org.openscience.cdk.io

Interface IChemObjectReader

All Superinterfaces:

AutoCloseable, Closeable, IChemObjectIO

All Known Subinterfaces:

IIteratingChemObjectReader<T>, ISimpleChemObjectReader

All Known Implementing Classes:

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

public interface IChemObjectReader
extends IChemObjectIO

This interface specifies the common functionality all IO readers should provide. IO readers should not implement this interface directly, but rather implement one of its child interfaces: ISimpleChemObjectReader or IIteratingChemObjectReader. These sub-interfaces specify the information access methods: a simple read() method for the ISimpleChemObjectReader and more advanced iterator based access for the IIteratingChemObjectReader (suitable for large files)

Author:

Egon Willighagen <egonw@users.sf.net>

See Also:

ISimpleChemObjectReader, IIteratingChemObjectReader

Source code:

master

Belongs to CDK module:

io

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	IChemObjectReader.Mode

Method Summary

Modifier and Type	Method and Description
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	setErrorHandler(IChemObjectReaderErrorHandler handler) Sets an error handler that is sent events when file format issues occur.
void	setReader(InputStream reader) 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.
void	setReaderMode(IChemObjectReader.Mode mode) Sets the reader mode.

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

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

Method Detail

setReader

void setReader(Reader reader)
        throws CDKException

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

Throws:

CDKException

setReader

void setReader(InputStream reader)
        throws CDKException

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

Throws:

CDKException

setReaderMode

void setReaderMode(IChemObjectReader.Mode mode)

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.

Parameters:

mode -

setErrorHandler

void setErrorHandler(IChemObjectReaderErrorHandler handler)

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

Parameters:

handler - IChemObjectReaderErrorHandler to send error messages to.

handleError

void handleError(String message)
          throws CDKException

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

Parameters:

message - the error message.

Throws:

CDKException

handleError

void handleError(String message,
                 Exception exception)
          throws CDKException

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

Parameters:

message - the error message.

exception - the corresponding Exception.

Throws:

CDKException

handleError

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.

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

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.

Parameters:

message - the error message.

exception - the corresponding Exception.

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