriter; overridden method does not throw java.lang.Exception.

	Change	Effect
1	Removed java.lang.Exception exception thrown.	Recompilation of a client program may be terminated with the message: cannot override MDLRXNWriter(OutputStream) in MDLRXNWriter; overridden method does not throw java.lang.Exception.

	Change	Effect
1	Removed java.lang.Exception exception thrown.	Recompilation of a client program may be terminated with the message: cannot override MDLRXNWriter(Writer) in org.openscience.cdk.io.MDLRXNWriter; overridden method does not throw java.lang.Exception.

cdk-1.0.3.jar, MDLRXNWriter
package org.openscience.cdk.io
[+] MDLRXNWriter.MDLRXNWriter ( ) (1)
[+] MDLRXNWriter.MDLRXNWriter ( OutputStream output ) (1)
[+] MDLRXNWriter.MDLRXNWriter ( Writer out ) (1)

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Other Changes in Data Types (4)

	Change	Effect
1	Field mayclose 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 mayclose is ambiguous.

	Change	Effect
1	Field rdFields 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 rdFields is ambiguous.

	Change	Effect
1	Field OBJECT_UNIQUE_POLICY 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 OBJECT_UNIQUE_POLICY is ambiguous.
2	Field SET_UNIQUE_POLICY 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 SET_UNIQUE_POLICY is ambiguous.

cdk-1.0.3.jar
package org.openscience.cdk.applications.swing.editor
[+] ChemObjectEditor (1)

package org.openscience.cdk.io
[+] MDLRXNWriter (1)

package org.openscience.cdk.tools
[+] IDCreator (2)

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Java ARchives (1)

cdk-1.0.3.jar

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