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

Class DefaultExtendedMitabColumnFeeder

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.feeder.AbstractMitabColumnFeeder<BinaryInteraction,Participant>

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

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

All Implemented Interfaces:

MitabColumnFeeder<BinaryInteraction,Participant>

public class DefaultExtendedMitabColumnFeeder
extends DefaultMitabColumnFeeder

Default Mitab 2.5 extended feeder for interaction. 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
DefaultExtendedMitabColumnFeeder(Writer writer)	Constructor for DefaultExtendedMitabColumnFeeder.

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(Participant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	writeFeature(Feature feature)	Writes a feature

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

writeConfidence, writeExperimentalRole, writeFirstAuthor, writeHostOrganism, writeInteractionAnnotations, writeInteractionConfidences, writeInteractionDetectionMethod, writeInteractionIdentifiers, writeInteractionParameters, writeInteractionXrefs, writeNegativeProperty, writeParameter, writeParticipantIdentificationMethod, writePublicationIdentifiers, 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, 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

DefaultExtendedMitabColumnFeeder

public DefaultExtendedMitabColumnFeeder(Writer writer)

Constructor for DefaultExtendedMitabColumnFeeder.

Parameters:

writer - a Writer object.

Method Detail

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<BinaryInteraction,Participant>

Overrides:

writeAlias in class AbstractMitabColumnFeeder<BinaryInteraction,Participant>

Parameters:

alias - a Alias object.

Throws:

IOException - if any.

writeAlias

public void writeAlias(Participant 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<BinaryInteraction,Participant>

Overrides:

writeAlias in class DefaultMitabColumnFeeder

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<BinaryInteraction,Participant>

Overrides:

writeFeature in class AbstractMitabColumnFeeder<BinaryInteraction,Participant>

Parameters:

feature - a Feature object.

Throws:

IOException - if any.