test_class.declarator: logger = LoggingToolFactory.createLoggingTool(SMILESReaderTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(SMILESReaderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/smiles/src/test/java/org/openscience/cdk/io/SMILESReaderTest.java
test_class.identifier: SMILESReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test 
      public void badSmilesLine() throws CDKException {
          IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
          String input = "C\nn1cccc1\nc1ccccc1\n";
          DefaultChemObjectReader cor = new SMILESReader(new StringReader(input));
          IAtomContainerSet mols = cor.read(bldr.newInstance(IAtomContainerSet.class));
          assertThat(mols.getAtomContainerCount(), is(3));
          assertThat(mols.getAtomContainer(0).getAtomCount(), is(1));
          assertThat(mols.getAtomContainer(0).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
                     nullValue());
          assertThat(mols.getAtomContainer(1).getAtomCount(), is(0));
          assertThat(mols.getAtomContainer(1).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
                     notNullValue());
          assertThat(mols.getAtomContainer(2).getAtomCount(), is(6));
          assertThat(mols.getAtomContainer(2).getProperty(IteratingSMILESReader.BAD_SMILES_INPUT),
                     nullValue());
      }
test_case.class_method_signature: SMILESReaderTest.badSmilesLine()
test_case.full_signature: @Test public void badSmilesLine()
test_case.identifier: badSmilesLine
test_case.invocations: getInstance read newInstance assertThat getAtomContainerCount is assertThat getAtomCount getAtomContainer is assertThat getProperty getAtomContainer nullValue assertThat getAtomCount getAtomContainer is assertThat getProperty getAtomContainer notNullValue assertThat getAtomCount getAtomContainer is assertThat getProperty getAtomContainer nullValue
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void badSmilesLine()
focal_class.declarator: input  = null
focal_class.modifier: private
focal_class.original_string: private BufferedReader      input  = null;
focal_class.type: BufferedReader
focal_class.var_name: input
focal_class.declarator: sp     = null
focal_class.modifier: private
focal_class.original_string: private SmilesParser        sp     = null;
focal_class.type: SmilesParser
focal_class.var_name: sp
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(SMILESReader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(SMILESReader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java
focal_class.identifier: SMILESReader
focal_class.class_method_signature: SMILESReader.SMILESReader(Reader input)
focal_class.full_signature: public  SMILESReader(Reader input)
focal_class.identifier: SMILESReader
focal_class.modifiers: public
focal_class.parameters: (Reader input)
focal_class.signature:  SMILESReader(Reader input)
focal_class.class_method_signature: SMILESReader.SMILESReader(InputStream input)
focal_class.full_signature: public  SMILESReader(InputStream input)
focal_class.identifier: SMILESReader
focal_class.modifiers: public
focal_class.parameters: (InputStream input)
focal_class.signature:  SMILESReader(InputStream input)
focal_class.class_method_signature: SMILESReader.SMILESReader()
focal_class.full_signature: public  SMILESReader()
focal_class.identifier: SMILESReader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  SMILESReader()
focal_class.class_method_signature: SMILESReader.getFormat()
focal_class.full_signature: @Override public IResourceFormat getFormat()
focal_class.identifier: getFormat
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IResourceFormat
focal_class.signature: IResourceFormat getFormat()
focal_class.class_method_signature: SMILESReader.setReader(Reader input)
focal_class.full_signature: @Override public void setReader(Reader input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (Reader input)
focal_class.return: void
focal_class.signature: void setReader(Reader input)
focal_class.class_method_signature: SMILESReader.setReader(InputStream input)
focal_class.full_signature: @Override public void setReader(InputStream input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (InputStream input)
focal_class.return: void
focal_class.signature: void setReader(InputStream input)
focal_class.class_method_signature: SMILESReader.accepts(Class<? extends IChemObject> classObject)
focal_class.full_signature: @Override public boolean accepts(Class<? extends IChemObject> classObject)
focal_class.identifier: accepts
focal_class.modifiers: @Override public
focal_class.parameters: (Class<? extends IChemObject> classObject)
focal_class.return: boolean
focal_class.signature: boolean accepts(Class<? extends IChemObject> classObject)
focal_class.class_method_signature: SMILESReader.read(T object)
focal_class.full_signature: @Override public T read(T object)
focal_class.identifier: read
focal_class.modifiers: @Override public
focal_class.parameters: (T object)
focal_class.return: T
focal_class.signature: T read(T object)
focal_class.class_method_signature: SMILESReader.readAtomContainerSet(IAtomContainerSet som)
focal_class.full_signature: private IAtomContainerSet readAtomContainerSet(IAtomContainerSet som)
focal_class.identifier: readAtomContainerSet
focal_class.modifiers: private
focal_class.parameters: (IAtomContainerSet som)
focal_class.return: IAtomContainerSet
focal_class.signature: IAtomContainerSet readAtomContainerSet(IAtomContainerSet som)
focal_class.class_method_signature: SMILESReader.close()
focal_class.full_signature: @Override public void close()
focal_class.identifier: close
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void close()
focal_class.class_method_signature: SMILESReader.suffix(final String line)
focal_class.full_signature: private String suffix(final String line)
focal_class.identifier: suffix
focal_class.modifiers: private
focal_class.parameters: (final String line)
focal_class.return: String
focal_class.signature: String suffix(final String line)
focal_class.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public <T extends IChemObject> T read(T object) throws CDKException {
          sp = new SmilesParser(object.getBuilder());
  
          if (object instanceof IAtomContainerSet) {
              return (T) readAtomContainerSet((IAtomContainerSet) object);
          } else if (object instanceof IChemFile) {
              IChemFile file = (IChemFile) object;
              IChemSequence sequence = file.getBuilder().newInstance(IChemSequence.class);
              IChemModel chemModel = file.getBuilder().newInstance(IChemModel.class);
              chemModel.setMoleculeSet(readAtomContainerSet(file.getBuilder().newInstance(IAtomContainerSet.class)));
              sequence.addChemModel(chemModel);
              file.addChemSequence(sequence);
              return (T) file;
          } else {
              throw new CDKException("Only supported is reading of MoleculeSet objects.");
          }
      }
focal_method.class_method_signature: SMILESReader.read(T object)
focal_method.full_signature: @Override public T read(T object)
focal_method.identifier: read
focal_method.invocations: getBuilder readAtomContainerSet newInstance getBuilder newInstance getBuilder setMoleculeSet readAtomContainerSet newInstance getBuilder addChemModel addChemSequence
focal_method.modifiers: @Override public
focal_method.parameters: (T object)
focal_method.return: T
focal_method.signature: T read(T object)