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

Class MitabInteractionEvidenceFeeder

java.lang.Object

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

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

All Implemented Interfaces:

MitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

Direct Known Subclasses:

ExtendedMitabInteractionEvidenceFeeder

public class MitabInteractionEvidenceFeeder
extends AbstractMitabColumnFeeder<BinaryInteractionEvidence,ParticipantEvidence>

The Mitab 2.5 column feeder for interaction evidences

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MitabInteractionEvidenceFeeder(Writer writer)	Constructor for MitabInteractionEvidenceFeeder.

Method Summary

Modifier and Type	Method	Description
void	writeAlias(ParticipantEvidence participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	writeExperimentalRole(ParticipantEvidence participant)	writeExperimentalRole.
void	writeFirstAuthor(BinaryInteractionEvidence interaction)	writeFirstAuthor.
void	writeHostOrganism(BinaryInteractionEvidence interaction)	writeHostOrganism.
void	writeInteractionAnnotations(BinaryInteractionEvidence interaction)	writeInteractionAnnotations.
protected void	writeInteractionAnnotationTagsFrom(Publication pub)	writeInteractionAnnotationTagsFrom.
void	writeInteractionConfidences(BinaryInteractionEvidence interaction)	writeInteractionConfidences.
void	writeInteractionDetectionMethod(BinaryInteractionEvidence interaction)	writeInteractionDetectionMethod.
void	writeInteractionIdentifiers(BinaryInteractionEvidence interaction)	writeInteractionIdentifiers.
void	writeInteractionParameters(BinaryInteractionEvidence interaction)	writeInteractionParameters.
void	writeInteractionXrefs(BinaryInteractionEvidence interaction)	writeInteractionXrefs.
void	writeNegativeProperty(BinaryInteractionEvidence interaction)	writeNegativeProperty.
void	writeParticipantIdentificationMethod(ParticipantEvidence participant)	writeParticipantIdentificationMethod.
void	writePublicationIdentifiers(BinaryInteractionEvidence interaction)	writePublicationIdentifiers.
protected void	writePublicationImexId(Publication pub, boolean writeFieldSeparator)	writePublicationImexId.
void	writeSource(BinaryInteractionEvidence 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

MitabInteractionEvidenceFeeder

public MitabInteractionEvidenceFeeder(Writer writer)

Constructor for MitabInteractionEvidenceFeeder.

Parameters:

writer - a Writer object.

Method Detail

writeInteractionDetectionMethod

public void writeInteractionDetectionMethod(BinaryInteractionEvidence interaction)
                                     throws IOException

writeInteractionDetectionMethod.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeFirstAuthor

public void writeFirstAuthor(BinaryInteractionEvidence interaction)
                      throws IOException

writeFirstAuthor.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writePublicationIdentifiers

public void writePublicationIdentifiers(BinaryInteractionEvidence interaction)
                                 throws IOException

writePublicationIdentifiers.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeSource

public void writeSource(BinaryInteractionEvidence interaction)
                 throws IOException

writeSource.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeInteractionIdentifiers

public void writeInteractionIdentifiers(BinaryInteractionEvidence interaction)
                                 throws IOException

writeInteractionIdentifiers.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeInteractionConfidences

public void writeInteractionConfidences(BinaryInteractionEvidence interaction)
                                 throws IOException

writeInteractionConfidences.

Parameters:

interaction - a BinaryInteractionEvidence 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

Parameters:

participant - a P object.

alias - a Alias object.

Throws:

IOException - if any.

writeExperimentalRole

public void writeExperimentalRole(ParticipantEvidence participant)
                           throws IOException

writeExperimentalRole.

Parameters:

participant - a ParticipantEvidence object.

Throws:

IOException - if any.

writeInteractionXrefs

public void writeInteractionXrefs(BinaryInteractionEvidence interaction)
                           throws IOException

writeInteractionXrefs.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeInteractionAnnotations

public void writeInteractionAnnotations(BinaryInteractionEvidence interaction)
                                 throws IOException

writeInteractionAnnotations.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeHostOrganism

public void writeHostOrganism(BinaryInteractionEvidence interaction)
                       throws IOException

writeHostOrganism.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeInteractionParameters

public void writeInteractionParameters(BinaryInteractionEvidence interaction)
                                throws IOException

writeInteractionParameters.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeNegativeProperty

public void writeNegativeProperty(BinaryInteractionEvidence interaction)
                           throws IOException

writeNegativeProperty.

Parameters:

interaction - a BinaryInteractionEvidence object.

Throws:

IOException - if any.

writeParticipantIdentificationMethod

public void writeParticipantIdentificationMethod(ParticipantEvidence participant)
                                          throws IOException

writeParticipantIdentificationMethod.

Parameters:

participant - a ParticipantEvidence object.

Throws:

IOException - if any.

writePublicationImexId

protected void writePublicationImexId(Publication pub,
                                      boolean writeFieldSeparator)
                               throws IOException

writePublicationImexId.

Parameters:

pub - a Publication object.

writeFieldSeparator - a boolean.

Throws:

IOException - if any.

writeInteractionAnnotationTagsFrom

protected void writeInteractionAnnotationTagsFrom(Publication pub)
                                           throws IOException

writeInteractionAnnotationTagsFrom.

Parameters:

pub - a Publication object.

Throws:

IOException - if any.