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

Class LightMitabStreamSource

java.lang.Object

psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource<Interaction,Participant,Feature>

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

All Implemented Interfaces:

InteractionStream<Interaction>, MIDataSource, MIFileDataSource, MIFileParserListener, MitabStreamSource<Interaction>, MitabParserListener

public class LightMitabStreamSource
extends AbstractMitabStreamSource<Interaction,Participant,Feature>

A mitab datasource that loads very basic interactions and ignore experimental details, source, confidence and experimental details It will only provide an iterator of 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
LightMitabStreamSource()	Constructor for LightMitabStreamSource.
LightMitabStreamSource(File file)	Constructor for LightMitabStreamSource.
LightMitabStreamSource(InputStream input)	Constructor for LightMitabStreamSource.
LightMitabStreamSource(Reader reader)	Constructor for LightMitabStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<Interaction>	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

Constructor Detail

LightMitabStreamSource

public LightMitabStreamSource()

Constructor for LightMitabStreamSource.

LightMitabStreamSource

public LightMitabStreamSource(File file)
                       throws IOException

Constructor for LightMitabStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

LightMitabStreamSource

public LightMitabStreamSource(InputStream input)

Constructor for LightMitabStreamSource.

Parameters:

input - a InputStream object.

LightMitabStreamSource

public LightMitabStreamSource(Reader reader)

Constructor for LightMitabStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<Interaction,Participant,Feature>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<Interaction,Participant,Feature>

Parameters:

file - a File object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<Interaction,Participant,Feature>

Parameters:

input - a InputStream object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<Interaction,Participant,Feature>

Parameters:

url - a URL object.

createMitabIterator

protected Iterator<Interaction> createMitabIterator()
                                             throws MIIOException

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<Interaction,Participant,Feature>

Returns:

a Iterator object.

Throws:

MIIOException