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

Class MitabModelledInteractionFeeder

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.feeder.AbstractMitabColumnFeeder<ModelledBinaryInteraction,ModelledParticipant>

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

All Implemented Interfaces:

MitabColumnFeeder<ModelledBinaryInteraction,ModelledParticipant>

Direct Known Subclasses:

ExtendedMitabModelledInteractionFeeder

public class MitabModelledInteractionFeeder
extends AbstractMitabColumnFeeder<ModelledBinaryInteraction,ModelledParticipant>

The Mitab 2.5 column feeder for Modelled interactions

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MitabModelledInteractionFeeder(Writer writer)	Constructor for MitabModelledInteractionFeeder.

Method Summary

Modifier and Type	Method	Description
void	writeAlias(ModelledParticipant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	writeExperimentalRole(ModelledParticipant participant)	writeExperimentalRole.
void	writeFirstAuthor(ModelledBinaryInteraction interaction)	writeFirstAuthor.
void	writeHostOrganism(ModelledBinaryInteraction interaction)	writeHostOrganism.
void	writeInteractionAnnotations(ModelledBinaryInteraction interaction)	writeInteractionAnnotations.
void	writeInteractionConfidences(ModelledBinaryInteraction interaction)	writeInteractionConfidences.
void	writeInteractionDetectionMethod(ModelledBinaryInteraction interaction)	writeInteractionDetectionMethod.
void	writeInteractionIdentifiers(ModelledBinaryInteraction interaction)	writeInteractionIdentifiers.
void	writeInteractionParameters(ModelledBinaryInteraction interaction)	writeInteractionParameters.
void	writeInteractionXrefs(ModelledBinaryInteraction interaction)	writeInteractionXrefs.
void	writeNegativeProperty(ModelledBinaryInteraction interaction)	writeNegativeProperty.
void	writeParticipantIdentificationMethod(ModelledParticipant participant)	writeParticipantIdentificationMethod.
void	writePublicationIdentifiers(ModelledBinaryInteraction interaction)	writePublicationIdentifiers.
void	writeSource(ModelledBinaryInteraction interaction)	writeSource.

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

escapeAndWriteString, getWriter, writeAlias, writeAliases, writeAlternativeIdentifiers, writeAnnotation, writeBiologicalRole, writeChecksum, writeComplexExpansion, writeConfidence, writeCvTerm, writeCvTermName, writeDate, writeFeature, 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

MitabModelledInteractionFeeder

public MitabModelledInteractionFeeder(Writer writer)

Constructor for MitabModelledInteractionFeeder.

Parameters:

writer - a Writer object.

Method Detail

writeInteractionDetectionMethod

public void writeInteractionDetectionMethod(ModelledBinaryInteraction interaction)
                                     throws IOException

writeInteractionDetectionMethod.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeFirstAuthor

public void writeFirstAuthor(ModelledBinaryInteraction interaction)
                      throws IOException

writeFirstAuthor.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writePublicationIdentifiers

public void writePublicationIdentifiers(ModelledBinaryInteraction interaction)
                                 throws IOException

writePublicationIdentifiers.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeSource

public void writeSource(ModelledBinaryInteraction interaction)
                 throws IOException

writeSource.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeInteractionIdentifiers

public void writeInteractionIdentifiers(ModelledBinaryInteraction interaction)
                                 throws IOException

writeInteractionIdentifiers.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeInteractionConfidences

public void writeInteractionConfidences(ModelledBinaryInteraction interaction)
                                 throws IOException

writeInteractionConfidences.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeAlias

public void writeAlias(ModelledParticipant 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

Parameters:

participant - a P object.

alias - a Alias object.

Throws:

IOException - if any.

writeExperimentalRole

public void writeExperimentalRole(ModelledParticipant participant)
                           throws IOException

writeExperimentalRole.

Parameters:

participant - a ModelledParticipant object.

Throws:

IOException - if any.

writeInteractionXrefs

public void writeInteractionXrefs(ModelledBinaryInteraction interaction)
                           throws IOException

writeInteractionXrefs.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeInteractionAnnotations

public void writeInteractionAnnotations(ModelledBinaryInteraction interaction)
                                 throws IOException

writeInteractionAnnotations.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeHostOrganism

public void writeHostOrganism(ModelledBinaryInteraction interaction)
                       throws IOException

writeHostOrganism.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeInteractionParameters

public void writeInteractionParameters(ModelledBinaryInteraction interaction)
                                throws IOException

writeInteractionParameters.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeNegativeProperty

public void writeNegativeProperty(ModelledBinaryInteraction interaction)
                           throws IOException

writeNegativeProperty.

Parameters:

interaction - a ModelledBinaryInteraction object.

Throws:

IOException - if any.

writeParticipantIdentificationMethod

public void writeParticipantIdentificationMethod(ModelledParticipant participant)
                                          throws IOException

writeParticipantIdentificationMethod.

Parameters:

participant - a ModelledParticipant object.

Throws:

IOException - if any.