test_class.declarator: firstModel
test_class.modifier: private static
test_class.original_string: private static OakModel firstModel;
test_class.type: OakModel
test_class.var_name: firstModel
test_class.declarator: secondModel
test_class.modifier: private static
test_class.original_string: private static OakModel secondModel;
test_class.type: OakModel
test_class.var_name: secondModel
test_class.declarator: modelToModify
test_class.modifier: private static
test_class.original_string: private static OakModel modelToModify;
test_class.type: OakModel
test_class.var_name: modelToModify
test_class.declarator: anotherModelToModify
test_class.modifier: private static
test_class.original_string: private static Model anotherModelToModify;
test_class.type: Model
test_class.var_name: anotherModelToModify
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/OakModelTest.java
test_class.identifier: OakModelTest
test_case.body: @Test
      void getCopy() {
          final OakModel firstModelCopy = firstModel.getCopy();
          assertNotSame(firstModel, firstModelCopy);
          assertEquals(firstModel, firstModelCopy);
      }
test_case.class_method_signature: OakModelTest.getCopy()
test_case.full_signature: @Test void getCopy()
test_case.identifier: getCopy
test_case.invocations: getCopy assertNotSame assertEquals
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void getCopy()
focal_class.declarator: identifier
focal_class.modifier: private final
focal_class.original_string: private final Integer identifier;
focal_class.type: Integer
focal_class.var_name: identifier
focal_class.declarator: chains
focal_class.modifier: private final
focal_class.original_string: private final TreeMap<String, OakChain> chains;
focal_class.type: TreeMap<String, OakChain>
focal_class.var_name: chains
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/OakModel.java
focal_class.identifier: OakModel
focal_class.interfaces: implements Model
focal_class.class_method_signature: OakModel.OakModel(int identifier)
focal_class.full_signature: public  OakModel(int identifier)
focal_class.identifier: OakModel
focal_class.modifiers: public
focal_class.parameters: (int identifier)
focal_class.signature:  OakModel(int identifier)
focal_class.class_method_signature: OakModel.OakModel(OakModel model)
focal_class.full_signature: public  OakModel(OakModel model)
focal_class.identifier: OakModel
focal_class.modifiers: public
focal_class.parameters: (OakModel model)
focal_class.signature:  OakModel(OakModel model)
focal_class.class_method_signature: OakModel.getModelIdentifier()
focal_class.full_signature: @Override public Integer getModelIdentifier()
focal_class.identifier: getModelIdentifier
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getModelIdentifier()
focal_class.class_method_signature: OakModel.getFirstChain()
focal_class.full_signature: public Chain getFirstChain()
focal_class.identifier: getFirstChain
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Chain
focal_class.signature: Chain getFirstChain()
focal_class.class_method_signature: OakModel.getAllChains()
focal_class.full_signature: public List<Chain> getAllChains()
focal_class.identifier: getAllChains
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Chain>
focal_class.signature: List<Chain> getAllChains()
focal_class.class_method_signature: OakModel.getAllChainIdentifiers()
focal_class.full_signature: @Override public Set<String> getAllChainIdentifiers()
focal_class.identifier: getAllChainIdentifiers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Set<String>
focal_class.signature: Set<String> getAllChainIdentifiers()
focal_class.class_method_signature: OakModel.getChain(String chainIdentifier)
focal_class.full_signature: @Override public Optional<Chain> getChain(String chainIdentifier)
focal_class.identifier: getChain
focal_class.modifiers: @Override public
focal_class.parameters: (String chainIdentifier)
focal_class.return: Optional<Chain>
focal_class.signature: Optional<Chain> getChain(String chainIdentifier)
focal_class.class_method_signature: OakModel.addChain(OakChain chain)
focal_class.full_signature: public void addChain(OakChain chain)
focal_class.identifier: addChain
focal_class.modifiers: public
focal_class.parameters: (OakChain chain)
focal_class.return: void
focal_class.signature: void addChain(OakChain chain)
focal_class.class_method_signature: OakModel.removeChain(String chainIdentifier)
focal_class.full_signature: @Override public void removeChain(String chainIdentifier)
focal_class.identifier: removeChain
focal_class.modifiers: @Override public
focal_class.parameters: (String chainIdentifier)
focal_class.return: void
focal_class.signature: void removeChain(String chainIdentifier)
focal_class.class_method_signature: OakModel.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: OakModel.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: OakModel.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: OakModel.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: OakModel.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: OakModel.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: OakModel.getCopy()
focal_class.full_signature: @Override public OakModel getCopy()
focal_class.identifier: getCopy
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: OakModel
focal_class.signature: OakModel getCopy()
focal_class.class_method_signature: OakModel.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: OakModel.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: OakModel.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 OakModel getCopy() {
          return new OakModel(this);
      }
focal_method.class_method_signature: OakModel.getCopy()
focal_method.full_signature: @Override public OakModel getCopy()
focal_method.identifier: getCopy
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: OakModel
focal_method.signature: OakModel getCopy()