test_class.declarator: firstChain
test_class.modifier: private static
test_class.original_string: private static Chain firstChain;
test_class.type: Chain
test_class.var_name: firstChain
test_class.declarator: chainToModify
test_class.modifier: private static
test_class.original_string: private static Chain chainToModify;
test_class.type: Chain
test_class.var_name: chainToModify
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.file: singa-structure/src/test/java/bio/singa/structure/model/mmtf/MmtfChainTest.java
test_class.identifier: MmtfChainTest
test_case.body: @Test
      void getAllLeafSubstructures() {
          final List<LeafSubstructure<?>> leafSubstructures = firstChain.getAllLeafSubstructures();
          assertEquals(167, leafSubstructures.size());
      }
test_case.class_method_signature: MmtfChainTest.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: 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: chainIdentifier
focal_class.modifier: private final
focal_class.original_string: private final String chainIdentifier;
focal_class.type: String
focal_class.var_name: chainIdentifier
focal_class.declarator: cachedLeaves
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, MmtfLeafSubstructure<?>> cachedLeaves;
focal_class.type: Map<Integer, MmtfLeafSubstructure<?>>
focal_class.var_name: cachedLeaves
focal_class.declarator: relevantGroups
focal_class.modifier: private final
focal_class.original_string: private final List<Integer> relevantGroups;
focal_class.type: List<Integer>
focal_class.var_name: relevantGroups
focal_class.declarator: leafIdentifiers
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, LeafIdentifier> leafIdentifiers;
focal_class.type: Map<Integer, LeafIdentifier>
focal_class.var_name: leafIdentifiers
focal_class.declarator: atomRanges
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, Range<Integer>> atomRanges;
focal_class.type: Map<Integer, Range<Integer>>
focal_class.var_name: atomRanges
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/mmtf/MmtfChain.java
focal_class.identifier: MmtfChain
focal_class.interfaces: implements Chain
focal_class.class_method_signature: MmtfChain.MmtfChain(StructureDataInterface data, byte[] bytes, String chainIdentifier, List<Integer> internalChainIndices, int modelIndex)
focal_class.full_signature:   MmtfChain(StructureDataInterface data, byte[] bytes, String chainIdentifier, List<Integer> internalChainIndices, int modelIndex)
focal_class.identifier: MmtfChain
focal_class.parameters: (StructureDataInterface data, byte[] bytes, String chainIdentifier, List<Integer> internalChainIndices, int modelIndex)
focal_class.signature:  MmtfChain(StructureDataInterface data, byte[] bytes, String chainIdentifier, List<Integer> internalChainIndices, int modelIndex)
focal_class.class_method_signature: MmtfChain.MmtfChain(MmtfChain mmtfChain)
focal_class.full_signature: private  MmtfChain(MmtfChain mmtfChain)
focal_class.identifier: MmtfChain
focal_class.modifiers: private
focal_class.parameters: (MmtfChain mmtfChain)
focal_class.signature:  MmtfChain(MmtfChain mmtfChain)
focal_class.class_method_signature: MmtfChain.getChainIdentifier()
focal_class.full_signature: @Override public String getChainIdentifier()
focal_class.identifier: getChainIdentifier
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getChainIdentifier()
focal_class.class_method_signature: MmtfChain.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: MmtfChain.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: MmtfChain.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: MmtfChain.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: MmtfChain.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.full_signature: public void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.identifier: removeLeafSubstructuresNotRelevantFor
focal_class.modifiers: public
focal_class.parameters: (LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.return: void
focal_class.signature: void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
focal_class.class_method_signature: MmtfChain.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: MmtfChain.getInternalIndexForLeafIdentifier(LeafIdentifier leafIdentifier)
focal_class.full_signature: private int getInternalIndexForLeafIdentifier(LeafIdentifier leafIdentifier)
focal_class.identifier: getInternalIndexForLeafIdentifier
focal_class.modifiers: private
focal_class.parameters: (LeafIdentifier leafIdentifier)
focal_class.return: int
focal_class.signature: int getInternalIndexForLeafIdentifier(LeafIdentifier leafIdentifier)
focal_class.class_method_signature: MmtfChain.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: MmtfChain.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: MmtfChain.getCopy()
focal_class.full_signature: @Override public Chain getCopy()
focal_class.identifier: getCopy
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Chain
focal_class.signature: Chain getCopy()
focal_class.class_method_signature: MmtfChain.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: MmtfChain.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: MmtfChain.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<?>> results = new ArrayList<>();
          for (Integer relevantGroup : relevantGroups) {
              if (cachedLeaves.containsKey(relevantGroup)) {
                  results.add(cachedLeaves.get(relevantGroup));
              } else {
                  final Range<Integer> atomRange = atomRanges.get(relevantGroup);
                  MmtfLeafSubstructure<?> leaf = MmtfLeafFactory.createLeaf(data, bytes, leafIdentifiers.get(relevantGroup), relevantGroup, atomRange.getLowerBound(), atomRange.getUpperBound());
                  cachedLeaves.put(relevantGroup, leaf);
                  results.add(leaf);
              }
          }
          return results;
      }
focal_method.class_method_signature: MmtfChain.getAllLeafSubstructures()
focal_method.full_signature: @Override public List<LeafSubstructure<?>> getAllLeafSubstructures()
focal_method.identifier: getAllLeafSubstructures
focal_method.invocations: containsKey add get get createLeaf get getLowerBound getUpperBound put add
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: List<LeafSubstructure<?>>
focal_method.signature: List<LeafSubstructure<?>> getAllLeafSubstructures()