test_class.declarator: handler = new CDKRMapHandler()
test_class.modifier: private final
test_class.original_string: private final CDKRMapHandler handler = new CDKRMapHandler();
test_class.type: CDKRMapHandler
test_class.var_name: handler
test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandlerTest.java
test_class.identifier: CDKRMapHandlerTest
test_case.body: @Test
      public void testGetTarget() {
          IAtomContainer expResult = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
          handler.setTarget(expResult);
          IAtomContainer result = handler.getTarget();
          Assert.assertEquals(expResult, result);
      }
test_case.class_method_signature: CDKRMapHandlerTest.testGetTarget()
test_case.full_signature: @Test public void testGetTarget()
test_case.identifier: testGetTarget
test_case.invocations: newInstance getInstance setTarget getTarget assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetTarget()
focal_class.declarator: mappings
focal_class.modifier: private
focal_class.original_string: private List<Map<Integer, Integer>> mappings;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: mappings
focal_class.declarator: source
focal_class.modifier: private
focal_class.original_string: private IAtomContainer       source;
focal_class.type: IAtomContainer
focal_class.var_name: source
focal_class.declarator: target
focal_class.modifier: private
focal_class.original_string: private IAtomContainer       target;
focal_class.type: IAtomContainer
focal_class.var_name: target
focal_class.declarator: timeoutFlag = false
focal_class.modifier: private
focal_class.original_string: private boolean                     timeoutFlag = false;
focal_class.type: boolean
focal_class.var_name: timeoutFlag
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java
focal_class.identifier: CDKRMapHandler
focal_class.class_method_signature: CDKRMapHandler.CDKRMapHandler()
focal_class.full_signature: public  CDKRMapHandler()
focal_class.identifier: CDKRMapHandler
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  CDKRMapHandler()
focal_class.class_method_signature: CDKRMapHandler.getSource()
focal_class.full_signature: public IAtomContainer getSource()
focal_class.identifier: getSource
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getSource()
focal_class.class_method_signature: CDKRMapHandler.setSource(IAtomContainer aSource)
focal_class.full_signature: public void setSource(IAtomContainer aSource)
focal_class.identifier: setSource
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer aSource)
focal_class.return: void
focal_class.signature: void setSource(IAtomContainer aSource)
focal_class.class_method_signature: CDKRMapHandler.getTarget()
focal_class.full_signature: public IAtomContainer getTarget()
focal_class.identifier: getTarget
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getTarget()
focal_class.class_method_signature: CDKRMapHandler.setTarget(IAtomContainer aTarget)
focal_class.full_signature: public void setTarget(IAtomContainer aTarget)
focal_class.identifier: setTarget
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer aTarget)
focal_class.return: void
focal_class.signature: void setTarget(IAtomContainer aTarget)
focal_class.class_method_signature: CDKRMapHandler.calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.full_signature: public void calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.identifier: calculateOverlapsAndReduce
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKRMapHandler.calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2,
              boolean shouldMatchBonds)
focal_class.full_signature: public void calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2,
              boolean shouldMatchBonds)
focal_class.identifier: calculateOverlapsAndReduceExactMatch
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule1, IAtomContainer molecule2,
              boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKRMapHandler.calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.full_signature: public void calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.identifier: calculateSubGraphs
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKRMapHandler.calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.full_signature: public void calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.identifier: calculateIsomorphs
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKRMapHandler.removeSubGraph(List<List<CDKRMap>> overlaps)
focal_class.full_signature: protected List<List<CDKRMap>> removeSubGraph(List<List<CDKRMap>> overlaps)
focal_class.identifier: removeSubGraph
focal_class.modifiers: protected
focal_class.parameters: (List<List<CDKRMap>> overlaps)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> removeSubGraph(List<List<CDKRMap>> overlaps)
focal_class.class_method_signature: CDKRMapHandler.removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
focal_class.full_signature: protected List<CDKRMap> removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
focal_class.identifier: removeRedundantMappingsForSingleAtomCase
focal_class.modifiers: protected
focal_class.parameters: (List<CDKRMap> overlaps)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
focal_class.class_method_signature: CDKRMapHandler.makeAtomsMapOfBondsMap(List<CDKRMap> rMapList, IAtomContainer graph1,
              IAtomContainer graph2)
focal_class.full_signature: private static List<List<CDKRMap>> makeAtomsMapOfBondsMap(List<CDKRMap> rMapList, IAtomContainer graph1,
              IAtomContainer graph2)
focal_class.identifier: makeAtomsMapOfBondsMap
focal_class.modifiers: private static
focal_class.parameters: (List<CDKRMap> rMapList, IAtomContainer graph1,
              IAtomContainer graph2)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> makeAtomsMapOfBondsMap(List<CDKRMap> rMapList, IAtomContainer graph1,
              IAtomContainer graph2)
focal_class.class_method_signature: CDKRMapHandler.makeAtomsMapOfBondsMapSingleBond(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.full_signature: private static List<List<CDKRMap>> makeAtomsMapOfBondsMapSingleBond(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.identifier: makeAtomsMapOfBondsMapSingleBond
focal_class.modifiers: private static
focal_class.parameters: (List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> makeAtomsMapOfBondsMapSingleBond(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.class_method_signature: CDKRMapHandler.getMaximum(List overlaps)
focal_class.full_signature: protected List getMaximum(List overlaps)
focal_class.identifier: getMaximum
focal_class.modifiers: protected
focal_class.parameters: (List overlaps)
focal_class.return: List
focal_class.signature: List getMaximum(List overlaps)
focal_class.class_method_signature: CDKRMapHandler.getAllMaximum(List<List<CDKRMap>> overlaps)
focal_class.full_signature: protected Stack<List<CDKRMap>> getAllMaximum(List<List<CDKRMap>> overlaps)
focal_class.identifier: getAllMaximum
focal_class.modifiers: protected
focal_class.parameters: (List<List<CDKRMap>> overlaps)
focal_class.return: Stack<List<CDKRMap>>
focal_class.signature: Stack<List<CDKRMap>> getAllMaximum(List<List<CDKRMap>> overlaps)
focal_class.class_method_signature: CDKRMapHandler.identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target)
focal_class.full_signature: protected void identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target)
focal_class.identifier: identifyMatchedParts
focal_class.modifiers: protected
focal_class.parameters: (List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target)
focal_class.return: void
focal_class.signature: void identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target)
focal_class.class_method_signature: CDKRMapHandler.identifySingleAtomsMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target)
focal_class.full_signature: protected void identifySingleAtomsMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target)
focal_class.identifier: identifySingleAtomsMatchedParts
focal_class.modifiers: protected
focal_class.parameters: (List<CDKRMap> list, IAtomContainer source, IAtomContainer target)
focal_class.return: void
focal_class.signature: void identifySingleAtomsMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target)
focal_class.class_method_signature: CDKRMapHandler.isSubgraph(List<CDKRMap> rmaps1, List<CDKRMap> rmaps2)
focal_class.full_signature: protected boolean isSubgraph(List<CDKRMap> rmaps1, List<CDKRMap> rmaps2)
focal_class.identifier: isSubgraph
focal_class.modifiers: protected
focal_class.parameters: (List<CDKRMap> rmaps1, List<CDKRMap> rmaps2)
focal_class.return: boolean
focal_class.signature: boolean isSubgraph(List<CDKRMap> rmaps1, List<CDKRMap> rmaps2)
focal_class.class_method_signature: CDKRMapHandler.isSameRMap(CDKRMap sourceRMap, CDKRMap targetRMap)
focal_class.full_signature: protected boolean isSameRMap(CDKRMap sourceRMap, CDKRMap targetRMap)
focal_class.identifier: isSameRMap
focal_class.modifiers: protected
focal_class.parameters: (CDKRMap sourceRMap, CDKRMap targetRMap)
focal_class.return: boolean
focal_class.signature: boolean isSameRMap(CDKRMap sourceRMap, CDKRMap targetRMap)
focal_class.class_method_signature: CDKRMapHandler.getMappings()
focal_class.full_signature: public List<Map<Integer, Integer>> getMappings()
focal_class.identifier: getMappings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Map<Integer, Integer>>
focal_class.signature: List<Map<Integer, Integer>> getMappings()
focal_class.class_method_signature: CDKRMapHandler.setMappings(List<Map<Integer, Integer>> mappings)
focal_class.full_signature: public void setMappings(List<Map<Integer, Integer>> mappings)
focal_class.identifier: setMappings
focal_class.modifiers: public
focal_class.parameters: (List<Map<Integer, Integer>> mappings)
focal_class.return: void
focal_class.signature: void setMappings(List<Map<Integer, Integer>> mappings)
focal_class.class_method_signature: CDKRMapHandler.isTimeoutFlag()
focal_class.full_signature: public boolean isTimeoutFlag()
focal_class.identifier: isTimeoutFlag
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isTimeoutFlag()
focal_class.class_method_signature: CDKRMapHandler.setTimeoutFlag(boolean timeoutFlag)
focal_class.full_signature: public void setTimeoutFlag(boolean timeoutFlag)
focal_class.identifier: setTimeoutFlag
focal_class.modifiers: public
focal_class.parameters: (boolean timeoutFlag)
focal_class.return: void
focal_class.signature: void setTimeoutFlag(boolean timeoutFlag)
focal_method.body: public IAtomContainer getTarget() {
          return target;
      }
focal_method.class_method_signature: CDKRMapHandler.getTarget()
focal_method.full_signature: public IAtomContainer getTarget()
focal_method.identifier: getTarget
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: IAtomContainer
focal_method.signature: IAtomContainer getTarget()