test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingHandlerTest.java
test_class.identifier: SingleMappingHandlerTest
test_class.superclass: extends AbstractMCSAlgorithmTest
test_case.body: @Test
      @Override
      public void testSearchMCS() {
          IAtom atomSource = new Atom("R");
          IAtom atomTarget = new Atom("R");
          IAtomContainer source = new AtomContainer();
          source.addAtom(atomSource);
          IAtomContainer target = new AtomContainer();
          target.addAtom(atomTarget);
          boolean removeHydrogen = false;
          SingleMappingHandler instance = new SingleMappingHandler(removeHydrogen);
          MolHandler mol1 = new MolHandler(source, true, true);
          MolHandler mol2 = new MolHandler(target, true, true);
          instance.set(mol1, mol2);
          instance.searchMCS(true);
          assertNotNull(instance.getAllMapping());
          assertEquals(1, instance.getAllMapping().size());
      }
test_case.class_method_signature: SingleMappingHandlerTest.testSearchMCS()
test_case.full_signature: @Test @Override public void testSearchMCS()
test_case.identifier: testSearchMCS
test_case.invocations: addAtom addAtom set searchMCS assertNotNull getAllMapping assertEquals size getAllMapping
test_case.modifiers: @Test @Override public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testSearchMCS()
focal_class.declarator: allAtomMCS     = null
focal_class.modifier: private static
focal_class.original_string: private static List<Map<IAtom, IAtom>>     allAtomMCS     = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: allAtomMCS
focal_class.declarator: atomsMCS       = null
focal_class.modifier: private static
focal_class.original_string: private static Map<IAtom, IAtom>           atomsMCS       = null;
focal_class.type: Map<IAtom, IAtom>
focal_class.var_name: atomsMCS
focal_class.declarator: firstMCS       = null
focal_class.modifier: private static
focal_class.original_string: private static 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 static
focal_class.original_string: private static List<Map<Integer, Integer>> allMCS         = null;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: allMCS
focal_class.declarator: source         = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer                     source         = null;
focal_class.type: IAtomContainer
focal_class.var_name: source
focal_class.declarator: smartSource    = null
focal_class.modifier: private
focal_class.original_string: private IQueryAtomContainer                smartSource    = null;
focal_class.type: IQueryAtomContainer
focal_class.var_name: smartSource
focal_class.declarator: target         = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer                     target         = null;
focal_class.type: IAtomContainer
focal_class.var_name: target
focal_class.declarator: removeHydrogen = false
focal_class.modifier: private
focal_class.original_string: private boolean                            removeHydrogen = false;
focal_class.type: boolean
focal_class.var_name: removeHydrogen
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingHandler.java
focal_class.identifier: SingleMappingHandler
focal_class.interfaces: implements IMCSBase
focal_class.class_method_signature: SingleMappingHandler.SingleMappingHandler(boolean removeH)
focal_class.full_signature: public  SingleMappingHandler(boolean removeH)
focal_class.identifier: SingleMappingHandler
focal_class.modifiers: public
focal_class.parameters: (boolean removeH)
focal_class.signature:  SingleMappingHandler(boolean removeH)
focal_class.class_method_signature: SingleMappingHandler.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: SingleMappingHandler.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: SingleMappingHandler.searchMCS(boolean bondTypeMatch)
focal_class.full_signature: @Override public void searchMCS(boolean bondTypeMatch)
focal_class.identifier: searchMCS
focal_class.modifiers: @Override public
focal_class.parameters: (boolean bondTypeMatch)
focal_class.return: void
focal_class.signature: void searchMCS(boolean bondTypeMatch)
focal_class.class_method_signature: SingleMappingHandler.setAllMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.full_signature: private void setAllMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.identifier: setAllMapping
focal_class.modifiers: private
focal_class.parameters: (List<Map<IAtom, IAtom>> mappings)
focal_class.return: void
focal_class.signature: void setAllMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.class_method_signature: SingleMappingHandler.setAllAtomMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.full_signature: private synchronized void setAllAtomMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.identifier: setAllAtomMapping
focal_class.modifiers: private synchronized
focal_class.parameters: (List<Map<IAtom, IAtom>> mappings)
focal_class.return: void
focal_class.signature: void setAllAtomMapping(List<Map<IAtom, IAtom>> mappings)
focal_class.class_method_signature: SingleMappingHandler.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: SingleMappingHandler.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: SingleMappingHandler.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: SingleMappingHandler.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: SingleMappingHandler.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: SingleMappingHandler.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 void searchMCS(boolean bondTypeMatch) {
          SingleMapping singleMapping = new SingleMapping();
          List<Map<IAtom, IAtom>> mappings = null;
          try {
              if (this.smartSource == null) {
                  mappings = singleMapping.getOverLaps(source, target, removeHydrogen);
              } else {
                  mappings = singleMapping.getOverLaps(smartSource, target, removeHydrogen);
              }
          } catch (CDKException ex) {
              Logger.getLogger(SingleMappingHandler.class.getName()).log(Level.SEVERE, null, ex);
          }
  
          setAllAtomMapping(mappings);
          setAllMapping(mappings);
          setFirstMapping();
          setFirstAtomMapping();
          //setStereoScore();
      }
focal_method.class_method_signature: SingleMappingHandler.searchMCS(boolean bondTypeMatch)
focal_method.full_signature: @Override public void searchMCS(boolean bondTypeMatch)
focal_method.identifier: searchMCS
focal_method.invocations: getOverLaps getOverLaps log getLogger getName setAllAtomMapping setAllMapping setFirstMapping setFirstAtomMapping
focal_method.modifiers: @Override public
focal_method.parameters: (boolean bondTypeMatch)
focal_method.return: void
focal_method.signature: void searchMCS(boolean bondTypeMatch)