Package org.openscience.cdk.io.iterator

Class IteratingPCSubstancesXMLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

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

org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader

All Implemented Interfaces:

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

public class IteratingPCSubstancesXMLReader
extends DefaultIteratingChemObjectReader<IChemModel>

Iterating PubChem PC-Substances ASN.1 XML reader.

Author:

Egon Willighagen <egonw@users.sf.net>

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
IteratingPCSubstancesXMLReader(InputStream in, IChemObjectBuilder builder)	Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCSubstancesXMLReader(Reader in, IChemObjectBuilder builder)	Constructs a new IteratingPCSubstancesXMLReader 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()
IChemModel	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

IteratingPCSubstancesXMLReader

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

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

Parameters:

in - The input stream

builder - The builder

Throws:

IOException - if there is error in getting the IsotopeFactory

XMLStreamException - an error in reading XML

IteratingPCSubstancesXMLReader

public IteratingPCSubstancesXMLReader(InputStream in,
                                      IChemObjectBuilder builder)
                               throws Exception

Constructs a new IteratingPCSubstancesXMLReader 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 IChemModel 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<IChemModel>

Overrides:

remove in class DefaultIteratingChemObjectReader<IChemModel>

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