Package psidev.psi.mi.jami.tab.io.writer.feeder.extended

Class ExtendedMitabInteractionEvidenceFeeder

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.feeder.AbstractMitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

psidev.psi.mi.jami.tab.io.writer.feeder.MitabInteractionEvidenceFeeder

psidev.psi.mi.jami.tab.io.writer.feeder.extended.ExtendedMitabInteractionEvidenceFeeder

All Implemented Interfaces:

MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

public class ExtendedMitabInteractionEvidenceFeeder
extends MitabInteractionEvidenceFeeder

Mitab 2.6 extended feeder for interaction evidence. It will cast Alias with MitabAlias to write a specified dbsource, it will cast Feature with DefaultMitabFeature to write a specific feature text and it will cast Confidence with MitabConfidence to write a specific text

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
ExtendedMitabInteractionEvidenceFeeder(Writer writer)	Constructor for ExtendedMitabInteractionEvidenceFeeder.

Method Summary

Modifier and Type	Method	Description
void	writeAlias(Alias alias)	This methods write the dbsource, alias name and alias type of an alias
void	writeAlias(ParticipantEvidence participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	writeConfidence(Confidence conf)	This method will write a confidence with a text if text is not null
void	writeFeature(Feature feature)	Writes a feature

Methods inherited from class psidev.psi.mi.jami.tab.io.writer.feeder.MitabInteractionEvidenceFeeder

writeExperimentalRole, writeFirstAuthor, writeHostOrganism, writeInteractionAnnotations, writeInteractionAnnotationTagsFrom, writeInteractionConfidences, writeInteractionDetectionMethod, writeInteractionIdentifiers, writeInteractionParameters, writeInteractionXrefs, writeNegativeProperty, writeParticipantIdentificationMethod, writePublicationIdentifiers, writePublicationImexId, writeSource

Methods inherited from class psidev.psi.mi.jami.tab.io.writer.feeder.AbstractMitabColumnFeeder

escapeAndWriteString, getWriter, writeAliases, writeAlternativeIdentifiers, writeAnnotation, writeBiologicalRole, writeChecksum, writeComplexExpansion, writeCvTerm, writeCvTermName, writeDate, writeIdentifier, writeInteractionCausalRegulatoryMechanism, writeInteractionCausalStatement, writeInteractionChecksums, writeInteractionType, writeInteractorOrganism, writeInteractorType, writeOrganism, writeParameter, writeParticipantAnnotations, writeParticipantBiologicalEffect, writeParticipantChecksums, writeParticipantFeatures, writeParticipantStoichiometry, writeParticipantXrefs, writeUniqueIdentifier, writeXref

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExtendedMitabInteractionEvidenceFeeder

public ExtendedMitabInteractionEvidenceFeeder(Writer writer)

Constructor for ExtendedMitabInteractionEvidenceFeeder.

Parameters:

writer - a Writer object.

Method Detail

writeConfidence

public void writeConfidence(Confidence conf)
                     throws IOException

This method will write a confidence with a text if text is not null

Specified by:

writeConfidence in interface MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Overrides:

writeConfidence in class AbstractMitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Parameters:

conf - a Confidence object.

Throws:

IOException - if any.

writeAlias

public void writeAlias(Alias alias)
                throws IOException

This methods write the dbsource, alias name and alias type of an alias

Specified by:

writeAlias in interface MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Overrides:

writeAlias in class AbstractMitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Parameters:

alias - a Alias object.

Throws:

IOException - if any.

writeAlias

public void writeAlias(ParticipantEvidence participant,
                       Alias alias)
                throws IOException

This methods write the dbsource, alias name and alias type of an alias. It can use the modelled participant to find dbsource

Specified by:

writeAlias in interface MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Overrides:

writeAlias in class MitabInteractionEvidenceFeeder

Parameters:

participant - a P object.

alias - a Alias object.

Throws:

IOException - if any.

writeFeature

public void writeFeature(Feature feature)
                  throws IOException

Writes a feature

Specified by:

writeFeature in interface MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Overrides:

writeFeature in class AbstractMitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Parameters:

feature - a Feature object.

Throws:

IOException - if any.