test_class.declarator: structure2N5E
test_class.modifier: private static
test_class.original_string: private static Structure structure2N5E;
test_class.type: Structure
test_class.var_name: structure2N5E
test_class.declarator: structure1C0A
test_class.modifier: private static
test_class.original_string: private static Structure structure1C0A;
test_class.type: Structure
test_class.var_name: structure1C0A
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/mmtf/MmtfStructureTest.java
test_class.identifier: MmtfStructureTest
test_case.body: @Test
      void shouldIgnoreAlternativePosition() throws IOException {
          final Structure mmtfStructure = new MmtfStructure(ReaderUtils.getByteArrayFromUrl("1dlf"));
          final Structure oakStructure = StructureParser.pdb().pdbIdentifier("1dlf").parse();
          final LeafIdentifier leafIdentifier = new LeafIdentifier("1dlf", 1, "H", 70);
  
          LeafSubstructure mmtfLeaf = mmtfStructure.getLeafSubstructure(leafIdentifier).get();
          LeafSubstructure oakLeaf = oakStructure.getLeafSubstructure(leafIdentifier).get();
          mmtfLeaf.getAllAtoms();
          assertEquals(oakLeaf.getAllAtoms().size(), mmtfLeaf.getAllAtoms().size());
  
      }
test_case.class_method_signature: MmtfStructureTest.shouldIgnoreAlternativePosition()
test_case.full_signature: @Test void shouldIgnoreAlternativePosition()
test_case.identifier: shouldIgnoreAlternativePosition
test_case.invocations: getByteArrayFromUrl parse pdbIdentifier pdb get getLeafSubstructure get getLeafSubstructure getAllAtoms assertEquals size getAllAtoms size getAllAtoms
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldIgnoreAlternativePosition()
focal_class.declarator: bytes
focal_class.modifier: private final
focal_class.original_string: private final byte[] bytes;
focal_class.type: byte[]
focal_class.var_name: bytes
focal_class.declarator: data
focal_class.modifier: private final
focal_class.original_string: private final StructureDataInterface data;
focal_class.type: StructureDataInterface
focal_class.var_name: data
focal_class.declarator: removedModels
focal_class.modifier: private
focal_class.original_string: private Set<Integer> removedModels;
focal_class.type: Set<Integer>
focal_class.var_name: removedModels
focal_class.declarator: cachedModels
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, MmtfModel> cachedModels;
focal_class.type: Map<Integer, MmtfModel>
focal_class.var_name: cachedModels
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/mmtf/MmtfStructure.java
focal_class.identifier: MmtfStructure
focal_class.interfaces: implements Structure
focal_class.class_method_signature: MmtfStructure.MmtfStructure(byte[] bytes)
focal_class.full_signature: public  MmtfStructure(byte[] bytes)
focal_class.identifier: MmtfStructure
focal_class.modifiers: public
focal_class.parameters: (byte[] bytes)
focal_class.signature:  MmtfStructure(byte[] bytes)
focal_class.class_method_signature: MmtfStructure.MmtfStructure(byte[] bytes, boolean deflate)
focal_class.full_signature: public  MmtfStructure(byte[] bytes, boolean deflate)
focal_class.identifier: MmtfStructure
focal_class.modifiers: public
focal_class.parameters: (byte[] bytes, boolean deflate)
focal_class.signature:  MmtfStructure(byte[] bytes, boolean deflate)
focal_class.class_method_signature: MmtfStructure.MmtfStructure(MmtfStructure mmtfStructure)
focal_class.full_signature: private  MmtfStructure(MmtfStructure mmtfStructure)
focal_class.identifier: MmtfStructure
focal_class.modifiers: private
focal_class.parameters: (MmtfStructure mmtfStructure)
focal_class.signature:  MmtfStructure(MmtfStructure mmtfStructure)
focal_class.class_method_signature: MmtfStructure.bytesToStructureData(byte[] bytes, boolean deflate)
focal_class.full_signature: static StructureDataInterface bytesToStructureData(byte[] bytes, boolean deflate)
focal_class.identifier: bytesToStructureData
focal_class.modifiers: static
focal_class.parameters: (byte[] bytes, boolean deflate)
focal_class.return: StructureDataInterface
focal_class.signature: StructureDataInterface bytesToStructureData(byte[] bytes, boolean deflate)
focal_class.class_method_signature: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.full_signature: @Override public void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.identifier: removeLeafSubstructuresNotRelevantFor
focal_class.modifiers: @Override public
focal_class.parameters: (LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.return: void
focal_class.signature: void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.class_method_signature: MmtfStructure.getNumberOfLeafSubstructures()
focal_class.full_signature: @Override public int getNumberOfLeafSubstructures()
focal_class.identifier: getNumberOfLeafSubstructures
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getNumberOfLeafSubstructures()
focal_class.class_method_signature: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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: MmtfStructure.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 Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier) {
          Optional<Chain> chainOptional = getChain(leafIdentifier.getModelIdentifier(), leafIdentifier.getChainIdentifier());
          return chainOptional.flatMap(chain -> chain.getLeafSubstructure(leafIdentifier));
      }
focal_method.class_method_signature: MmtfStructure.getLeafSubstructure(LeafIdentifier leafIdentifier)
focal_method.full_signature: @Override public Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)
focal_method.identifier: getLeafSubstructure
focal_method.invocations: getChain getModelIdentifier getChainIdentifier flatMap getLeafSubstructure
focal_method.modifiers: @Override public
focal_method.parameters: (LeafIdentifier leafIdentifier)
focal_method.return: Optional<LeafSubstructure<?>>
focal_method.signature: Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)