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

Class MitabModelledBinaryStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

InteractionStream<ModelledBinaryInteraction>, MIDataSource, MIFileDataSource, ModelledBinaryInteractionStream, ModelledInteractionStream<ModelledBinaryInteraction>, MIFileParserListener, MitabStreamSource<ModelledBinaryInteraction>, MitabParserListener

public class MitabModelledBinaryStreamSource
extends AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>
implements ModelledBinaryInteractionStream

A mitab datasource that loads modelled binary interactions and ignore experimental details. It only provides an iterator of binary 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
MitabModelledBinaryStreamSource()	Constructor for MitabModelledBinaryStreamSource.
MitabModelledBinaryStreamSource(File file)	Constructor for MitabModelledBinaryStreamSource.
MitabModelledBinaryStreamSource(InputStream input)	Constructor for MitabModelledBinaryStreamSource.
MitabModelledBinaryStreamSource(Reader reader)	Constructor for MitabModelledBinaryStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<ModelledBinaryInteraction>	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

MitabModelledBinaryStreamSource

public MitabModelledBinaryStreamSource()

Constructor for MitabModelledBinaryStreamSource.

MitabModelledBinaryStreamSource

public MitabModelledBinaryStreamSource(File file)
                                throws IOException

Constructor for MitabModelledBinaryStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

MitabModelledBinaryStreamSource

public MitabModelledBinaryStreamSource(InputStream input)

Constructor for MitabModelledBinaryStreamSource.

Parameters:

input - a InputStream object.

MitabModelledBinaryStreamSource

public MitabModelledBinaryStreamSource(Reader reader)

Constructor for MitabModelledBinaryStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Parameters:

file - a File object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Parameters:

input - a InputStream object.

createMitabIterator

protected Iterator<ModelledBinaryInteraction> createMitabIterator()
                                                           throws MIIOException

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Returns:

a Iterator object.

Throws:

MIIOException

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Parameters:

url - a URL object.