test_class.file: storage/smiles/src/test/java/org/openscience/cdk/io/MoSSOutputReaderTest.java
test_class.identifier: MoSSOutputReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test
      public void testExampleFile_SupportColumns() throws Exception {
          String filename = "data/moss/TKO.mossoutput";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          MoSSOutputReader reader = new MoSSOutputReader(ins);
          IAtomContainerSet moleculeSet = new AtomContainerSet();
          moleculeSet = reader.read(moleculeSet);
          Assert.assertEquals(5.06, Double
                  .valueOf(moleculeSet.getAtomContainer(0).getProperty("focusSupport").toString()).doubleValue(), 0.01);
          Assert.assertEquals(1.74,
                  Double.valueOf(moleculeSet.getAtomContainer(0).getProperty("complementSupport").toString())
                          .doubleValue(), 0.01);
      }
test_case.class_method_signature: MoSSOutputReaderTest.testExampleFile_SupportColumns()
test_case.full_signature: @Test public void testExampleFile_SupportColumns()
test_case.identifier: testExampleFile_SupportColumns
test_case.invocations: getResourceAsStream getClassLoader getClass read assertEquals doubleValue valueOf toString getProperty getAtomContainer assertEquals doubleValue valueOf toString getProperty getAtomContainer
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testExampleFile_SupportColumns()
focal_class.declarator: input
focal_class.modifier: private
focal_class.original_string: private BufferedReader      input;
focal_class.type: BufferedReader
focal_class.var_name: input
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(MoSSOutputReader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MoSSOutputReader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/io/MoSSOutputReader.java
focal_class.identifier: MoSSOutputReader
focal_class.class_method_signature: MoSSOutputReader.MoSSOutputReader(Reader input)
focal_class.full_signature: public  MoSSOutputReader(Reader input)
focal_class.identifier: MoSSOutputReader
focal_class.modifiers: public
focal_class.parameters: (Reader input)
focal_class.signature:  MoSSOutputReader(Reader input)
focal_class.class_method_signature: MoSSOutputReader.MoSSOutputReader(InputStream input)
focal_class.full_signature: public  MoSSOutputReader(InputStream input)
focal_class.identifier: MoSSOutputReader
focal_class.modifiers: public
focal_class.parameters: (InputStream input)
focal_class.signature:  MoSSOutputReader(InputStream input)
focal_class.class_method_signature: MoSSOutputReader.MoSSOutputReader()
focal_class.full_signature: public  MoSSOutputReader()
focal_class.identifier: MoSSOutputReader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MoSSOutputReader()
focal_class.class_method_signature: MoSSOutputReader.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: MoSSOutputReader.setReader(Reader reader)
focal_class.full_signature: @Override public void setReader(Reader reader)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (Reader reader)
focal_class.return: void
focal_class.signature: void setReader(Reader reader)
focal_class.class_method_signature: MoSSOutputReader.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: MoSSOutputReader.accepts(Class<? extends IChemObject> testClass)
focal_class.full_signature: @Override public boolean accepts(Class<? extends IChemObject> testClass)
focal_class.identifier: accepts
focal_class.modifiers: @Override public
focal_class.parameters: (Class<? extends IChemObject> testClass)
focal_class.return: boolean
focal_class.signature: boolean accepts(Class<? extends IChemObject> testClass)
focal_class.class_method_signature: MoSSOutputReader.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: MoSSOutputReader.readAtomContainerSet(IAtomContainerSet molSet)
focal_class.full_signature: private IAtomContainerSet readAtomContainerSet(IAtomContainerSet molSet)
focal_class.identifier: readAtomContainerSet
focal_class.modifiers: private
focal_class.parameters: (IAtomContainerSet molSet)
focal_class.return: IAtomContainerSet
focal_class.signature: IAtomContainerSet readAtomContainerSet(IAtomContainerSet molSet)
focal_class.class_method_signature: MoSSOutputReader.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.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public <T extends IChemObject> T read(T object) throws CDKException {
          if (object instanceof IAtomContainerSet) {
              IAtomContainerSet cf = (IAtomContainerSet) object;
              try {
                  cf = readAtomContainerSet(cf);
              } catch (IOException e) {
                  logger.error("Input/Output error while reading from input.");
              }
              return (T) cf;
          } else if (object instanceof IChemFile) {
              IChemFile chemFile = (IChemFile) object;
              IChemSequence chemSeq = object.getBuilder().newInstance(IChemSequence.class);
              IChemModel chemModel = object.getBuilder().newInstance(IChemModel.class);
              IAtomContainerSet molSet = object.getBuilder().newInstance(IAtomContainerSet.class);
              try {
                  molSet = readAtomContainerSet(molSet);
              } catch (IOException e) {
                  logger.error("Input/Output error while reading from input.");
              }
              chemModel.setMoleculeSet(molSet);
              chemSeq.addChemModel(chemModel);
              chemFile.addChemSequence(chemSeq);
              return (T) chemFile;
          } else {
              throw new CDKException("Only supported is reading of IAtomContainerSet.");
          }
      }
focal_method.class_method_signature: MoSSOutputReader.read(T object)
focal_method.full_signature: @Override public T read(T object)
focal_method.identifier: read
focal_method.invocations: readAtomContainerSet error newInstance getBuilder newInstance getBuilder newInstance getBuilder readAtomContainerSet error setMoleculeSet addChemModel addChemSequence
focal_method.modifiers: @Override public
focal_method.parameters: (T object)
focal_method.return: T
focal_method.signature: T read(T object)