test_class.declarator: firstChain
test_class.modifier: private static
test_class.original_string: private static OakChain firstChain;
test_class.type: OakChain
test_class.var_name: firstChain
test_class.declarator: chainToModify
test_class.modifier: private static
test_class.original_string: private static OakChain chainToModify;
test_class.type: OakChain
test_class.var_name: chainToModify
test_class.declarator: anotherChain
test_class.modifier: private static
test_class.original_string: private static OakChain anotherChain;
test_class.type: OakChain
test_class.var_name: anotherChain
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/OakChainTest.java
test_class.identifier: OakChainTest
test_case.body: @Test
      void getNextLeafIdentifier() {
          final LeafIdentifier actual = anotherChain.getNextLeafIdentifier();
          assertEquals(new LeafIdentifier("1brr", 1, "A", 1004), actual);
      }
test_case.class_method_signature: OakChainTest.getNextLeafIdentifier()
test_case.full_signature: @Test void getNextLeafIdentifier()
test_case.identifier: getNextLeafIdentifier
test_case.invocations: getNextLeafIdentifier assertEquals
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void getNextLeafIdentifier()
focal_class.declarator: identifier
focal_class.modifier: private final
focal_class.original_string: private final String identifier;
focal_class.type: String
focal_class.var_name: identifier
focal_class.declarator: leafSubstructures
focal_class.modifier: private final
focal_class.original_string: private final TreeMap<LeafIdentifier, OakLeafSubstructure<?>> leafSubstructures;
focal_class.type: TreeMap<LeafIdentifier, OakLeafSubstructure<?>>
focal_class.var_name: leafSubstructures
focal_class.declarator: consecutiveIdentifiers
focal_class.modifier: private final
focal_class.original_string: private final Set<LeafIdentifier> consecutiveIdentifiers;
focal_class.type: Set<LeafIdentifier>
focal_class.var_name: consecutiveIdentifiers
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/OakChain.java
focal_class.identifier: OakChain
focal_class.interfaces: implements Chain
focal_class.class_method_signature: OakChain.OakChain(String chainIdentifier)
focal_class.full_signature: public  OakChain(String chainIdentifier)
focal_class.identifier: OakChain
focal_class.modifiers: public
focal_class.parameters: (String chainIdentifier)
focal_class.signature:  OakChain(String chainIdentifier)
focal_class.class_method_signature: OakChain.OakChain(OakChain chain)
focal_class.full_signature: public  OakChain(OakChain chain)
focal_class.identifier: OakChain
focal_class.modifiers: public
focal_class.parameters: (OakChain chain)
focal_class.signature:  OakChain(OakChain chain)
focal_class.class_method_signature: OakChain.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: OakChain.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: OakChain.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: OakChain.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: OakChain.addLeafSubstructure(OakLeafSubstructure leafSubstructure, boolean consecutivePart)
focal_class.full_signature: public void addLeafSubstructure(OakLeafSubstructure leafSubstructure, boolean consecutivePart)
focal_class.identifier: addLeafSubstructure
focal_class.modifiers: public
focal_class.parameters: (OakLeafSubstructure leafSubstructure, boolean consecutivePart)
focal_class.return: void
focal_class.signature: void addLeafSubstructure(OakLeafSubstructure leafSubstructure, boolean consecutivePart)
focal_class.class_method_signature: OakChain.addLeafSubstructure(OakLeafSubstructure leafSubstructure)
focal_class.full_signature: public void addLeafSubstructure(OakLeafSubstructure leafSubstructure)
focal_class.identifier: addLeafSubstructure
focal_class.modifiers: public
focal_class.parameters: (OakLeafSubstructure leafSubstructure)
focal_class.return: void
focal_class.signature: void addLeafSubstructure(OakLeafSubstructure leafSubstructure)
focal_class.class_method_signature: OakChain.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: OakChain.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: OakChain.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: OakChain.connectChainBackbone()
focal_class.full_signature: public void connectChainBackbone()
focal_class.identifier: connectChainBackbone
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void connectChainBackbone()
focal_class.class_method_signature: OakChain.connectPeptideBonds(OakAminoAcid source, OakAminoAcid target)
focal_class.full_signature: public void connectPeptideBonds(OakAminoAcid source, OakAminoAcid target)
focal_class.identifier: connectPeptideBonds
focal_class.modifiers: public
focal_class.parameters: (OakAminoAcid source, OakAminoAcid target)
focal_class.return: void
focal_class.signature: void connectPeptideBonds(OakAminoAcid source, OakAminoAcid target)
focal_class.class_method_signature: OakChain.connectNucleotideBonds(OakNucleotide source, OakNucleotide target)
focal_class.full_signature: public void connectNucleotideBonds(OakNucleotide source, OakNucleotide target)
focal_class.identifier: connectNucleotideBonds
focal_class.modifiers: public
focal_class.parameters: (OakNucleotide source, OakNucleotide target)
focal_class.return: void
focal_class.signature: void connectNucleotideBonds(OakNucleotide source, OakNucleotide target)
focal_class.class_method_signature: OakChain.getConsecutivePart()
focal_class.full_signature: public List<LeafSubstructure<?>> getConsecutivePart()
focal_class.identifier: getConsecutivePart
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<LeafSubstructure<?>>
focal_class.signature: List<LeafSubstructure<?>> getConsecutivePart()
focal_class.class_method_signature: OakChain.getNonConsecutivePart()
focal_class.full_signature: public List<LeafSubstructure<?>> getNonConsecutivePart()
focal_class.identifier: getNonConsecutivePart
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<LeafSubstructure<?>>
focal_class.signature: List<LeafSubstructure<?>> getNonConsecutivePart()
focal_class.class_method_signature: OakChain.getNextLeafIdentifier()
focal_class.full_signature: public LeafIdentifier getNextLeafIdentifier()
focal_class.identifier: getNextLeafIdentifier
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: LeafIdentifier
focal_class.signature: LeafIdentifier getNextLeafIdentifier()
focal_class.class_method_signature: OakChain.getCopy()
focal_class.full_signature: @Override public OakChain getCopy()
focal_class.identifier: getCopy
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: OakChain
focal_class.signature: OakChain getCopy()
focal_class.class_method_signature: OakChain.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: OakChain.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: OakChain.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: public LeafIdentifier getNextLeafIdentifier() {
          LeafIdentifier lastLeafIdentifier = leafSubstructures.lastEntry().getKey();
          return new LeafIdentifier(lastLeafIdentifier.getPdbIdentifier(), lastLeafIdentifier.getModelIdentifier(),
                  lastLeafIdentifier.getChainIdentifier(), lastLeafIdentifier.getSerial() + 1);
      }
focal_method.class_method_signature: OakChain.getNextLeafIdentifier()
focal_method.full_signature: public LeafIdentifier getNextLeafIdentifier()
focal_method.identifier: getNextLeafIdentifier
focal_method.invocations: getKey lastEntry getPdbIdentifier getModelIdentifier getChainIdentifier getSerial
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: LeafIdentifier
focal_method.signature: LeafIdentifier getNextLeafIdentifier()