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 testReading() throws Exception {
          String filename = "data/smiles/smiles.smi";
          logger.info("Testing: " + filename);
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          SMILESReader reader = new SMILESReader(ins);
          IAtomContainerSet som = reader.read(new AtomContainerSet());
          Assert.assertEquals(8, som.getAtomContainerCount());
      }
test_case.class_method_signature: SMILESReaderTest.testReading()
test_case.full_signature: @Test public void testReading()
test_case.identifier: testReading
test_case.invocations: info getResourceAsStream getClassLoader getClass read assertEquals getAtomContainerCount
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testReading()
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)