ambit2.core.io

Class RawIteratingWrapper<R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader>

java.lang.Object

ambit2.core.io.RawIteratingWrapper<R>

All Implemented Interfaces:

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

public class RawIteratingWrapper<R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader>
extends Object
implements IRawReader<IStructureRecord>, ICiteable

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 IStructureRecord	r
protected R	reader
protected ILiteratureEntry	reference
protected MoleculeWriter	writer

Constructor Summary

Constructors

Constructor and Description
RawIteratingWrapper(R reader)

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class 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()
protected IStructureRecord	createStructureRecord()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
org.openscience.cdk.io.setting.IOSetting[]	getIOSettings()
Collection<org.openscience.cdk.io.listener.IChemObjectIOListener>	getListeners()
ILiteratureEntry	getReference()
<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 message)
void	handleError(String message, Exception exception)
void	handleError(String message, int row, int colStart, int colEnd)
void	handleError(String message, int row, int colStart, int colEnd, Exception exception)
boolean	hasNext()
boolean	hasSetting(String name)
Object	next()
IStructureRecord	nextRecord()
void	remove()
void	removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener arg0)
void	setErrorHandler(org.openscience.cdk.io.IChemObjectReaderErrorHandler handler)
void	setReader(InputStream reader)
void	setReader(Reader reader)
void	setReaderMode(org.openscience.cdk.io.IChemObjectReader.Mode mode)
void	setReference(ILiteratureEntry reference)
protected Object	transform(Object o)

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

reader

protected R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader reader

writer

protected MoleculeWriter writer

reference

protected ILiteratureEntry reference

r

protected IStructureRecord r

Constructor Detail

RawIteratingWrapper

public RawIteratingWrapper(R reader)

Method Detail

createStructureRecord

protected IStructureRecord createStructureRecord()

getReference

public ILiteratureEntry getReference()

Specified by:

getReference in interface ICiteable

setReference

public void setReference(ILiteratureEntry reference)

Specified by:

setReference in interface ICiteable

setReader

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

Specified by:

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

Throws:

org.openscience.cdk.exception.CDKException

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

accepts

public boolean accepts(Class 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

transform

protected Object transform(Object o)

next

public Object next()

Specified by:

next in interface Iterator

remove

public void remove()

Specified by:

remove in interface Iterator

setReaderMode

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

Specified by:

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

setErrorHandler

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

Specified by:

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

handleError

public void handleError(String message)
                 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 message,
                        Exception exception)
                 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 message,
                        int row,
                        int colStart,
                        int colEnd)
                 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 message,
                        int row,
                        int colStart,
                        int colEnd,
                        Exception exception)
                 throws org.openscience.cdk.exception.CDKException

Specified by:

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

Throws:

org.openscience.cdk.exception.CDKException

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