test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandlerTest.java
test_class.identifier: CDKMCSHandlerTest
test_class.superclass: extends AbstractMCSAlgorithmTest
test_case.body: @Test
      public void testGetAllMapping() throws InvalidSmilesException {
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
          IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");
  
          CDKMCSHandler smsd1 = new CDKMCSHandler();
          MolHandler mol1 = new MolHandler(queryac, true, true);
          MolHandler mol2 = new MolHandler(target, true, true);
          smsd1.set(mol1, mol2);
          smsd1.searchMCS(true);
          smsd1.searchMCS(true);
          assertNotNull(smsd1.getFirstMapping());
  
          assertEquals(4, smsd1.getAllMapping().size());
      }
test_case.class_method_signature: CDKMCSHandlerTest.testGetAllMapping()
test_case.full_signature: @Test public void testGetAllMapping()
test_case.identifier: testGetAllMapping
test_case.invocations: getInstance parseSmiles parseSmiles set searchMCS searchMCS assertNotNull getFirstMapping assertEquals size getAllMapping
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetAllMapping()
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: rOnPFlag     = false
focal_class.modifier: private
focal_class.original_string: private boolean                     rOnPFlag     = false;
focal_class.type: boolean
focal_class.var_name: rOnPFlag
focal_class.declarator: allAtomMCS   = null
focal_class.modifier: private
focal_class.original_string: private List<Map<IAtom, IAtom>>     allAtomMCS   = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: allAtomMCS
focal_class.declarator: firstAtomMCS = null
focal_class.modifier: private
focal_class.original_string: private Map<IAtom, IAtom>           firstAtomMCS = null;
focal_class.type: Map<IAtom, IAtom>
focal_class.var_name: firstAtomMCS
focal_class.declarator: firstMCS     = null
focal_class.modifier: private
focal_class.original_string: private Map<Integer, Integer>       firstMCS     = null;
focal_class.type: Map<Integer, Integer>
focal_class.var_name: firstMCS
focal_class.declarator: allMCS       = null
focal_class.modifier: private
focal_class.original_string: private List<Map<Integer, Integer>> allMCS       = null;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: allMCS
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandler.java
focal_class.identifier: CDKMCSHandler
focal_class.interfaces: implements IMCSBase
focal_class.class_method_signature: CDKMCSHandler.CDKMCSHandler()
focal_class.full_signature: public  CDKMCSHandler()
focal_class.identifier: CDKMCSHandler
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  CDKMCSHandler()
focal_class.class_method_signature: CDKMCSHandler.set(MolHandler source, MolHandler target)
focal_class.full_signature: @Override public void set(MolHandler source, MolHandler target)
focal_class.identifier: set
focal_class.modifiers: @Override public
focal_class.parameters: (MolHandler source, MolHandler target)
focal_class.return: void
focal_class.signature: void set(MolHandler source, MolHandler target)
focal_class.class_method_signature: CDKMCSHandler.set(IQueryAtomContainer source, IAtomContainer target)
focal_class.full_signature: @Override public void set(IQueryAtomContainer source, IAtomContainer target)
focal_class.identifier: set
focal_class.modifiers: @Override public
focal_class.parameters: (IQueryAtomContainer source, IAtomContainer target)
focal_class.return: void
focal_class.signature: void set(IQueryAtomContainer source, IAtomContainer target)
focal_class.class_method_signature: CDKMCSHandler.searchMCS(boolean shouldMatchBonds)
focal_class.full_signature: @Override public void searchMCS(boolean shouldMatchBonds)
focal_class.identifier: searchMCS
focal_class.modifiers: @Override public
focal_class.parameters: (boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void searchMCS(boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCSHandler.getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
focal_class.full_signature: protected IAtomContainerSet getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
focal_class.identifier: getUncommon
focal_class.modifiers: protected
focal_class.parameters: (IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
focal_class.return: IAtomContainerSet
focal_class.signature: IAtomContainerSet getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCSHandler.setAllMapping()
focal_class.full_signature: private synchronized void setAllMapping()
focal_class.identifier: setAllMapping
focal_class.modifiers: private synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setAllMapping()
focal_class.class_method_signature: CDKMCSHandler.setAllAtomMapping()
focal_class.full_signature: private synchronized void setAllAtomMapping()
focal_class.identifier: setAllAtomMapping
focal_class.modifiers: private synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setAllAtomMapping()
focal_class.class_method_signature: CDKMCSHandler.setFirstMapping()
focal_class.full_signature: private synchronized void setFirstMapping()
focal_class.identifier: setFirstMapping
focal_class.modifiers: private synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setFirstMapping()
focal_class.class_method_signature: CDKMCSHandler.setFirstAtomMapping()
focal_class.full_signature: private synchronized void setFirstAtomMapping()
focal_class.identifier: setFirstAtomMapping
focal_class.modifiers: private synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setFirstAtomMapping()
focal_class.class_method_signature: CDKMCSHandler.getAllMapping()
focal_class.full_signature: @Override public List<Map<Integer, Integer>> getAllMapping()
focal_class.identifier: getAllMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Map<Integer, Integer>>
focal_class.signature: List<Map<Integer, Integer>> getAllMapping()
focal_class.class_method_signature: CDKMCSHandler.getFirstMapping()
focal_class.full_signature: @Override public Map<Integer, Integer> getFirstMapping()
focal_class.identifier: getFirstMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<Integer, Integer>
focal_class.signature: Map<Integer, Integer> getFirstMapping()
focal_class.class_method_signature: CDKMCSHandler.getAllAtomMapping()
focal_class.full_signature: @Override public List<Map<IAtom, IAtom>> getAllAtomMapping()
focal_class.identifier: getAllAtomMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Map<IAtom, IAtom>>
focal_class.signature: List<Map<IAtom, IAtom>> getAllAtomMapping()
focal_class.class_method_signature: CDKMCSHandler.getFirstAtomMapping()
focal_class.full_signature: @Override public Map<IAtom, IAtom> getFirstAtomMapping()
focal_class.identifier: getFirstAtomMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<IAtom, IAtom>
focal_class.signature: Map<IAtom, IAtom> getFirstAtomMapping()
focal_class.superclass: extends AbstractMCSAlgorithm
focal_method.body: @Override
      public List<Map<Integer, Integer>> getAllMapping() {
          return Collections.unmodifiableList(allMCS);
      }
focal_method.class_method_signature: CDKMCSHandler.getAllMapping()
focal_method.full_signature: @Override public List<Map<Integer, Integer>> getAllMapping()
focal_method.identifier: getAllMapping
focal_method.invocations: unmodifiableList
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: List<Map<Integer, Integer>>
focal_method.signature: List<Map<Integer, Integer>> getAllMapping()