Package org.openscience.cdk.io

Class CMLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.CMLReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class CMLReader
extends DefaultChemObjectReader

Reads a molecule in CML 1.x and 2.0 format. CML is an XML based application [Murray-Rust, P. and Rzepa, H.S.. Journal of Chemical Information and Computer Sciences. 1999. 39], and this Reader applies the method described in [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4].

Author:

Egon L. Willighagen

This class is affected by these bug(s):

1544406

Source code:

main

Belongs to CDK module:

io

Keywords:

file format, CML

Created on:

2001-02-01

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
CMLReader()
CMLReader(InputStream input)	Reads CML from an java.io.InputStream, for example the FileInputStream.
CMLReader(String url)	Define this CMLReader to take the input from a java.io.Reader class.

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)	Read a IChemObject from input.
void	registerConvention(String convention, ICMLModule conv)
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

CMLReader

public CMLReader(InputStream input)

Reads CML from an java.io.InputStream, for example the FileInputStream.

Parameters:

input - InputStream type input

CMLReader

public CMLReader()

CMLReader

public CMLReader(String url)

Define this CMLReader to take the input from a java.io.Reader class. Possible readers are (among others) StringReader and FileReader.

Parameters:

url - String url which points to the file to be read

Method Detail

registerConvention

public void registerConvention(String convention,
                               ICMLModule conv)

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

Read a IChemObject from input.

Parameters:

object - the type of object to return

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.