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

Class LightMitabBinaryStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

BinaryInteractionStream<BinaryInteraction>, InteractionStream<BinaryInteraction>, MIDataSource, MIFileDataSource, MIFileParserListener, MitabStreamSource<BinaryInteraction>, MitabParserListener

public class LightMitabBinaryStreamSource
extends AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>
implements BinaryInteractionStream<BinaryInteraction>

A mitab datasource that loads very basic binary interactions and ignore experimental details, source, confidence and 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
LightMitabBinaryStreamSource()	Constructor for LightMitabBinaryStreamSource.
LightMitabBinaryStreamSource(File file)	Constructor for LightMitabBinaryStreamSource.
LightMitabBinaryStreamSource(InputStream input)	Constructor for LightMitabBinaryStreamSource.
LightMitabBinaryStreamSource(Reader reader)	Constructor for LightMitabBinaryStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<BinaryInteraction>	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

LightMitabBinaryStreamSource

public LightMitabBinaryStreamSource()

Constructor for LightMitabBinaryStreamSource.

LightMitabBinaryStreamSource

public LightMitabBinaryStreamSource(File file)
                             throws IOException

Constructor for LightMitabBinaryStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

LightMitabBinaryStreamSource

public LightMitabBinaryStreamSource(InputStream input)

Constructor for LightMitabBinaryStreamSource.

Parameters:

input - a InputStream object.

LightMitabBinaryStreamSource

public LightMitabBinaryStreamSource(Reader reader)

Constructor for LightMitabBinaryStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)
                                  throws MIIOException

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>

Parameters:

file - a File object.

Throws:

MIIOException

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>

Parameters:

input - a InputStream object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)
                                  throws MIIOException

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>

Parameters:

url - a URL object.

Throws:

MIIOException

createMitabIterator

protected Iterator<BinaryInteraction> createMitabIterator()
                                                   throws MIIOException

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<BinaryInteraction,Participant,Feature>

Returns:

a Iterator object.

Throws:

MIIOException