Package psidev.psi.mi.jami.tab.extension.datasource

Class MitabModelledStreamSource

java.lang.Object

psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

psidev.psi.mi.jami.tab.extension.datasource.MitabModelledStreamSource

All Implemented Interfaces:

InteractionStream<ModelledInteraction>, MIDataSource, MIFileDataSource, ModelledInteractionStream<ModelledInteraction>, MIFileParserListener, MitabStreamSource<ModelledInteraction>, MitabParserListener

public class MitabModelledStreamSource
extends AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>
implements ModelledInteractionStream<ModelledInteraction>

A mitab datasource that loads modelled interactions and ignore experimental details It only provides an iterator of modelled interactions

Since:

21/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource

FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors

Constructor	Description
MitabModelledStreamSource()	Constructor for MitabModelledStreamSource.
MitabModelledStreamSource(File file)	Constructor for MitabModelledStreamSource.
MitabModelledStreamSource(InputStream input)	Constructor for MitabModelledStreamSource.
MitabModelledStreamSource(Reader reader)	Constructor for MitabModelledStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<ModelledInteraction>	createMitabIterator()	createMitabIterator.
protected void	initialiseMitabLineParser(File file)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(InputStream input)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(Reader reader)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(URL url)	initialiseMitabLineParser.

Methods inherited from class psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource

close, getFileParserListener, getInteractionsIterator, getInteractorFactory, getLineParser, initialiseContext, onAliasWithoutDbSource, onAliasWithoutName, onAnnotationWithoutTopic, onEmptyUniqueIdentifiers, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingExpansionId, onMissingInteractorIdentifierColumns, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSeveralCreatedDateFound, onSeveralCvTermsFound, onSeveralFirstAuthorFound, onSeveralHostOrganismFound, onSeveralOrganismFound, onSeveralSourceFound, onSeveralStoichiometryFound, onSeveralUniqueIdentifiers, onSeveralUpdatedDateFound, onSyntaxWarning, onTextFoundInConfidence, onTextFoundInIdentifier, onXrefWithoutDatabase, onXrefWithoutId, reInit, reset, setFileParserListener, setInteractorFactory, setLineParser, setMIFileParserListener, setMitabFileParserListener, setOriginalFile, setOriginalReader, setOriginalStream, setOriginalURL, validateSyntax, validateSyntax

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.datasource.InteractionStream

getInteractionsIterator

Methods inherited from interface psidev.psi.mi.jami.datasource.MIDataSource

close, initialiseContext, reset

Constructor Detail

MitabModelledStreamSource

public MitabModelledStreamSource()

Constructor for MitabModelledStreamSource.

MitabModelledStreamSource

public MitabModelledStreamSource(File file)
                          throws IOException

Constructor for MitabModelledStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

MitabModelledStreamSource

public MitabModelledStreamSource(InputStream input)

Constructor for MitabModelledStreamSource.

Parameters:

input - a InputStream object.

MitabModelledStreamSource

public MitabModelledStreamSource(Reader reader)

Constructor for MitabModelledStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

Parameters:

file - a File object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

Parameters:

input - a InputStream object.

createMitabIterator

protected Iterator<ModelledInteraction> createMitabIterator()
                                                     throws MIIOException

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

Returns:

a Iterator object.

Throws:

MIIOException

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledInteraction,ModelledParticipant,ModelledFeature>

Parameters:

url - a URL object.