Package 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, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

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.

Source code:

main

Belongs to CDK module:

smiles

Keywords:

MoSS

Nested Class Summary

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

IChemObjectReader.Mode

Field Summary

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

errorHandler, mode

Constructor Summary

Constructors

Constructor	Description
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

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> 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 IAtomContainerSet 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

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

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

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

Methods inherited from class java.lang.Object

clone, equals, finalize, 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 Details

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 Details

getFormat

public IResourceFormat getFormat()

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader reader)
               throws CDKException

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

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

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

Throws:

CDKException

accepts

public boolean accepts(Class<? extends IChemObject> 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 IAtomContainerSet from the input source.

Parameters:

object - an IAtomContainerSet into which the data is stored.

Returns:

the content in a IAtomContainerSet object

Throws:

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

close

public void close()
           throws IOException

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.