Package psidev.psi.mi.jami.crosslink.extension

Class CsvBinaryInteractionEvidence

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractInteraction<T>

psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction<ParticipantEvidence>

psidev.psi.mi.jami.binary.impl.DefaultBinaryInteractionEvidence

psidev.psi.mi.jami.crosslink.extension.CsvBinaryInteractionEvidence

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, CrosslinkCsvInteraction, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence

public class CsvBinaryInteractionEvidence
extends DefaultBinaryInteractionEvidence
implements FileSourceContext, CrosslinkCsvInteraction

Crosslink CSV implementation of BinaryInteractionEvidence

Since:

20/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
CsvBinaryInteractionEvidence()	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, CvTerm type)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(CvTerm complexExpansion)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for CsvBinaryInteractionEvidence.
CsvBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for CsvBinaryInteractionEvidence.

Method Summary

Modifier and Type	Method	Description
String	getNaryGroup()	getNaryGroup.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setNaryGroup(String bait)	setNaryGroup.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

Methods inherited from class psidev.psi.mi.jami.binary.impl.DefaultBinaryInteractionEvidence

assignImexId, clearPropertiesLinkedToXrefs, getAvailability, getConfidences, getExperiment, getImexId, getParameters, getVariableParameterValues, initialiseExperimentalConfidences, initialiseExperimentalConfidencesWith, initialiseExperimentalParameters, initialiseExperimentalParametersWith, initialiseVariableParameterValueSets, initialiseVariableParameterValueSetsWith, initialiseXrefs, isInferred, isNegative, processAddedXrefEvent, processRemovedXrefEvent, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setNegative

Methods inherited from class psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction

addAllParticipants, addParticipant, getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, getParticipants, removeAllParticipants, removeParticipant, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

Methods inherited from class psidev.psi.mi.jami.model.impl.AbstractInteraction

clearPropertiesLinkedToChecksums, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.binary.BinaryInteraction

getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

Methods inherited from interface psidev.psi.mi.jami.model.Interaction

addAllParticipants, addParticipant, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Methods inherited from interface psidev.psi.mi.jami.model.InteractionEvidence

assignImexId, getAvailability, getConfidences, getExperiment, getImexId, getParameters, getVariableParameterValues, isInferred, isNegative, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setNegative

Constructor Detail

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence()

Constructor for CsvBinaryInteractionEvidence.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    CvTerm type)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(ParticipantEvidence participantA,
                                    ParticipantEvidence participantB)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    ParticipantEvidence participantA,
                                    ParticipantEvidence participantB)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    CvTerm type,
                                    ParticipantEvidence participantA,
                                    ParticipantEvidence participantB)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(CvTerm complexExpansion)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

complexExpansion - a CvTerm object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    CvTerm type,
                                    CvTerm complexExpansion)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(ParticipantEvidence participantA,
                                    ParticipantEvidence participantB,
                                    CvTerm complexExpansion)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    ParticipantEvidence participantA,
                                    ParticipantEvidence participantB,
                                    CvTerm complexExpansion)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

CsvBinaryInteractionEvidence

public CsvBinaryInteractionEvidence(String shortName,
                                    CvTerm type,
                                    ParticipantEvidence participantA,
                                    ParticipantEvidence participantB,
                                    CvTerm complexExpansion)

Constructor for CsvBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

getNaryGroup

public String getNaryGroup()

getNaryGroup.

Specified by:

getNaryGroup in interface CrosslinkCsvInteraction

Returns:

a String object.

setNaryGroup

public void setNaryGroup(String bait)

setNaryGroup.

Specified by:

setNaryGroup in interface CrosslinkCsvInteraction

Parameters:

bait - : n-ary group name used for this interaction

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultBinaryInteractionEvidence

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties