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

Class FullXmlModelledBinaryParser

java.lang.Object

psidev.psi.mi.jami.xml.io.parser.AbstractPsixmlBinaryParser<ModelledInteraction,ModelledBinaryInteraction>

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

All Implemented Interfaces:

FullPsiXmlParser<ModelledInteraction>, PsiXmlParser<ModelledBinaryInteraction>

public class FullXmlModelledBinaryParser
extends AbstractPsixmlBinaryParser<ModelledInteraction,ModelledBinaryInteraction>
implements FullPsiXmlParser<ModelledInteraction>

Full Parser generating binary modelled 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
FullXmlModelledBinaryParser(File file)	Constructor for FullXmlModelledBinaryParser.
FullXmlModelledBinaryParser(InputStream inputStream)	Constructor for FullXmlModelledBinaryParser.
FullXmlModelledBinaryParser(Reader reader)	Constructor for FullXmlModelledBinaryParser.
FullXmlModelledBinaryParser(URL url)	Constructor for FullXmlModelledBinaryParser.

Method Summary

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

FullXmlModelledBinaryParser

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

Constructor for FullXmlModelledBinaryParser.

Parameters:

file - a File object.

Throws:

javax.xml.bind.JAXBException - if any.

FileNotFoundException - if any.

FullXmlModelledBinaryParser

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

Constructor for FullXmlModelledBinaryParser.

Parameters:

inputStream - a InputStream object.

Throws:

javax.xml.bind.JAXBException - if any.

FullXmlModelledBinaryParser

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

Constructor for FullXmlModelledBinaryParser.

Parameters:

url - a URL object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

FullXmlModelledBinaryParser

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

Constructor for FullXmlModelledBinaryParser.

Parameters:

reader - a Reader object.

Throws:

javax.xml.bind.JAXBException - if any.

Method Detail

initialiseDefaultExpansionMethod

protected ComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction> initialiseDefaultExpansionMethod()

initialiseDefaultExpansionMethod.

Specified by:

initialiseDefaultExpansionMethod in class AbstractPsixmlBinaryParser<ModelledInteraction,ModelledBinaryInteraction>

Returns:

a ComplexExpansionMethod object.

getEntrySet

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

getEntrySet.

Specified by:

getEntrySet in interface FullPsiXmlParser<ModelledInteraction>

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.