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

Class AbstractPsiXmlParser<T extends Interaction>

java.lang.Object

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

All Implemented Interfaces:

PsiXmlParser<T>

Direct Known Subclasses:

LightXmlParser, XmlComplexParser, XmlEvidenceParser, XmlModelledParser, XmlParser

public abstract class AbstractPsiXmlParser<T extends Interaction>
extends Object
implements PsiXmlParser<T>

Parser for PSI-XML Returns an Iterator of interactions. // Needs to parse each entry. Between each entry, clear the XmlEntryContext and resolve references // for each entry, read all experiments and interactors and stop when reading interactions

Since:

14/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected boolean	containsUnresolvedReferences(XmlEntryContext entryContext)	containsUnresolvedReferences.
protected abstract javax.xml.bind.Unmarshaller	createJAXBUnmarshaller()	createJAXBUnmarshaller.
protected PsiXmlParserException	createPsiXmlExceptionFrom(String message, Exception e)	createPsiXmlExceptionFrom.
protected String	getCurrentElement()	Getter for the field currentElement.
XmlInteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
PsiXmlParserListener	getListener()	Getter for the field listener.
protected String	getNextPsiXmlStartElement()	getNextPsiXmlStartElement.
protected XMLStreamReader	getStreamReader()	Getter for the field streamReader.
PsiXmlVersion	getVersion()	Getter for the field version.
boolean	hasFinished()	hasFinished.
protected void	loadEntry(XmlEntryContext entryContext, T currentInteraction)	Some interactions contains references and we want to load the remaining interactions until the end of the entry
protected void	parseAttributeList(XmlEntryContext entryContext)	parseAttributeList.
protected void	parseAvailabilityList(XmlEntryContext entryContext)	parseAvailabilityList.
protected void	parseExperimentList()	parseExperimentList.
protected T	parseInteractionList(XmlEntryContext entryContext, T loadedInteraction)	parseInteractionList.
protected T	parseInteractionTag(XmlEntryContext entryContext)	The unmarshaller must be able to return the expected interaction type
protected void	parseInteractorList()	parseInteractorList.
T	parseNextInteraction()	parseNextInteraction.
protected T	parseNextPreLoadedInteraction()	parseNextPreLoadedInteraction.
protected void	parseSource(XmlEntryContext entryContext)	parseSource.
protected void	processAvailabilityList(XmlEntryContext entryContext)	processAvailabilityList.
protected T	processEntry(XmlEntryContext entryContext)	Creates a new Entry, parses the entry and return the next available interaction
protected T	processEntryAndLoadNextInteraction(XmlEntryContext entryContext, Location startEntry)	Process an entry that is opened (source, experimentList, etc) and read the first interaction
protected void	processUnexpectedNode()	processUnexpectedNode.
void	reInit()	reInit.
void	setCacheOfObjects(PsiXmlIdCache indexOfObjects)	setCacheOfObjects.
protected void	setCurrentElement(String currentElement)	Setter for the field currentElement.
void	setInteractorFactory(XmlInteractorFactory interactorFactory)	setInteractorFactory.
void	setListener(PsiXmlParserListener listener)	setListener.
protected void	skipNextElement()	skipNextElement.
protected T	unmarshallInteraction()	unmarshallInteraction.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractPsiXmlParser

public AbstractPsiXmlParser(File file)

Constructor for AbstractPsiXmlParser.

Parameters:

file - a File object.

AbstractPsiXmlParser

public AbstractPsiXmlParser(InputStream inputStream)

Constructor for AbstractPsiXmlParser.

Parameters:

inputStream - a InputStream object.

AbstractPsiXmlParser

public AbstractPsiXmlParser(URL url)

Constructor for AbstractPsiXmlParser.

Parameters:

url - a URL object.

AbstractPsiXmlParser

public AbstractPsiXmlParser(Reader reader)

Constructor for AbstractPsiXmlParser.

Parameters:

reader - a Reader object.

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 PsiXmlParser<T extends Interaction>

Throws:

MIIOException - if any.

hasFinished

public boolean hasFinished()
                    throws PsiXmlParserException

hasFinished.

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 PsiXmlParser<T extends Interaction>

Throws:

MIIOException - if any.

getListener

public PsiXmlParserListener getListener()

Getter for the field listener.

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 PsiXmlParser<T extends Interaction>

Parameters:

listener - a PsiXmlParserListener object.

setCacheOfObjects

public void setCacheOfObjects(PsiXmlIdCache indexOfObjects)

setCacheOfObjects.

Specified by:

setCacheOfObjects in interface PsiXmlParser<T extends Interaction>

Parameters:

indexOfObjects - a PsiXmlIdCache object.

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.

getNextPsiXmlStartElement

protected String getNextPsiXmlStartElement()
                                    throws PsiXmlParserException

getNextPsiXmlStartElement.

Returns:

a String 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.

createJAXBUnmarshaller

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

createJAXBUnmarshaller.

Returns:

the unmarshaller with the class context

Throws:

javax.xml.bind.JAXBException - if any.

processEntryAndLoadNextInteraction

protected T processEntryAndLoadNextInteraction(XmlEntryContext entryContext,
                                               Location startEntry)
                                        throws PsiXmlParserException

Process an entry that is opened (source, experimentList, etc) and read the first interaction

Parameters:

entryContext - a XmlEntryContext object.

startEntry - a Location object.

Returns:

a T object.

Throws:

PsiXmlParserException - if any.

parseAttributeList

protected void parseAttributeList(XmlEntryContext entryContext)
                           throws PsiXmlParserException

parseAttributeList.

Parameters:

entryContext - a XmlEntryContext object.

Throws:

PsiXmlParserException - if any.

parseInteractionList

protected T parseInteractionList(XmlEntryContext entryContext,
                                 T loadedInteraction)
                          throws PsiXmlParserException

parseInteractionList.

Parameters:

entryContext - a XmlEntryContext object.

loadedInteraction - a T object.

Returns:

a T object.

Throws:

PsiXmlParserException - if any.

parseInteractorList

protected void parseInteractorList()
                            throws PsiXmlParserException

parseInteractorList.

Throws:

PsiXmlParserException - if any.

parseExperimentList

protected void parseExperimentList()
                            throws PsiXmlParserException

parseExperimentList.

Throws:

PsiXmlParserException - if any.

parseAvailabilityList

protected void parseAvailabilityList(XmlEntryContext entryContext)
                              throws PsiXmlParserException

parseAvailabilityList.

Parameters:

entryContext - a XmlEntryContext object.

Throws:

PsiXmlParserException - if any.

parseSource

protected void parseSource(XmlEntryContext entryContext)
                    throws PsiXmlParserException

parseSource.

Parameters:

entryContext - a XmlEntryContext object.

Throws:

PsiXmlParserException - if any.

processEntry

protected T processEntry(XmlEntryContext entryContext)
                  throws PsiXmlParserException

Creates a new Entry, parses the entry and return the next available interaction

Parameters:

entryContext - a XmlEntryContext object.

Returns:

a T object.

Throws:

PsiXmlParserException - if any.

loadEntry

protected void loadEntry(XmlEntryContext entryContext,
                         T currentInteraction)
                  throws PsiXmlParserException

Some interactions contains references and we want to load the remaining interactions until the end of the entry

Parameters:

entryContext - a XmlEntryContext object.

currentInteraction - a T object.

Throws:

PsiXmlParserException - if any.

parseNextPreLoadedInteraction

protected T parseNextPreLoadedInteraction()
                                   throws PsiXmlParserException

parseNextPreLoadedInteraction.

Returns:

the next interaction preloaded in the interactionIterator. Deletes the returned interaction

Throws:

PsiXmlParserException - if any.

parseInteractionTag

protected T parseInteractionTag(XmlEntryContext entryContext)
                         throws PsiXmlParserException

The unmarshaller must be able to return the expected interaction type

Parameters:

entryContext - a XmlEntryContext object.

Returns:

next interaction parsed in the interaction list. Will load the all entry if we have references to solve

Throws:

PsiXmlParserException - if any.

containsUnresolvedReferences

protected boolean containsUnresolvedReferences(XmlEntryContext entryContext)

containsUnresolvedReferences.

Parameters:

entryContext - a XmlEntryContext object.

Returns:

a boolean.

unmarshallInteraction

protected T unmarshallInteraction()
                           throws javax.xml.bind.JAXBException

unmarshallInteraction.

Returns:

a T object.

Throws:

javax.xml.bind.JAXBException - if any.

processAvailabilityList

protected void processAvailabilityList(XmlEntryContext entryContext)
                                throws PsiXmlParserException

processAvailabilityList.

Parameters:

entryContext - a XmlEntryContext object.

Throws:

PsiXmlParserException - if any.

getStreamReader

protected XMLStreamReader getStreamReader()

Getter for the field streamReader.

Returns:

a XMLStreamReader object.

getCurrentElement

protected String getCurrentElement()

Getter for the field currentElement.

Returns:

a String object.

setCurrentElement

protected void setCurrentElement(String currentElement)

Setter for the field currentElement.

Parameters:

currentElement - a String object.

skipNextElement

protected void skipNextElement()
                        throws PsiXmlParserException

skipNextElement.

Throws:

PsiXmlParserException - if any.

processUnexpectedNode

protected void processUnexpectedNode()
                              throws PsiXmlParserException

processUnexpectedNode.

Throws:

PsiXmlParserException - if any.

getVersion

public PsiXmlVersion getVersion()

Getter for the field version.

Specified by:

getVersion in interface PsiXmlParser<T extends Interaction>

Returns:

a PsiXmlVersion object.