ambit2.rest.rdf.chembl

Class ChEMBLRawReader

java.lang.Object

ambit2.rest.rdf.chembl.ChEMBLRawReader

All Implemented Interfaces:

IRawReader<IStructureRecord>, Closeable, AutoCloseable, Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

public class ChEMBLRawReader
extends Object
implements IRawReader<IStructureRecord>

Reads SPARQL results from http://rdf.farmbio.uu.se/chembl/ into iterator

Author:

nina

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
protected com.hp.hpl.jena.query.QueryExecution	ex
protected IStructureRecord	record
protected com.hp.hpl.jena.query.ResultSet	results
String	sparql
static String	sparqlEndpoint

Constructor Summary

Constructors

Constructor and Description
ChEMBLRawReader()

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends org.openscience.cdk.interfaces.IChemObject> arg0)
void	addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener arg0)
<S extends org.openscience.cdk.io.setting.IOSetting> S	addSetting(org.openscience.cdk.io.setting.IOSetting setting)
void	addSettings(Collection<org.openscience.cdk.io.setting.IOSetting> settings)
void	close()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
org.openscience.cdk.io.setting.IOSetting[]	getIOSettings()
Collection<org.openscience.cdk.io.listener.IChemObjectIOListener>	getListeners()
<S extends org.openscience.cdk.io.setting.IOSetting> S	getSetting(String name)
<S extends org.openscience.cdk.io.setting.IOSetting> S	getSetting(String name, Class<S> c)
Collection<org.openscience.cdk.io.setting.IOSetting>	getSettings()
void	handleError(String arg0)
void	handleError(String arg0, Exception arg1)
void	handleError(String arg0, int arg1, int arg2, int arg3)
void	handleError(String arg0, int arg1, int arg2, int arg3, Exception arg4)
boolean	hasNext()
boolean	hasSetting(String name)
Object	next()
IStructureRecord	nextRecord()
IStructureRecord	processSolution(com.hp.hpl.jena.query.QuerySolution row)
void	remove()
void	removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener arg0)
void	setErrorHandler(org.openscience.cdk.io.IChemObjectReaderErrorHandler arg0)
void	setReader(InputStream arg0)
void	setReader(Reader arg0)
void	setReaderMode(org.openscience.cdk.io.IChemObjectReader.Mode arg0)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

ex

protected com.hp.hpl.jena.query.QueryExecution ex

results

protected com.hp.hpl.jena.query.ResultSet results

record

protected IStructureRecord record

sparqlEndpoint

public static final String sparqlEndpoint

See Also:

Constant Field Values

sparql

public final String sparql

See Also:

Constant Field Values

Constructor Detail

ChEMBLRawReader

public ChEMBLRawReader()

Method Detail

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

handleError

public void handleError(String arg0)
                 throws org.openscience.cdk.exception.CDKException

Specified by:

handleError in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

handleError

public void handleError(String arg0,
                        Exception arg1)
                 throws org.openscience.cdk.exception.CDKException

Specified by:

handleError in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

handleError

public void handleError(String arg0,
                        int arg1,
                        int arg2,
                        int arg3)
                 throws org.openscience.cdk.exception.CDKException

Specified by:

handleError in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

handleError

public void handleError(String arg0,
                        int arg1,
                        int arg2,
                        int arg3,
                        Exception arg4)
                 throws org.openscience.cdk.exception.CDKException

Specified by:

handleError in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

setErrorHandler

public void setErrorHandler(org.openscience.cdk.io.IChemObjectReaderErrorHandler arg0)

Specified by:

setErrorHandler in interface org.openscience.cdk.io.IChemObjectReader

setReader

public void setReader(Reader arg0)
               throws org.openscience.cdk.exception.CDKException

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(InputStream arg0)
               throws org.openscience.cdk.exception.CDKException

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

setReaderMode

public void setReaderMode(org.openscience.cdk.io.IChemObjectReader.Mode arg0)

Specified by:

setReaderMode in interface org.openscience.cdk.io.IChemObjectReader

accepts

public boolean accepts(Class<? extends org.openscience.cdk.interfaces.IChemObject> arg0)

Specified by:

accepts in interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener

public void addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener arg0)

Specified by:

addChemObjectIOListener in interface org.openscience.cdk.io.IChemObjectIO

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in interface org.openscience.cdk.io.IChemObjectIO

Throws:

IOException

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

Specified by:

getFormat in interface org.openscience.cdk.io.IChemObjectIO

getIOSettings

public org.openscience.cdk.io.setting.IOSetting[] getIOSettings()

Specified by:

getIOSettings in interface org.openscience.cdk.io.IChemObjectIO

removeChemObjectIOListener

public void removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener arg0)

Specified by:

removeChemObjectIOListener in interface org.openscience.cdk.io.IChemObjectIO

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

processSolution

public IStructureRecord processSolution(com.hp.hpl.jena.query.QuerySolution row)
                                 throws Exception

Throws:

Exception

next

public Object next()

Specified by:

next in interface Iterator

remove

public void remove()

Specified by:

remove in interface Iterator

getListeners

public Collection<org.openscience.cdk.io.listener.IChemObjectIOListener> getListeners()

Specified by:

getListeners in interface org.openscience.cdk.io.IChemObjectIO

addSetting

public <S extends org.openscience.cdk.io.setting.IOSetting> S addSetting(org.openscience.cdk.io.setting.IOSetting setting)

Specified by:

addSetting in interface org.openscience.cdk.io.IChemObjectIO

addSettings

public void addSettings(Collection<org.openscience.cdk.io.setting.IOSetting> settings)

Specified by:

addSettings in interface org.openscience.cdk.io.IChemObjectIO

hasSetting

public boolean hasSetting(String name)

Specified by:

hasSetting in interface org.openscience.cdk.io.IChemObjectIO

getSetting

public <S extends org.openscience.cdk.io.setting.IOSetting> S getSetting(String name)

Specified by:

getSetting in interface org.openscience.cdk.io.IChemObjectIO

getSetting

public <S extends org.openscience.cdk.io.setting.IOSetting> S getSetting(String name,
                                                                         Class<S> c)

Specified by:

getSetting in interface org.openscience.cdk.io.IChemObjectIO

getSettings

public Collection<org.openscience.cdk.io.setting.IOSetting> getSettings()

Specified by:

getSettings in interface org.openscience.cdk.io.IChemObjectIO