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

Class DefaultMitabColumnFeeder

java.lang.Object

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

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

All Implemented Interfaces:

MitabColumnFeeder<BinaryInteraction,Participant>

Direct Known Subclasses:

DefaultExtendedMitabColumnFeeder

public class DefaultMitabColumnFeeder
extends AbstractMitabColumnFeeder<BinaryInteraction,Participant>

The default Mitab 2.5 column feeder for interactions

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
DefaultMitabColumnFeeder(Writer writer)	Constructor for DefaultMitabColumnFeeder.

Method Summary

Modifier and Type	Method	Description
void	writeAlias(Participant 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	writeExperimentalRole(Participant participant)	Writes the experimentsl role of a participant evidence
void	writeFirstAuthor(BinaryInteraction interaction)	Writes the first author of a publication in an experiment
void	writeHostOrganism(BinaryInteraction interaction)	Writes experiment host organism
void	writeInteractionAnnotations(BinaryInteraction interaction)	Writes interaction annotations
void	writeInteractionConfidences(BinaryInteraction interaction)	Writes the confidences of an interaction evidence
void	writeInteractionDetectionMethod(BinaryInteraction interaction)	Writes the interaction detection method of the experiment.
void	writeInteractionIdentifiers(BinaryInteraction interaction)	Writes the interaction identifiers of an interaction.
void	writeInteractionParameters(BinaryInteraction interaction)	Writes interaction parameters
void	writeInteractionXrefs(BinaryInteraction interaction)	Write interaction Xref r
void	writeNegativeProperty(BinaryInteraction interaction)	Writes interaction negative property if true
void	writeParameter(Parameter parameter)	Writes the parameter
void	writeParticipantIdentificationMethod(Participant participant)	Writes participant identification method(s)
void	writePublicationIdentifiers(BinaryInteraction interaction)	Writes the publication identifiers of a publication in an experiment.
void	writeSource(BinaryInteraction interaction)	Writes the interaction source from the modelled interaction

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

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

DefaultMitabColumnFeeder

public DefaultMitabColumnFeeder(Writer writer)

Constructor for DefaultMitabColumnFeeder.

Parameters:

writer - a Writer object.

Method Detail

writeInteractionDetectionMethod

public void writeInteractionDetectionMethod(BinaryInteraction interaction)
                                     throws IOException

Writes the interaction detection method of the experiment.

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeFirstAuthor

public void writeFirstAuthor(BinaryInteraction interaction)
                      throws IOException

Writes the first author of a publication in an experiment

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writePublicationIdentifiers

public void writePublicationIdentifiers(BinaryInteraction interaction)
                                 throws IOException

Writes the publication identifiers of a publication in an experiment. This method will write the first publication identifier (pubmed before doi) and also the IMEx id

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeSource

public void writeSource(BinaryInteraction interaction)
                 throws IOException

Writes the interaction source from the modelled interaction

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionIdentifiers

public void writeInteractionIdentifiers(BinaryInteraction interaction)
                                 throws IOException

Writes the interaction identifiers of an interaction. This method will write the first interaction identifier and also the IMEx id

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionConfidences

public void writeInteractionConfidences(BinaryInteraction interaction)
                                 throws IOException

Writes the confidences of an interaction evidence

Parameters:

interaction - a T 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

Parameters:

participant - a P object.

alias - a Alias object.

Throws:

IOException - if any.

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<BinaryInteraction,Participant>

Overrides:

writeConfidence in class AbstractMitabColumnFeeder<BinaryInteraction,Participant>

Parameters:

conf - a Confidence object.

Throws:

IOException - if any.

writeParameter

public void writeParameter(Parameter parameter)
                    throws IOException

Writes the parameter

Specified by:

writeParameter in interface MitabColumnFeeder<BinaryInteraction,Participant>

Overrides:

writeParameter in class AbstractMitabColumnFeeder<BinaryInteraction,Participant>

Parameters:

parameter - a Parameter object.

Throws:

IOException - if any.

writeNegativeProperty

public void writeNegativeProperty(BinaryInteraction interaction)
                           throws IOException

Writes interaction negative property if true

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeHostOrganism

public void writeHostOrganism(BinaryInteraction interaction)
                       throws IOException

Writes experiment host organism

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionParameters

public void writeInteractionParameters(BinaryInteraction interaction)
                                throws IOException

Writes interaction parameters

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionAnnotations

public void writeInteractionAnnotations(BinaryInteraction interaction)
                                 throws IOException

Writes interaction annotations

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionXrefs

public void writeInteractionXrefs(BinaryInteraction interaction)
                           throws IOException

Write interaction Xref r

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeExperimentalRole

public void writeExperimentalRole(Participant participant)
                           throws IOException

Writes the experimentsl role of a participant evidence

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantIdentificationMethod

public void writeParticipantIdentificationMethod(Participant participant)
                                          throws IOException

Writes participant identification method(s)

Parameters:

participant - a P object.

Throws:

IOException - if any.