org.openscience.cdk.io
Class MoSSOutputReader

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.DefaultChemObjectReader
          org.openscience.cdk.io.MoSSOutputReader

All Implemented Interfaces:

Closeable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@TestClass(value="org.openscience.cdk.io.MoSSOutputReaderTest")
public class MoSSOutputReader
extends DefaultChemObjectReader

Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study. These files look like:

 id,description,nodes,edges,s_abs,s_rel,c_abs,c_rel
 1,S-c:c:c:c:c:c,7,6,491,5.055081,5,1.7421603
 2,S-c:c:c:c:c,6,5,493,5.0756717,5,1.7421603
 

Caution: the output contains substructures, not full molecules, even though they are read as such right now.

Keywords:

MoSS

Belongs to CDK module:

smiles

Source code:

cdk-1.4.x

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Constructor Summary

MoSSOutputReader()
Create a reader for MoSS output files from an empty string.

MoSSOutputReader(InputStream input)
Create a reader for MoSS output files from an InputStream.

MoSSOutputReader(Reader input)
Create a reader for MoSS output files from a Reader.

Method Summary

boolean	accepts(Class testClass) Returns whether the given IChemObject can be read or written.
void	close() Closes this IChemObjectIO's resources.
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object) Read a IMoleculeSet from the input source.
void	setReader(InputStream input) Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader reader) Sets the Reader from which this ChemObjectReader should read the contents.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader

handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Constructor Detail

MoSSOutputReader

public MoSSOutputReader(Reader input)

Create a reader for MoSS output files from a Reader.

Parameters:

input - source of CIF data

MoSSOutputReader

public MoSSOutputReader(InputStream input)

Create a reader for MoSS output files from an InputStream.

Parameters:

input - source of CIF data

MoSSOutputReader

public MoSSOutputReader()

Create a reader for MoSS output files from an empty string.

Method Detail

getFormat

@TestMethod(value="testGetFormat")
public IResourceFormat getFormat()

Returns the IResourceFormat class for this IO class.

setReader

@TestMethod(value="testSetReader_Reader")
public void setReader(Reader reader)
               throws CDKException

Sets the Reader from which this ChemObjectReader should read the contents.

Throws:

CDKException

setReader

@TestMethod(value="testSetReader_InputStream")
public void setReader(InputStream input)
               throws CDKException

Sets the InputStream from which this ChemObjectReader should read the contents.

Throws:

CDKException

accepts

@TestMethod(value="testAccepts")
public boolean accepts(Class testClass)

Returns whether the given IChemObject can be read or written.

Parameters:

testClass - IChemObject of which is tested if it can be handled.

Returns:

true, if the IChemObject can be handled.

read

public <T extends IChemObject> T read(T object)
                           throws CDKException

Read a IMoleculeSet from the input source.

Parameters:

object - an IMoleculeSet into which the data is stored.

Returns:

the content in a IMoleculeSet object

Throws:

CDKException - it is thrown if the type of information is not available from the input

close

@TestMethod(value="testClose")
public void close()
           throws IOException

Closes this IChemObjectIO's resources.

Throws:

IOException