Package org.openscience.cdk.io.iterator

Class IteratingPCCompoundXMLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

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

org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader

All Implemented Interfaces:

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

public class IteratingPCCompoundXMLReader
extends DefaultIteratingChemObjectReader<IAtomContainer>

Iterating PubChem PCCompound ASN.1 XML reader.

Author:

Egon Willighagen <egonw@users.sf.net>

See Also:

PCCompoundASNReader

Source code:

main

Belongs to CDK module:

io

Keywords:

file format, ASN, PubChem

Created on:

2008-05-05

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.iterator.DefaultIteratingChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor	Description
IteratingPCCompoundXMLReader(InputStream in, IChemObjectBuilder builder)	Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCCompoundXMLReader(Reader in, IChemObjectBuilder builder)	Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes this IChemObjectIO's resources.
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
boolean	hasNext()
IAtomContainer	next()
void	remove()	File IO generally does not support removing of entries.
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.

Methods inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts, 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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

IteratingPCCompoundXMLReader

public IteratingPCCompoundXMLReader(Reader in,
                                    IChemObjectBuilder builder)
                             throws IOException,
                                    XMLStreamException

Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.

Parameters:

in - The input stream

builder - The builder

Throws:

XMLStreamException - if there is an error in setting up the XML parser

IOException

IteratingPCCompoundXMLReader

public IteratingPCCompoundXMLReader(InputStream in,
                                    IChemObjectBuilder builder)
                             throws Exception

Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.

Parameters:

in - The input stream

builder - The builder. In general, use DefaultChemObjectBuilder

Throws:

Exception - if there is a problem creating an InputStreamReader

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

hasNext

public boolean hasNext()

next

public IAtomContainer next()

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.

remove

public void remove()

Description copied from class: DefaultIteratingChemObjectReader

File IO generally does not support removing of entries.

Specified by:

remove in interface Iterator<IAtomContainer>

Overrides:

remove in class DefaultIteratingChemObjectReader<IAtomContainer>

setReader

public void setReader(Reader reader)
               throws CDKException

Description copied from interface: IChemObjectReader

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

Throws:

CDKException

setReader

public void setReader(InputStream reader)
               throws CDKException

Description copied from interface: IChemObjectReader

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

Throws:

CDKException