Package psidev.psi.mi.jami.xml.io.parser

Class LightFullXmlBinaryParser

java.lang.Object

psidev.psi.mi.jami.xml.io.parser.AbstractPsixmlBinaryParser<Interaction,BinaryInteraction>

psidev.psi.mi.jami.xml.io.parser.LightFullXmlBinaryParser

All Implemented Interfaces:

FullPsiXmlParser<Interaction<? extends Participant>>, PsiXmlParser<BinaryInteraction>

public class LightFullXmlBinaryParser
extends AbstractPsixmlBinaryParser<Interaction,BinaryInteraction>
implements FullPsiXmlParser<Interaction<? extends Participant>>

Full Parser generating basic binary interaction objects and ignoring all experimental details. It will load the all entrySet so is consuming a lot of memory in case of large files but is very performant for small files

Since:

08/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
LightFullXmlBinaryParser(File file)	Constructor for LightFullXmlBinaryParser.
LightFullXmlBinaryParser(InputStream inputStream)	Constructor for LightFullXmlBinaryParser.
LightFullXmlBinaryParser(Reader reader)	Constructor for LightFullXmlBinaryParser.
LightFullXmlBinaryParser(URL url)	Constructor for LightFullXmlBinaryParser.

Method Summary

Modifier and Type	Method	Description
AbstractEntrySet<AbstractBaseEntry<Interaction<? extends Participant>>>	getEntrySet()	getEntrySet.
protected ComplexExpansionMethod<Interaction,BinaryInteraction>	initialiseDefaultExpansionMethod()	initialiseDefaultExpansionMethod.

Methods inherited from class psidev.psi.mi.jami.xml.io.parser.AbstractPsixmlBinaryParser

close, getDelegateParser, getExpansionMethod, getInteractorFactory, getListener, getVersion, hasFinished, instantiateInteractionFactory, parseNextInteraction, reInit, setCacheOfObjects, setExpansionMethod, setInteractorFactory, setListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface psidev.psi.mi.jami.xml.io.parser.FullPsiXmlParser

close, getListener, hasFinished, reInit, setCacheOfObjects, setListener

Constructor Detail

LightFullXmlBinaryParser

public LightFullXmlBinaryParser(File file)
                         throws javax.xml.bind.JAXBException,
                                FileNotFoundException

Constructor for LightFullXmlBinaryParser.

Parameters:

file - a File object.

Throws:

javax.xml.bind.JAXBException - if any.

FileNotFoundException - if any.

LightFullXmlBinaryParser

public LightFullXmlBinaryParser(InputStream inputStream)
                         throws javax.xml.bind.JAXBException

Constructor for LightFullXmlBinaryParser.

Parameters:

inputStream - a InputStream object.

Throws:

javax.xml.bind.JAXBException - if any.

LightFullXmlBinaryParser

public LightFullXmlBinaryParser(URL url)
                         throws IOException,
                                javax.xml.bind.JAXBException

Constructor for LightFullXmlBinaryParser.

Parameters:

url - a URL object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

LightFullXmlBinaryParser

public LightFullXmlBinaryParser(Reader reader)
                         throws javax.xml.bind.JAXBException

Constructor for LightFullXmlBinaryParser.

Parameters:

reader - a Reader object.

Throws:

javax.xml.bind.JAXBException - if any.

Method Detail

initialiseDefaultExpansionMethod

protected ComplexExpansionMethod<Interaction,BinaryInteraction> initialiseDefaultExpansionMethod()

initialiseDefaultExpansionMethod.

Specified by:

initialiseDefaultExpansionMethod in class AbstractPsixmlBinaryParser<Interaction,BinaryInteraction>

Returns:

a ComplexExpansionMethod object.

getEntrySet

public AbstractEntrySet<AbstractBaseEntry<Interaction<? extends Participant>>> getEntrySet()
                                                                                    throws PsiXmlParserException

getEntrySet.

Specified by:

getEntrySet in interface FullPsiXmlParser<Interaction<? extends Participant>>

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.