test_class.declarator: structure2N5E
test_class.modifier: private static
test_class.original_string: private static OakStructure structure2N5E;
test_class.type: OakStructure
test_class.var_name: structure2N5E
test_class.declarator: structure1C0A
test_class.modifier: private static
test_class.original_string: private static OakStructure structure1C0A;
test_class.type: OakStructure
test_class.var_name: structure1C0A
test_class.declarator: structureToModify
test_class.modifier: private static
test_class.original_string: private static OakStructure structureToModify;
test_class.type: OakStructure
test_class.var_name: structureToModify
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/OakStructureTest.java
test_class.identifier: OakStructureTest
test_case.body: @Test
      void getAllLeafSubstructures() {
          List<LeafSubstructure<?>> leafSubstructures = structure2N5E.getAllLeafSubstructures();
          assertEquals(3340, leafSubstructures.size());
      }
test_case.class_method_signature: OakStructureTest.getAllLeafSubstructures()
test_case.full_signature: @Test void getAllLeafSubstructures()
test_case.identifier: getAllLeafSubstructures
test_case.invocations: getAllLeafSubstructures assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void getAllLeafSubstructures()
focal_class.declarator: models
focal_class.modifier: private final
focal_class.original_string: private final TreeMap<Integer, OakModel> models;
focal_class.type: TreeMap<Integer, OakModel>
focal_class.var_name: models
focal_class.declarator: pdbIdentifier
focal_class.modifier: private
focal_class.original_string: private String pdbIdentifier;
focal_class.type: String
focal_class.var_name: pdbIdentifier
focal_class.declarator: title
focal_class.modifier: private
focal_class.original_string: private String title;
focal_class.type: String
focal_class.var_name: title
focal_class.declarator: lastAddedAtomIdentifier
focal_class.modifier: private
focal_class.original_string: private int lastAddedAtomIdentifier;
focal_class.type: int
focal_class.var_name: lastAddedAtomIdentifier
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/OakStructure.java
focal_class.identifier: OakStructure
focal_class.interfaces: implements Structure
focal_class.class_method_signature: OakStructure.OakStructure()
focal_class.full_signature: public  OakStructure()
focal_class.identifier: OakStructure
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  OakStructure()
focal_class.class_method_signature: OakStructure.OakStructure(OakStructure structure)
focal_class.full_signature: public  OakStructure(OakStructure structure)
focal_class.identifier: OakStructure
focal_class.modifiers: public
focal_class.parameters: (OakStructure structure)
focal_class.signature:  OakStructure(OakStructure structure)
focal_class.class_method_signature: OakStructure.getPdbIdentifier()
focal_class.full_signature: @Override public String getPdbIdentifier()
focal_class.identifier: getPdbIdentifier
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getPdbIdentifier()
focal_class.class_method_signature: OakStructure.setPdbIdentifier(String pdbIdentifier)
focal_class.full_signature: public void setPdbIdentifier(String pdbIdentifier)
focal_class.identifier: setPdbIdentifier
focal_class.modifiers: public
focal_class.parameters: (String pdbIdentifier)
focal_class.return: void
focal_class.signature: void setPdbIdentifier(String pdbIdentifier)
focal_class.class_method_signature: OakStructure.getTitle()
focal_class.full_signature: @Override public String getTitle()
focal_class.identifier: getTitle
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getTitle()
focal_class.class_method_signature: OakStructure.setTitle(String title)
focal_class.full_signature: public void setTitle(String title)
focal_class.identifier: setTitle
focal_class.modifiers: public
focal_class.parameters: (String title)
focal_class.return: void
focal_class.signature: void setTitle(String title)
focal_class.class_method_signature: OakStructure.getAllModels()
focal_class.full_signature: @Override public List<Model> getAllModels()
focal_class.identifier: getAllModels
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Model>
focal_class.signature: List<Model> getAllModels()
focal_class.class_method_signature: OakStructure.getAllModelIdentifiers()
focal_class.full_signature: @Override public Set<Integer> getAllModelIdentifiers()
focal_class.identifier: getAllModelIdentifiers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Set<Integer>
focal_class.signature: Set<Integer> getAllModelIdentifiers()
focal_class.class_method_signature: OakStructure.getFirstModel()
focal_class.full_signature: @Override public Model getFirstModel()
focal_class.identifier: getFirstModel
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Model
focal_class.signature: Model getFirstModel()
focal_class.class_method_signature: OakStructure.getModel(int modelIdentifier)
focal_class.full_signature: @Override public Optional<Model> getModel(int modelIdentifier)
focal_class.identifier: getModel
focal_class.modifiers: @Override public
focal_class.parameters: (int modelIdentifier)
focal_class.return: Optional<Model>
focal_class.signature: Optional<Model> getModel(int modelIdentifier)
focal_class.class_method_signature: OakStructure.removeModel(int modelIdentifier)
focal_class.full_signature: @Override public void removeModel(int modelIdentifier)
focal_class.identifier: removeModel
focal_class.modifiers: @Override public
focal_class.parameters: (int modelIdentifier)
focal_class.return: void
focal_class.signature: void removeModel(int modelIdentifier)
focal_class.class_method_signature: OakStructure.addModel(OakModel model)
focal_class.full_signature: public void addModel(OakModel model)
focal_class.identifier: addModel
focal_class.modifiers: public
focal_class.parameters: (OakModel model)
focal_class.return: void
focal_class.signature: void addModel(OakModel model)
focal_class.class_method_signature: OakStructure.getChain(int modelIdentifier, String chainIdentifier)
focal_class.full_signature: @Override public Optional<Chain> getChain(int modelIdentifier, String chainIdentifier)
focal_class.identifier: getChain
focal_class.modifiers: @Override public
focal_class.parameters: (int modelIdentifier, String chainIdentifier)
focal_class.return: Optional<Chain>
focal_class.signature: Optional<Chain> getChain(int modelIdentifier, String chainIdentifier)
focal_class.class_method_signature: OakStructure.getAllChains()
focal_class.full_signature: @Override public List<Chain> getAllChains()
focal_class.identifier: getAllChains
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Chain>
focal_class.signature: List<Chain> getAllChains()
focal_class.class_method_signature: OakStructure.getFirstChain()
focal_class.full_signature: @Override public Chain getFirstChain()
focal_class.identifier: getFirstChain
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Chain
focal_class.signature: Chain getFirstChain()
focal_class.class_method_signature: OakStructure.getAllLeafSubstructures()
focal_class.full_signature: @Override public List<LeafSubstructure<?>> getAllLeafSubstructures()
focal_class.identifier: getAllLeafSubstructures
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<LeafSubstructure<?>>
focal_class.signature: List<LeafSubstructure<?>> getAllLeafSubstructures()
focal_class.class_method_signature: OakStructure.getLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.full_signature: @Override public Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.identifier: getLeafSubstructure
focal_class.modifiers: @Override public
focal_class.parameters: (LeafIdentifier leafIdentifier)
focal_class.return: Optional<LeafSubstructure<?>>
focal_class.signature: Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.class_method_signature: OakStructure.getFirstLeafSubstructure()
focal_class.full_signature: @Override public LeafSubstructure<?> getFirstLeafSubstructure()
focal_class.identifier: getFirstLeafSubstructure
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: LeafSubstructure<?>
focal_class.signature: LeafSubstructure<?> getFirstLeafSubstructure()
focal_class.class_method_signature: OakStructure.removeLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.full_signature: @Override public boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.identifier: removeLeafSubstructure
focal_class.modifiers: @Override public
focal_class.parameters: (LeafIdentifier leafIdentifier)
focal_class.return: boolean
focal_class.signature: boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.class_method_signature: OakStructure.getAtom(Integer atomIdentifier)
focal_class.full_signature: @Override public Optional<Atom> getAtom(Integer atomIdentifier)
focal_class.identifier: getAtom
focal_class.modifiers: @Override public
focal_class.parameters: (Integer atomIdentifier)
focal_class.return: Optional<Atom>
focal_class.signature: Optional<Atom> getAtom(Integer atomIdentifier)
focal_class.class_method_signature: OakStructure.getUniqueAtomEntry(int atomSerial)
focal_class.full_signature: public Optional<Map.Entry<UniqueAtomIdentifer, Atom>> getUniqueAtomEntry(int atomSerial)
focal_class.identifier: getUniqueAtomEntry
focal_class.modifiers: public
focal_class.parameters: (int atomSerial)
focal_class.return: Optional<Map.Entry<UniqueAtomIdentifer, Atom>>
focal_class.signature: Optional<Map.Entry<UniqueAtomIdentifer, Atom>> getUniqueAtomEntry(int atomSerial)
focal_class.class_method_signature: OakStructure.getAtomByCoordinate(Vector3D coordinate, double eps)
focal_class.full_signature: public Optional<Map.Entry<UniqueAtomIdentifer, Atom>> getAtomByCoordinate(Vector3D coordinate, double eps)
focal_class.identifier: getAtomByCoordinate
focal_class.modifiers: public
focal_class.parameters: (Vector3D coordinate, double eps)
focal_class.return: Optional<Map.Entry<UniqueAtomIdentifer, Atom>>
focal_class.signature: Optional<Map.Entry<UniqueAtomIdentifer, Atom>> getAtomByCoordinate(Vector3D coordinate, double eps)
focal_class.class_method_signature: OakStructure.addAtom(String chainIdentifier, String threeLetterCode, Vector3D position)
focal_class.full_signature: public void addAtom(String chainIdentifier, String threeLetterCode, Vector3D position)
focal_class.identifier: addAtom
focal_class.modifiers: public
focal_class.parameters: (String chainIdentifier, String threeLetterCode, Vector3D position)
focal_class.return: void
focal_class.signature: void addAtom(String chainIdentifier, String threeLetterCode, Vector3D position)
focal_class.class_method_signature: OakStructure.removeAtom(Integer atomIdentifier)
focal_class.full_signature: @Override public void removeAtom(Integer atomIdentifier)
focal_class.identifier: removeAtom
focal_class.modifiers: @Override public
focal_class.parameters: (Integer atomIdentifier)
focal_class.return: void
focal_class.signature: void removeAtom(Integer atomIdentifier)
focal_class.class_method_signature: OakStructure.getLastAddedAtomIdentifier()
focal_class.full_signature: public int getLastAddedAtomIdentifier()
focal_class.identifier: getLastAddedAtomIdentifier
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getLastAddedAtomIdentifier()
focal_class.class_method_signature: OakStructure.setLastAddedAtomIdentifier(int lastAddedAtomIdentifier)
focal_class.full_signature: public void setLastAddedAtomIdentifier(int lastAddedAtomIdentifier)
focal_class.identifier: setLastAddedAtomIdentifier
focal_class.modifiers: public
focal_class.parameters: (int lastAddedAtomIdentifier)
focal_class.return: void
focal_class.signature: void setLastAddedAtomIdentifier(int lastAddedAtomIdentifier)
focal_class.class_method_signature: OakStructure.getCopy()
focal_class.full_signature: @Override public Structure getCopy()
focal_class.identifier: getCopy
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Structure
focal_class.signature: Structure getCopy()
focal_class.class_method_signature: OakStructure.equals(Object o)
focal_class.full_signature: @Override public boolean equals(Object o)
focal_class.identifier: equals
focal_class.modifiers: @Override public
focal_class.parameters: (Object o)
focal_class.return: boolean
focal_class.signature: boolean equals(Object o)
focal_class.class_method_signature: OakStructure.hashCode()
focal_class.full_signature: @Override public int hashCode()
focal_class.identifier: hashCode
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int hashCode()
focal_class.class_method_signature: OakStructure.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_method.body: @Override
      public List<LeafSubstructure<?>> getAllLeafSubstructures() {
          List<LeafSubstructure<?>> allLeafSubstructures = new ArrayList<>();
          for (OakModel model : models.values()) {
              allLeafSubstructures.addAll(model.getAllLeafSubstructures());
          }
          return allLeafSubstructures;
      }
focal_method.class_method_signature: OakStructure.getAllLeafSubstructures()
focal_method.full_signature: @Override public List<LeafSubstructure<?>> getAllLeafSubstructures()
focal_method.identifier: getAllLeafSubstructures
focal_method.invocations: values addAll getAllLeafSubstructures
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: List<LeafSubstructure<?>>
focal_method.signature: List<LeafSubstructure<?>> getAllLeafSubstructures()