test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: public static
test_class.original_string: public static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.file: tool/group/src/test/java/org/openscience/cdk/group/BondRefinableTest.java
test_class.identifier: BondRefinableTest
test_case.body: @Test
      public void neighboursInBlock() {
          String acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(1),2:3(1)";
          BondRefinable bondRefinable = refinable(acpString);
          Set<Integer> block = new HashSet<Integer>();
          block.add(1);
          block.add(3);
          assertEquals(new IntegerInvariant(1), bondRefinable.neighboursInBlock(block, 0));
          assertEquals(new IntegerInvariant(1), bondRefinable.neighboursInBlock(block, 2));
      }
test_case.class_method_signature: BondRefinableTest.neighboursInBlock()
test_case.full_signature: @Test public void neighboursInBlock()
test_case.identifier: neighboursInBlock
test_case.invocations: refinable add add assertEquals neighboursInBlock assertEquals neighboursInBlock
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void neighboursInBlock()
focal_class.declarator: atomContainer
focal_class.modifier: private final
focal_class.original_string: private final IAtomContainer atomContainer;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.declarator: connectionTable
focal_class.modifier: private
focal_class.original_string: private int[][] connectionTable;
focal_class.type: int[][]
focal_class.var_name: connectionTable
focal_class.declarator: ignoreBondOrders
focal_class.modifier: private
focal_class.original_string: private boolean ignoreBondOrders;
focal_class.type: boolean
focal_class.var_name: ignoreBondOrders
focal_class.file: tool/group/src/main/java/org/openscience/cdk/group/BondRefinable.java
focal_class.identifier: BondRefinable
focal_class.interfaces: implements Refinable
focal_class.class_method_signature: BondRefinable.BondRefinable(IAtomContainer atomContainer)
focal_class.full_signature: public  BondRefinable(IAtomContainer atomContainer)
focal_class.identifier: BondRefinable
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.signature:  BondRefinable(IAtomContainer atomContainer)
focal_class.class_method_signature: BondRefinable.BondRefinable(IAtomContainer atomContainer, boolean ignoreBondOrders)
focal_class.full_signature: public  BondRefinable(IAtomContainer atomContainer, boolean ignoreBondOrders)
focal_class.identifier: BondRefinable
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, boolean ignoreBondOrders)
focal_class.signature:  BondRefinable(IAtomContainer atomContainer, boolean ignoreBondOrders)
focal_class.class_method_signature: BondRefinable.getVertexCount()
focal_class.full_signature: @Override public int getVertexCount()
focal_class.identifier: getVertexCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getVertexCount()
focal_class.class_method_signature: BondRefinable.getConnectivity(int vertexI, int vertexJ)
focal_class.full_signature: @Override public int getConnectivity(int vertexI, int vertexJ)
focal_class.identifier: getConnectivity
focal_class.modifiers: @Override public
focal_class.parameters: (int vertexI, int vertexJ)
focal_class.return: int
focal_class.signature: int getConnectivity(int vertexI, int vertexJ)
focal_class.class_method_signature: BondRefinable.neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.full_signature: @Override public Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.identifier: neighboursInBlock
focal_class.modifiers: @Override public
focal_class.parameters: (Set<Integer> block, int vertexIndex)
focal_class.return: Invariant
focal_class.signature: Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.class_method_signature: BondRefinable.getConnectedIndices(int vertexIndex)
focal_class.full_signature: private int[] getConnectedIndices(int vertexIndex)
focal_class.identifier: getConnectedIndices
focal_class.modifiers: private
focal_class.parameters: (int vertexIndex)
focal_class.return: int[]
focal_class.signature: int[] getConnectedIndices(int vertexIndex)
focal_class.class_method_signature: BondRefinable.getInitialPartition()
focal_class.full_signature: public Partition getInitialPartition()
focal_class.identifier: getInitialPartition
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Partition
focal_class.signature: Partition getInitialPartition()
focal_class.class_method_signature: BondRefinable.setupConnectionTable(IAtomContainer atomContainer)
focal_class.full_signature: private void setupConnectionTable(IAtomContainer atomContainer)
focal_class.identifier: setupConnectionTable
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void setupConnectionTable(IAtomContainer atomContainer)
focal_method.body: @Override
      public Invariant neighboursInBlock(Set<Integer> block, int vertexIndex) {
          int neighbours = 0;
          for (int connected : getConnectedIndices(vertexIndex)) {
              if (block.contains(connected)) {
                  neighbours++;
              }
          }
          return new IntegerInvariant(neighbours);
      }
focal_method.class_method_signature: BondRefinable.neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_method.full_signature: @Override public Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_method.identifier: neighboursInBlock
focal_method.invocations: getConnectedIndices contains
focal_method.modifiers: @Override public
focal_method.parameters: (Set<Integer> block, int vertexIndex)
focal_method.return: Invariant
focal_method.signature: Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)