Binary 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 | 0 |
| Low | 3 |
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 )
[mangled: org/openscience/cdk/applications/swing/editor/AtomEditor."<init>":(Lorg/openscience/cdk/interfaces/IChemModel;Ljavax/swing/undo/UndoableEditSupport;)V]
cdk-1.0.4.jar, ChemFileManipulator.class
package org.openscience.cdk.tools.manipulator
ChemFileManipulator.getAllReactions ( IChemFile file ) [static] : List
[mangled: org/openscience/cdk/tools/manipulator/ChemFileManipulator.getAllReactions:(Lorg/openscience/cdk/interfaces/IChemFile;)Ljava/util/List;]
cdk-1.0.4.jar, ChemObjectEditor.class
package org.openscience.cdk.applications.swing.editor
ChemObjectEditor.getMayclose ( ) : boolean
[mangled: org/openscience/cdk/applications/swing/editor/ChemObjectEditor.getMayclose:()Z]
cdk-1.0.4.jar, ConvertToAtomEdit.class
package org.openscience.cdk.applications.undoredo
ConvertToAtomEdit.canRedo ( ) : boolean
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit.canRedo:()Z]
ConvertToAtomEdit.canUndo ( ) : boolean
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit.canUndo:()Z]
ConvertToAtomEdit.ConvertToAtomEdit ( IAtomContainer relevantContainer, IPseudoAtom pseudo, IAtom atom )
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit."<init>":(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/interfaces/IPseudoAtom;Lorg/openscience/cdk/interfaces/IAtom;)V]
ConvertToAtomEdit.getPresentationName ( ) : String
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit.getPresentationName:()Ljava/lang/String;]
ConvertToAtomEdit.redo ( ) : void
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit.redo:()V]
ConvertToAtomEdit.undo ( ) : void
[mangled: org/openscience/cdk/applications/undoredo/ConvertToAtomEdit.undo:()V]
cdk-1.0.4.jar, GeometryTools.class
package org.openscience.cdk.geometry
GeometryTools.center ( IReaction reaction, Dimension areaDim, HashMap renderingCoordinates ) [static] : void
[mangled: org/openscience/cdk/geometry/GeometryTools.center:(Lorg/openscience/cdk/interfaces/IReaction;Ljava/awt/Dimension;Ljava/util/HashMap;)V]
GeometryTools.translate2D ( IReaction reaction, double transX, double transY, HashMap renderingCoordinates ) [static] : void
[mangled: org/openscience/cdk/geometry/GeometryTools.translate2D:(Lorg/openscience/cdk/interfaces/IReaction;DDLjava/util/HashMap;)V]
GeometryTools.translate2D ( IReaction reaction, Vector2d vector, HashMap renderingCoordinates ) [static] : void
[mangled: org/openscience/cdk/geometry/GeometryTools.translate2D:(Lorg/openscience/cdk/interfaces/IReaction;Ljavax/vecmath/Vector2d;Ljava/util/HashMap;)V]
GeometryTools.translateAllPositive ( IReaction reaction, HashMap renderingCoordinates ) [static] : void
[mangled: org/openscience/cdk/geometry/GeometryTools.translateAllPositive:(Lorg/openscience/cdk/interfaces/IReaction;Ljava/util/HashMap;)V]
cdk-1.0.4.jar, IDCreator.class
package org.openscience.cdk.tools
IDCreator.setIDPolicy ( int policy ) [static] : void
[mangled: org/openscience/cdk/tools/IDCreator.setIDPolicy:(I)V]
cdk-1.0.4.jar, MDLRXNWriter.class
package org.openscience.cdk.io
MDLRXNWriter.setRdFields ( Map map ) : void
[mangled: org/openscience/cdk/io/MDLRXNWriter.setRdFields:(Ljava/util/Map;)V]
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Removed Methods (46)
cdk-1.0.3.jar, AtomEditor.class
package org.openscience.cdk.applications.swing.editor
AtomEditor.AtomEditor ( )
[mangled: org/openscience/cdk/applications/swing/editor/AtomEditor."<init>":()V]
cdk-1.0.3.jar, EquivalentClassesDeterministicGenerator.class
package org.openscience.cdk.structgen.deterministic
EquivalentClassesDeterministicGenerator.EquivalentClassesDeterministicGenerator ( )
[mangled: org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator."<init>":()V]
EquivalentClassesDeterministicGenerator.setAtomContainer ( IAtomContainer ac ) : void
[mangled: org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.setAtomContainer:(Lorg/openscience/cdk/interfaces/IAtomContainer;)V]
cdk-1.0.3.jar, GENMDeterministicGenerator.class
package org.openscience.cdk.structgen.deterministic
GENMDeterministicGenerator.addListener ( IStructureGenerationListener x ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.addListener:(Lorg/openscience/cdk/structgen/IStructureGenerationListener;)V]
GENMDeterministicGenerator.analyseMolecularFormula ( MFAnalyser mfa ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.analyseMolecularFormula:(Lorg/openscience/cdk/tools/MFAnalyser;)V]
GENMDeterministicGenerator.checkAdmissibility ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.checkAdmissibility:(ILjava/util/List;[[I)Z]
GENMDeterministicGenerator.checkConstraint ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix, IAtomContainer ac ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.checkConstraint:(ILjava/util/List;[[ILorg/openscience/cdk/interfaces/IAtomContainer;)Z]
GENMDeterministicGenerator.convertToMol ( List set, int[ ][ ] matrix, List structures ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.convertToMol:(Ljava/util/List;[[ILjava/util/List;)V]
GENMDeterministicGenerator.DFSM ( int[ ][ ] adjacency, int number, boolean[ ] isVisited ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.DFSM:([[II[Z)V]
GENMDeterministicGenerator.fireChange ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.fireChange:()V]
GENMDeterministicGenerator.forceFilling ( int step, List setOfBasicFragment, int[ ][ ] adjacencyMatrix, int[ ][ ] previousMatrix ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.forceFilling:(ILjava/util/List;[[I[[I)I]
GENMDeterministicGenerator.generate ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.generate:()V]
GENMDeterministicGenerator.generateBasicFragments ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.generateBasicFragments:()V]
GENMDeterministicGenerator.generateBasicUnits ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.generateBasicUnits:()V]
GENMDeterministicGenerator.generateIsomers ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.generateIsomers:()V]
GENMDeterministicGenerator.GENMDeterministicGenerator ( String mf, String path )
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator."<init>":(Ljava/lang/String;Ljava/lang/String;)V]
GENMDeterministicGenerator.getAtomContainer ( ) : IAtomContainer
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getAtomContainer:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
GENMDeterministicGenerator.getBasicUnit ( List basicUnits ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getBasicUnit:(Ljava/util/List;)V]
GENMDeterministicGenerator.getEquivalentClass ( List setOfBasicFragment, int[ ] setOfStability ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getEquivalentClass:(Ljava/util/List;[I)I]
GENMDeterministicGenerator.getFinalStructure ( List setOfBasicFragment, int[ ][ ] adjacencyMatrix, GENMDeterministicGenerator.IntArray storedSymbolOfStructure, int[ ] totalNumberOfThisSet, int totalNumberOfAtomAndBond ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getFinalStructure:(Ljava/util/List;[[ILorg/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator$IntArray;[II)V]
GENMDeterministicGenerator.getMaximumWCF ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacency, int[ ][ ] previousMatrix, int[ ] parentID ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getMaximumWCF:(Ljava/util/List;I[I[[I[[I[I)Z]
GENMDeterministicGenerator.getNextWCF ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacencyMatrix, int[ ][ ] previousMatrix, int[ ] parentID ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getNextWCF:(Ljava/util/List;I[I[[I[[I[I)Z]
GENMDeterministicGenerator.getNumberOfStructures ( ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getNumberOfStructures:()I]
GENMDeterministicGenerator.getOrderOfBasicFragmentSet ( List setOfBasicFragment, int[ ] parentID ) : List
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getOrderOfBasicFragmentSet:(Ljava/util/List;[I)Ljava/util/List;]
GENMDeterministicGenerator.getReturnedStructureCount ( ) : long
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getReturnedStructureCount:()J]
GENMDeterministicGenerator.getSetOfStability ( List setOfBasicFragment, int step, int[ ] rowMatrix, int[ ][ ] adjacency, int[ ] setOfStability, int[ ] parentID ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getSetOfStability:(Ljava/util/List;I[I[[I[I[I)V]
GENMDeterministicGenerator.getStructures ( ) : List
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getStructures:()Ljava/util/List;]
GENMDeterministicGenerator.getStructuresAtATime ( ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getStructuresAtATime:()I]
GENMDeterministicGenerator.getSymmetryFromAllPath ( int size, int[ ][ ] connectivity, int[ ] classID ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getSymmetryFromAllPath:(I[[I[I)I]
GENMDeterministicGenerator.getSymmetryFromNeighbour ( int size, int number, int[ ][ ] connectivity, int[ ] classID ) : int
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.getSymmetryFromNeighbour:(II[[I[I)I]
GENMDeterministicGenerator.hasMoreStructures ( ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.hasMoreStructures:()Z]
GENMDeterministicGenerator.initializeMatrix ( List setOfBasicFragment, int[ ] bondAttribute, int[ ][ ] adjacency, int[ ][ ] previousMatrix ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.initializeMatrix:(Ljava/util/List;[I[[I[[I)V]
GENMDeterministicGenerator.initializeParameters ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.initializeParameters:()V]
GENMDeterministicGenerator.isForceFilling ( int step, int[ ][ ] previousMatrix, int[ ][ ] adjacency ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.isForceFilling:(I[[I[[I)Z]
GENMDeterministicGenerator.normalization ( List setOfBasicFragment, int[ ][ ] adjacencyMatrix ) : int[ ][ ]
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.normalization:(Ljava/util/List;[[I)[[I]
GENMDeterministicGenerator.removeChangeListener ( IStructureGenerationListener x ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.removeChangeListener:(Lorg/openscience/cdk/structgen/IStructureGenerationListener;)V]
GENMDeterministicGenerator.restoreMatrix ( int step, int[ ] freeValence, int[ ][ ] sourceMatrix, int[ ][ ] destMatrix ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.restoreMatrix:(I[I[[I[[I)V]
GENMDeterministicGenerator.setAtomContainer ( IAtomContainer atomContainer ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.setAtomContainer:(Lorg/openscience/cdk/interfaces/IAtomContainer;)V]
GENMDeterministicGenerator.setBasicUnits ( List basicUnits ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.setBasicUnits:(Ljava/util/List;)V]
GENMDeterministicGenerator.setReturnedStructureCount ( long returnedStructureCount ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.setReturnedStructureCount:(J)V]
GENMDeterministicGenerator.setStructuresAtATime ( int structuresAtATime ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.setStructuresAtATime:(I)V]
GENMDeterministicGenerator.testBasicFragment ( ) : boolean
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.testBasicFragment:()Z]
GENMDeterministicGenerator.writeToFile ( List setOfBasicFragment, int number, int[ ][ ] adjacency ) : void
[mangled: org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.writeToFile:(Ljava/util/List;I[[I)V]
cdk-1.0.3.jar, Graph.class
package org.openscience.cdk.structgen.deterministic
Graph.getNumberOfClasses ( ) : int
[mangled: org/openscience/cdk/structgen/deterministic/Graph.getNumberOfClasses:()I]
Graph.Graph ( )
[mangled: org/openscience/cdk/structgen/deterministic/Graph."<init>":()V]
Graph.partition ( ) : void
[mangled: org/openscience/cdk/structgen/deterministic/Graph.partition:()V]
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Problems with Data Types, High Severity (3)
cdk-1.0.3.jar
package org.openscience.cdk.structgen.deterministic
[+] EquivalentClassesDeterministicGenerator (1)
| Change | Effect |
|---|
| 1 | This class has been removed. | A client program may be interrupted by NoClassDefFoundError exception. |
|---|
[+] affected methods (2)
EquivalentClassesDeterministicGenerator ( )This constructor is from 'EquivalentClassesDeterministicGenerator' class.
setAtomContainer ( IAtomContainer )This method is from 'EquivalentClassesDeterministicGenerator' class.
[+] GENMDeterministicGenerator (1)
| Change | Effect |
|---|
| 1 | This class has been removed. | A client program may be interrupted by NoClassDefFoundError exception. |
|---|
[+] affected methods (40)
GENMDeterministicGenerator ( String, String )This constructor is from 'GENMDeterministicGenerator' class.
addListener ( IStructureGenerationListener )This method is from 'GENMDeterministicGenerator' class.
analyseMolecularFormula ( MFAnalyser )This method is from 'GENMDeterministicGenerator' class.
checkAdmissibility ( int, List, int[ ][ ] )This method is from 'GENMDeterministicGenerator' class.
checkConstraint ( int, List, int[ ][ ], IAtomContainer )This method is from 'GENMDeterministicGenerator' class.
convertToMol ( List, int[ ][ ], List )This method is from 'GENMDeterministicGenerator' class.
DFSM ( int[ ][ ], int, boolean[ ] )This method is from 'GENMDeterministicGenerator' class.
fireChange ( )This method is from 'GENMDeterministicGenerator' class.
forceFilling ( int, List, int[ ][ ], int[ ][ ] )This method is from 'GENMDeterministicGenerator' class.
generate ( )This method is from 'GENMDeterministicGenerator' class.
generateBasicFragments ( )This method is from 'GENMDeterministicGenerator' class.
generateBasicUnits ( )This method is from 'GENMDeterministicGenerator' class.
...
[+] Graph (1)
| Change | Effect |
|---|
| 1 | This class has been removed. | A client program may be interrupted by NoClassDefFoundError exception. |
|---|
[+] affected methods (3)
Graph ( )This constructor is from 'Graph' class.
getNumberOfClasses ( )This method is from 'Graph' class.
partition ( )This method is from 'Graph' class.
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Problems with Methods, Low Severity (3)
cdk-1.0.3.jar, MDLRXNWriter
package org.openscience.cdk.io
[+] MDLRXNWriter.MDLRXNWriter ( ) (1)
[mangled: org/openscience/cdk/io/MDLRXNWriter."<init>":()V]
| Change | Effect |
|---|
| 1 | Removed java.lang.Exception exception thrown.
| A client program may change behavior because the removed exception will not be thrown any more and client will not catch and handle it. |
|---|
[+] MDLRXNWriter.MDLRXNWriter ( OutputStream output ) (1)
[mangled: org/openscience/cdk/io/MDLRXNWriter."<init>":(Ljava/io/OutputStream;)V]
| Change | Effect |
|---|
| 1 | Removed java.lang.Exception exception thrown.
| A client program may change behavior because the removed exception will not be thrown any more and client will not catch and handle it. |
|---|
[+] MDLRXNWriter.MDLRXNWriter ( Writer out ) (1)
[mangled: org/openscience/cdk/io/MDLRXNWriter."<init>":(Ljava/io/Writer;)V]
| Change | Effect |
|---|
| 1 | Removed java.lang.Exception exception thrown.
| A client program may change behavior because the removed exception will not be thrown any more and client will not catch and handle it. |
|---|
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Other Changes in Data Types (4)
cdk-1.0.3.jar
package org.openscience.cdk.applications.swing.editor
[+] ChemObjectEditor (1)
| 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 and cause IncompatibleClassChangeError exception. |
|---|
[+] affected methods (3)
ChemObjectEditor ( )This constructor is from 'ChemObjectEditor' abstract class.
applyChanges ( )This method is from 'ChemObjectEditor' abstract class.
setChemObject ( IChemObject )This method is from 'ChemObjectEditor' abstract class.
package org.openscience.cdk.io
[+] MDLRXNWriter (1)
| 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 and cause IncompatibleClassChangeError exception. |
|---|
[+] affected methods (9)
MDLRXNWriter ( )This constructor is from 'MDLRXNWriter' class.
MDLRXNWriter ( OutputStream )This constructor is from 'MDLRXNWriter' class.
MDLRXNWriter ( Writer )This constructor is from 'MDLRXNWriter' class.
accepts ( Class )This method is from 'MDLRXNWriter' class.
close ( )This method is from 'MDLRXNWriter' class.
getFormat ( )This method is from 'MDLRXNWriter' class.
setWriter ( OutputStream )This method is from 'MDLRXNWriter' class.
setWriter ( Writer )This method is from 'MDLRXNWriter' class.
write ( IChemObject )This method is from 'MDLRXNWriter' class.
package org.openscience.cdk.tools
[+] IDCreator (2)
| 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 and cause IncompatibleClassChangeError exception. |
|---|
| 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 and cause IncompatibleClassChangeError exception. |
|---|
[+] affected methods (2)
IDCreator ( )This constructor is from 'IDCreator' abstract class.
createIDs ( IChemObject )This method is from 'IDCreator' abstract class.
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Java ARchives (1)
cdk-1.0.3.jar
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