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

Class AbstractMitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.feeder.AbstractMitabColumnFeeder<T,P>

All Implemented Interfaces:

MitabColumnFeeder<T,P>

Direct Known Subclasses:

DefaultMitabColumnFeeder, MitabInteractionEvidenceFeeder, MitabModelledInteractionFeeder

public abstract class AbstractMitabColumnFeeder<T extends BinaryInteraction,P extends Participant>
extends Object
implements MitabColumnFeeder<T,P>

Abstract Mitab 2.5 column feeder

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractMitabColumnFeeder(Writer writer)	Constructor for AbstractMitabColumnFeeder.

Method Summary

Modifier and Type	Method	Description
void	escapeAndWriteString(String stringToEscape)	This method replaces line breaks and tab characters with a space.
protected Writer	getWriter()	Getter for the field writer.
void	writeAlias(Alias alias)	This methods write the dbsource, alias name and alias type of an alias
void	writeAliases(P participant)	writeAliases.
void	writeAlternativeIdentifiers(P participant)	writeAlternativeIdentifiers.
void	writeAnnotation(Annotation annotation)	Writes an annotation
void	writeBiologicalRole(P participant)	writeBiologicalRole.
void	writeChecksum(Checksum checksum)	Writes the checksum
void	writeComplexExpansion(T binary)	writeComplexExpansion.
void	writeConfidence(Confidence conf)	This method will write a confidence with a text if text is not null
void	writeCvTerm(CvTerm cv)	Write the CvTerm.
protected void	writeCvTermName(CvTerm cv)	Write full name if not null, otherwise write shortname
void	writeDate(Date date)	Writes created date of an interaction
void	writeFeature(Feature feature)	Writes a feature
void	writeIdentifier(Xref identifier)	This methods write the database, id and version of an identifier
void	writeInteractionCausalRegulatoryMechanism(T interaction)	writeInteractionType.
void	writeInteractionCausalStatement(T interaction)	writeInteractionType.
void	writeInteractionChecksums(T interaction)	writeInteractionChecksums.
void	writeInteractionType(T interaction)	writeInteractionType.
void	writeInteractorOrganism(P participant)	writeInteractorOrganism.
void	writeInteractorType(P participant)	writeInteractorType.
void	writeOrganism(Organism organism)	Write an organism.
void	writeParameter(Parameter parameter)	Writes the parameter
void	writeParticipantAnnotations(P participant)	writeParticipantAnnotations.
void	writeParticipantBiologicalEffect(P participant)	writeBiologicalRole.
void	writeParticipantChecksums(P participant)	writeParticipantChecksums.
void	writeParticipantFeatures(P participant)	writeParticipantFeatures.
void	writeParticipantStoichiometry(P participant)	writeParticipantStoichiometry.
void	writeParticipantXrefs(P participant)	writeParticipantXrefs.
void	writeUniqueIdentifier(P participant)	writeUniqueIdentifier.
void	writeXref(Xref xref)	This methods write the database, id, version and qualifier of an xref

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.tab.io.writer.feeder.MitabColumnFeeder

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

Constructor Detail

AbstractMitabColumnFeeder

public AbstractMitabColumnFeeder(Writer writer)

Constructor for AbstractMitabColumnFeeder.

Parameters:

writer - a Writer object.

Method Detail

writeUniqueIdentifier

public void writeUniqueIdentifier(P participant)
                           throws IOException

writeUniqueIdentifier.

Specified by:

writeUniqueIdentifier in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeAlternativeIdentifiers

public void writeAlternativeIdentifiers(P participant)
                                 throws IOException

writeAlternativeIdentifiers.

Specified by:

writeAlternativeIdentifiers in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeAliases

public void writeAliases(P participant)
                  throws IOException

writeAliases.

Specified by:

writeAliases in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeInteractorOrganism

public void writeInteractorOrganism(P participant)
                             throws IOException

writeInteractorOrganism.

Specified by:

writeInteractorOrganism in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeInteractionType

public void writeInteractionType(T interaction)
                          throws IOException

writeInteractionType.

Specified by:

writeInteractionType in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

interaction - a T 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<T extends BinaryInteraction,P extends 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<T extends BinaryInteraction,P extends Participant>

Parameters:

parameter - a Parameter object.

Throws:

IOException - if any.

writeOrganism

public void writeOrganism(Organism organism)
                   throws IOException

Write an organism. Will duplicate taxid if needs to provide both common name and scientific name

Specified by:

writeOrganism in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

organism - a Organism object.

Throws:

IOException - if any.

writeCvTerm

public void writeCvTerm(CvTerm cv)
                 throws IOException

Write the CvTerm. If it is null, it writes an empty column (-)

Specified by:

writeCvTerm in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

cv - a CvTerm 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<T extends BinaryInteraction,P extends Participant>

Parameters:

alias - a Alias object.

Throws:

IOException - if any.

writeIdentifier

public void writeIdentifier(Xref identifier)
                     throws IOException

This methods write the database, id and version of an identifier

Specified by:

writeIdentifier in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

identifier - a Xref object.

Throws:

IOException - if any.

escapeAndWriteString

public void escapeAndWriteString(String stringToEscape)
                          throws IOException

This method replaces line breaks and tab characters with a space. It escapes the StringToEscape with doble quote if it finds a special MITAB character

Specified by:

escapeAndWriteString in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

stringToEscape - a String object.

Throws:

IOException - if any.

writeComplexExpansion

public void writeComplexExpansion(T binary)
                           throws IOException

writeComplexExpansion.

Specified by:

writeComplexExpansion in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

binary - a T object.

Throws:

IOException - if any.

writeBiologicalRole

public void writeBiologicalRole(P participant)
                         throws IOException

writeBiologicalRole.

Specified by:

writeBiologicalRole in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeInteractorType

public void writeInteractorType(P participant)
                         throws IOException

writeInteractorType.

Specified by:

writeInteractorType in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantXrefs

public void writeParticipantXrefs(P participant)
                           throws IOException

writeParticipantXrefs.

Specified by:

writeParticipantXrefs in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantAnnotations

public void writeParticipantAnnotations(P participant)
                                 throws IOException

writeParticipantAnnotations.

Specified by:

writeParticipantAnnotations in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeDate

public void writeDate(Date date)
               throws IOException

Writes created date of an interaction

Specified by:

writeDate in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

date - a Date object.

Throws:

IOException - if any.

writeParticipantChecksums

public void writeParticipantChecksums(P participant)
                               throws IOException

writeParticipantChecksums.

Specified by:

writeParticipantChecksums in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeInteractionChecksums

public void writeInteractionChecksums(T interaction)
                               throws IOException

writeInteractionChecksums.

Specified by:

writeInteractionChecksums in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeChecksum

public void writeChecksum(Checksum checksum)
                   throws IOException

Writes the checksum

Specified by:

writeChecksum in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

checksum - a Checksum object.

Throws:

IOException - if any.

writeAnnotation

public void writeAnnotation(Annotation annotation)
                     throws IOException

Writes an annotation

Specified by:

writeAnnotation in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

annotation - a Annotation object.

Throws:

IOException - if any.

writeXref

public void writeXref(Xref xref)
               throws IOException

This methods write the database, id, version and qualifier of an xref

Specified by:

writeXref in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

xref - a Xref object.

Throws:

IOException - if any.

writeParticipantFeatures

public void writeParticipantFeatures(P participant)
                              throws IOException

writeParticipantFeatures.

Specified by:

writeParticipantFeatures in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantStoichiometry

public void writeParticipantStoichiometry(P participant)
                                   throws IOException

writeParticipantStoichiometry.

Specified by:

writeParticipantStoichiometry in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeFeature

public void writeFeature(Feature feature)
                  throws IOException

Writes a feature

Specified by:

writeFeature in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

feature - a Feature object.

Throws:

IOException - if any.

writeParticipantBiologicalEffect

public void writeParticipantBiologicalEffect(P participant)
                                      throws IOException

writeBiologicalRole.

Specified by:

writeParticipantBiologicalEffect in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeInteractionCausalRegulatoryMechanism

public void writeInteractionCausalRegulatoryMechanism(T interaction)
                                               throws IOException

writeInteractionType.

Specified by:

writeInteractionCausalRegulatoryMechanism in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeInteractionCausalStatement

public void writeInteractionCausalStatement(T interaction)
                                     throws IOException

writeInteractionType.

Specified by:

writeInteractionCausalStatement in interface MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.

writeCvTermName

protected void writeCvTermName(CvTerm cv)
                        throws IOException

Write full name if not null, otherwise write shortname

Parameters:

cv - a CvTerm object.

Throws:

IOException - if any.