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

Class DefaultMitabSource

java.lang.Object

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

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

All Implemented Interfaces:

InteractionSource, InteractionStream, MIDataSource, MIFileDataSource, MIFileParserListener, MitabSource, MitabStreamSource, MitabParserListener

public class DefaultMitabSource
extends DefaultMitabStreamSource
implements MitabSource

Abstract class for an InteractionSource coming from a MITAB file. This datasource provides interaction iterator and collection

Since:

08/11/13

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
DefaultMitabSource()	Constructor for DefaultMitabSource.

Method Summary

Modifier and Type	Method	Description
protected MitabSource	getDelegate()	Getter for the field delegate.
Collection<Interaction>	getInteractions()	getInteractions.
long	getNumberOfInteractions()	getNumberOfInteractions.
protected void	initialiseDelegate(Map<String,Object> options, MitabDataSourceFactory factory, InteractionCategory category, ComplexType type)	initialiseDelegate.

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

close, getFileParserListener, getInteractionsIterator, 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, reset, setDelegate, setFileParserListener, 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

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

getFileParserListener, setFileParserListener, validateSyntax, validateSyntax

Methods inherited from interface psidev.psi.mi.jami.listener.MIFileParserListener

onAliasWithoutName, onAnnotationWithoutTopic, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSyntaxWarning, onXrefWithoutDatabase, onXrefWithoutId

Methods inherited from interface psidev.psi.mi.jami.tab.listener.MitabParserListener

onAliasWithoutDbSource, onEmptyUniqueIdentifiers, onMissingExpansionId, onMissingInteractorIdentifierColumns, onSeveralCreatedDateFound, onSeveralCvTermsFound, onSeveralFirstAuthorFound, onSeveralHostOrganismFound, onSeveralOrganismFound, onSeveralSourceFound, onSeveralStoichiometryFound, onSeveralUniqueIdentifiers, onSeveralUpdatedDateFound, onTextFoundInConfidence, onTextFoundInIdentifier

Constructor Detail

DefaultMitabSource

public DefaultMitabSource()

Constructor for DefaultMitabSource.

Method Detail

initialiseDelegate

protected void initialiseDelegate(Map<String,Object> options,
                                  MitabDataSourceFactory factory,
                                  InteractionCategory category,
                                  ComplexType type)

initialiseDelegate.

Overrides:

initialiseDelegate in class DefaultMitabStreamSource

Parameters:

options - a Map object.

factory - a MitabDataSourceFactory object.

category - a InteractionCategory object.

type - a ComplexType object.

getInteractions

public Collection<Interaction> getInteractions()
                                        throws MIIOException

getInteractions.

Specified by:

getInteractions in interface InteractionSource

Returns:

a Collection object.

Throws:

MIIOException - if any.

getNumberOfInteractions

public long getNumberOfInteractions()

getNumberOfInteractions.

Specified by:

getNumberOfInteractions in interface InteractionSource

Returns:

a long.

getDelegate

protected MitabSource getDelegate()

Getter for the field delegate.

Overrides:

getDelegate in class DefaultMitabStreamSource

Returns:

a MitabStreamSource object.