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

Class AbstractFullPsiXmlParser<T extends Interaction>

java.lang.Object

psidev.psi.mi.jami.xml.io.parser.AbstractFullPsiXmlParser<T>

All Implemented Interfaces:

FullPsiXmlParser<T>, PsiXmlParser<T>

Direct Known Subclasses:

FullXmlComplexParser, FullXmlEvidenceParser, FullXmlModelledParser, FullXmlParser, LightFullXmlParser

public abstract class AbstractFullPsiXmlParser<T extends Interaction>
extends Object
implements PsiXmlParser<T>, FullPsiXmlParser<T>

This class if for parser that will load the all file in memory

Since:

07/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected abstract javax.xml.bind.Unmarshaller	createJAXBUnmarshaller()	createJAXBUnmarshaller.
protected PsiXmlParserException	createPsiXmlExceptionFrom(String message, Exception e)	createPsiXmlExceptionFrom.
AbstractEntrySet<AbstractBaseEntry<T>>	getEntrySet()	Getter for the field entrySet.
XmlInteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
PsiXmlParserListener	getListener()	getListener.
PsiXmlVersion	getVersion()	Getter for the field version.
boolean	hasFinished()	hasFinished.
protected AbstractEntrySet<AbstractBaseEntry<T>>	parseEntrySet()	parseEntrySet.
T	parseNextInteraction()	parseNextInteraction.
void	reInit()	reInit.
void	setCacheOfObjects(PsiXmlIdCache indexOfObjects)	setCacheOfObjects.
void	setInteractorFactory(XmlInteractorFactory interactorFactory)	setInteractorFactory.
void	setListener(PsiXmlParserListener listener)	setListener.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractFullPsiXmlParser

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

Constructor for AbstractFullPsiXmlParser.

Parameters:

file - a File object.

Throws:

javax.xml.bind.JAXBException - if any.

FileNotFoundException - if any.

AbstractFullPsiXmlParser

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

Constructor for AbstractFullPsiXmlParser.

Parameters:

inputStream - a InputStream object.

Throws:

javax.xml.bind.JAXBException - if any.

AbstractFullPsiXmlParser

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

Constructor for AbstractFullPsiXmlParser.

Parameters:

url - a URL object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

AbstractFullPsiXmlParser

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

Constructor for AbstractFullPsiXmlParser.

Parameters:

reader - a Reader object.

Throws:

javax.xml.bind.JAXBException - if any.

Method Detail

parseNextInteraction

public T parseNextInteraction()
                       throws PsiXmlParserException

parseNextInteraction.

Specified by:

parseNextInteraction in interface PsiXmlParser<T extends Interaction>

Returns:

a T object.

Throws:

PsiXmlParserException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface FullPsiXmlParser<T extends Interaction>

Specified by:

close in interface PsiXmlParser<T extends Interaction>

Throws:

MIIOException - if any.

getInteractorFactory

public XmlInteractorFactory getInteractorFactory()

Getter for the field interactorFactory.

Specified by:

getInteractorFactory in interface PsiXmlParser<T extends Interaction>

Returns:

a XmlInteractorFactory object.

setInteractorFactory

public void setInteractorFactory(XmlInteractorFactory interactorFactory)

setInteractorFactory.

Specified by:

setInteractorFactory in interface PsiXmlParser<T extends Interaction>

Parameters:

interactorFactory - a XmlInteractorFactory object.

hasFinished

public boolean hasFinished()
                    throws PsiXmlParserException

hasFinished.

Specified by:

hasFinished in interface FullPsiXmlParser<T extends Interaction>

Specified by:

hasFinished in interface PsiXmlParser<T extends Interaction>

Returns:

a boolean.

Throws:

PsiXmlParserException - if any.

reInit

public void reInit()
            throws MIIOException

reInit.

Specified by:

reInit in interface FullPsiXmlParser<T extends Interaction>

Specified by:

reInit in interface PsiXmlParser<T extends Interaction>

Throws:

MIIOException - if any.

getListener

public PsiXmlParserListener getListener()

getListener.

Specified by:

getListener in interface FullPsiXmlParser<T extends Interaction>

Specified by:

getListener in interface PsiXmlParser<T extends Interaction>

Returns:

a PsiXmlParserListener object.

setListener

public void setListener(PsiXmlParserListener listener)

setListener.

Specified by:

setListener in interface FullPsiXmlParser<T extends Interaction>

Specified by:

setListener in interface PsiXmlParser<T extends Interaction>

Parameters:

listener - a PsiXmlParserListener object.

setCacheOfObjects

public void setCacheOfObjects(PsiXmlIdCache indexOfObjects)

setCacheOfObjects.

Specified by:

setCacheOfObjects in interface FullPsiXmlParser<T extends Interaction>

Specified by:

setCacheOfObjects in interface PsiXmlParser<T extends Interaction>

Parameters:

indexOfObjects - a PsiXmlIdCache object.

getEntrySet

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

Getter for the field entrySet.

Specified by:

getEntrySet in interface FullPsiXmlParser<T extends Interaction>

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.

createJAXBUnmarshaller

protected abstract javax.xml.bind.Unmarshaller createJAXBUnmarshaller()
                                                               throws javax.xml.bind.JAXBException

createJAXBUnmarshaller.

Returns:

a Unmarshaller object.

Throws:

javax.xml.bind.JAXBException - if any.

parseEntrySet

protected AbstractEntrySet<AbstractBaseEntry<T>> parseEntrySet()
                                                        throws PsiXmlParserException

parseEntrySet.

Returns:

a AbstractEntrySet object.

Throws:

PsiXmlParserException - if any.

createPsiXmlExceptionFrom

protected PsiXmlParserException createPsiXmlExceptionFrom(String message,
                                                          Exception e)

createPsiXmlExceptionFrom.

Parameters:

message - a String object.

e - a Exception object.

Returns:

a PsiXmlParserException object.

getVersion

public PsiXmlVersion getVersion()

Getter for the field version.

Specified by:

getVersion in interface PsiXmlParser<T extends Interaction>

Returns:

a PsiXmlVersion object.