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

Class FullXmlBinaryParser

java.lang.Object

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

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

All Implemented Interfaces:

FullPsiXmlParser<Interaction>, PsiXmlParser<BinaryInteraction>

public class FullXmlBinaryParser
extends AbstractPsixmlBinaryParser<Interaction,BinaryInteraction>
implements FullPsiXmlParser<Interaction>

Full Parser generating binary interactions that could be a mix or abstract interactions and interaction evidences. 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
FullXmlBinaryParser(File file)	Constructor for FullXmlBinaryParser.
FullXmlBinaryParser(InputStream inputStream)	Constructor for FullXmlBinaryParser.
FullXmlBinaryParser(Reader reader)	Constructor for FullXmlBinaryParser.
FullXmlBinaryParser(URL url)	Constructor for FullXmlBinaryParser.

Method Summary

Modifier and Type	Method	Description
AbstractEntrySet<AbstractBaseEntry<Interaction>>	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

FullXmlBinaryParser

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

Constructor for FullXmlBinaryParser.

Parameters:

file - a File object.

Throws:

javax.xml.bind.JAXBException - if any.

FileNotFoundException - if any.

FullXmlBinaryParser

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

Constructor for FullXmlBinaryParser.

Parameters:

inputStream - a InputStream object.

Throws:

javax.xml.bind.JAXBException - if any.

FullXmlBinaryParser

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

Constructor for FullXmlBinaryParser.

Parameters:

url - a URL object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

FullXmlBinaryParser

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

Constructor for FullXmlBinaryParser.

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>> getEntrySet()
                                                             throws PsiXmlParserException

getEntrySet.

Specified by:

getEntrySet in interface FullPsiXmlParser<Interaction>

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.