Package org.openscience.cdk.io

Class INChIReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.INChIReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class INChIReader
extends DefaultChemObjectReader

Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document. See [Stein, S. and Heller, S.. Chemistry International. 2001. 23]. Recently a new INChI format was introduced an files generated with the latest INChI generator cannot be parsed with this class. This class needs to be updated.

The elements that are read are given in the INChIHandler class.

Author:

Egon Willighagen <egonw@sci.kun.nl>

Source code:

main

Belongs to CDK module:

extra

Keywords:

file format, INChI, chemical identifier

Created on:

2004-05-17

Requires:

java1.4+

Nested Class Summary

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

IChemObjectReader.Mode

Field Summary

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor	Description
INChIReader()
INChIReader(InputStream input)	Construct a INChI reader from a InputStream object.

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> classObject)	Returns whether the given IChemObject can be read or written.
void	close()	Closes this IChemObjectIO's resources.
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object)	Reads a IChemObject of type object from input.
void	setReader(InputStream input)	Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader reader)	This method must not be used; XML reading requires the use of an InputStream.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

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

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

Constructor Detail

INChIReader

public INChIReader(InputStream input)

Construct a INChI reader from a InputStream object.

Parameters:

input - the InputStream with the content

INChIReader

public INChIReader()

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader reader)
               throws CDKException

This method must not be used; XML reading requires the use of an InputStream. Use setReader(InputStream) instead.

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

Description copied from interface: IChemObjectReader

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

Throws:

CDKException

accepts

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

Description copied from interface: IChemObjectIO

Returns whether the given IChemObject can be read or written.

Parameters:

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

Returns:

true, if the IChemObject can be handled.

read

public <T extends IChemObject> T read(T object)
                               throws CDKException

Reads a IChemObject of type object from input. Supported types are: ChemFile.

Parameters:

object - type of requested IChemObject

Returns:

the content in a ChemFile object

Throws:

CDKException - it is thrown if the type of information is not available from the input

close

public void close()
           throws IOException

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.