Package org.openscience.cdk.io

Class DefaultChemObjectReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

Direct Known Subclasses:

CDKOWLReader, CIFReader, CMLReader, CrystClustReader, CTXReader, GamessReader, Gaussian03Reader, Gaussian98Reader, GhemicalMMReader, HINReader, INChIPlainTextReader, INChIReader, MDLReader, MDLRXNReader, MDLRXNV2000Reader, MDLRXNV3000Reader, MDLV2000Reader, MDLV3000Reader, Mol2Reader, Mopac7Reader, MoSSOutputReader, PCCompoundASNReader, PCCompoundXMLReader, PCSubstanceXMLReader, PDBReader, PMPReader, RGroupQueryReader, ShelXReader, SMILESReader, VASPReader, XYZReader, ZMatrixReader

public abstract class DefaultChemObjectReader
extends ChemObjectIO
implements ISimpleChemObjectReader

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

Source code:

main

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	Description
protected IChemObjectReaderErrorHandler	errorHandler
protected IChemObjectReader.Mode	mode

Constructor Summary

Constructors

Constructor	Description
DefaultChemObjectReader()

Method Summary

Modifier and Type	Method	Description
protected void	fireFrameRead()	Sends a frame read event to the registered ReaderListeners.
void	handleError(String message)	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	handleError(String message, Exception exception)	Redirects an error message to the IChemObjectReaderErrorHandler.
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.IChemObjectIO

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

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

setReader, setReader

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

read

Field Detail

mode

protected IChemObjectReader.Mode mode

errorHandler

protected IChemObjectReaderErrorHandler errorHandler

Constructor Detail

DefaultChemObjectReader

public DefaultChemObjectReader()

Method Detail

fireFrameRead

protected void fireFrameRead()

Sends a frame read event to the registered ReaderListeners.

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