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

Class FullXmlBinaryEvidenceParser

java.lang.Object

psidev.psi.mi.jami.xml.io.parser.AbstractPsixmlBinaryParser<InteractionEvidence,BinaryInteractionEvidence>

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

All Implemented Interfaces:

FullPsiXmlParser<InteractionEvidence>, PsiXmlParser<BinaryInteractionEvidence>

public class FullXmlBinaryEvidenceParser
extends AbstractPsixmlBinaryParser<InteractionEvidence,BinaryInteractionEvidence>
implements FullPsiXmlParser<InteractionEvidence>

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

Method Summary

Modifier and Type	Method	Description
AbstractEntrySet<AbstractBaseEntry<InteractionEvidence>>	getEntrySet()	getEntrySet.
protected ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>	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

FullXmlBinaryEvidenceParser

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

Constructor for FullXmlBinaryEvidenceParser.

Parameters:

file - a File object.

Throws:

javax.xml.bind.JAXBException - if any.

FileNotFoundException - if any.

FullXmlBinaryEvidenceParser

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

Constructor for FullXmlBinaryEvidenceParser.

Parameters:

inputStream - a InputStream object.

Throws:

javax.xml.bind.JAXBException - if any.

FullXmlBinaryEvidenceParser

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

Constructor for FullXmlBinaryEvidenceParser.

Parameters:

url - a URL object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

FullXmlBinaryEvidenceParser

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

Constructor for FullXmlBinaryEvidenceParser.

Parameters:

reader - a Reader object.

Throws:

javax.xml.bind.JAXBException - if any.

Method Detail

initialiseDefaultExpansionMethod

protected ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> initialiseDefaultExpansionMethod()

initialiseDefaultExpansionMethod.

Specified by:

initialiseDefaultExpansionMethod in class AbstractPsixmlBinaryParser<InteractionEvidence,BinaryInteractionEvidence>

Returns:

a ComplexExpansionMethod object.

getEntrySet

public AbstractEntrySet<AbstractBaseEntry<InteractionEvidence>> getEntrySet()
                                                                     throws PsiXmlParserException

getEntrySet.

Specified by:

getEntrySet in interface FullPsiXmlParser<InteractionEvidence>

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.