org.openscience.cdk.io.iterator

Class DefaultIteratingChemObjectReader<T extends IChemObject>

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader<T>

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator<T>, IChemObjectIO, IChemObjectReader, IIteratingChemObjectReader<T>

Direct Known Subclasses:

IteratingPCCompoundASNReader, IteratingPCCompoundXMLReader, IteratingPCSubstancesXMLReader, IteratingSDFReader, IteratingSMILESReader

public abstract class DefaultIteratingChemObjectReader<T extends IChemObject>
extends ChemObjectIO
implements IIteratingChemObjectReader<T>

Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.

Source code:

master

Belongs to CDK module:

io

Nested Class Summary

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

IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
protected IChemObjectReaderErrorHandler	errorHandler
protected IChemObjectReader.Mode	mode

Constructor Summary

Constructors

Constructor and Description
DefaultIteratingChemObjectReader()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> objectClass) Returns whether the given IChemObject can be read or written.
void	handleError(String message) Redirects an error message to the IChemObjectReaderErrorHandler.
void	handleError(String message, Exception exception) Redirects an error message to the IChemObjectReaderErrorHandler.
void	handleError(String message, int row, int colStart, int colEnd) Redirects an error message to the IChemObjectReaderErrorHandler.
void	handleError(String message, int row, int colStart, int colEnd, Exception exception) Redirects an error message to the IChemObjectReaderErrorHandler.
void	remove() File IO generally does not support removing of entries.
void	setErrorHandler(IChemObjectReaderErrorHandler handler) Sets an error handler that is sent events when file format issues occur.
void	setReaderMode(IChemObjectReader.Mode mode) Sets the reader mode.

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.IChemObjectReader

setReader, setReader

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

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

Methods inherited from interface java.util.Iterator

hasNext, next

Field Detail

mode

protected IChemObjectReader.Mode mode

errorHandler

protected IChemObjectReaderErrorHandler errorHandler

Constructor Detail

DefaultIteratingChemObjectReader

public DefaultIteratingChemObjectReader()

Method Detail

accepts

public boolean accepts(Class<? extends IChemObject> objectClass)

Description copied from interface: IChemObjectIO

Returns whether the given IChemObject can be read or written.

Specified by:

accepts in interface IChemObjectIO

Parameters:

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

Returns:

true, if the IChemObject can be handled.

remove

public void remove()

File IO generally does not support removing of entries.

Specified by:

remove in interface Iterator<T extends IChemObject>

setReaderMode

public void setReaderMode(IChemObjectReader.Mode mode)

Description copied from interface: IChemObjectReader

Sets the reader mode. If Mode.STRICT, then the reader will fail on any problem in the format of the read file, instead of trying to recover from that.

Specified by:

setReaderMode in interface IChemObjectReader

setErrorHandler

public void setErrorHandler(IChemObjectReaderErrorHandler handler)

Sets an error handler that is sent events when file format issues occur.

Specified by:

setErrorHandler in interface IChemObjectReader

Parameters:

handler - IChemObjectReaderErrorHandler to send error messages to.

handleError

public void handleError(String message)
                 throws CDKException

Redirects an error message to the IChemObjectReaderErrorHandler. Throws an CDKException when in STRICT IChemObjectReader.Mode.

Specified by:

handleError in interface IChemObjectReader

Parameters:

message - the error message.

Throws:

CDKException

handleError

public void handleError(String message,
               Exception exception)
                 throws CDKException

Redirects an error message to the IChemObjectReaderErrorHandler. Throws an CDKException when in STRICT IChemObjectReader.Mode.

Specified by:

handleError in interface IChemObjectReader

Parameters:

message - the error message.

exception - the corresponding Exception.

Throws:

CDKException

handleError

public void handleError(String message,
               int row,
               int colStart,
               int colEnd)
                 throws CDKException

Redirects an error message to the IChemObjectReaderErrorHandler. Throws an CDKException when in STRICT IChemObjectReader.Mode.

Specified by:

handleError in interface IChemObjectReader

Parameters:

message - the error message.

row - Row in the file where the error is found.

colStart - Start column in the file where the error is found.

colEnd - End column in the file where the error is found.

Throws:

CDKException

handleError

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

Redirects an error message to the IChemObjectReaderErrorHandler. Throws an CDKException when in STRICT IChemObjectReader.Mode.

Specified by:

handleError in interface IChemObjectReader

Parameters:

message - the error message.

row - Row in the file where the error is found.

colStart - Start column in the file where the error is found.

colEnd - End column in the file where the error is found.

exception - the corresponding Exception.

Throws:

CDKException