Package psidev.psi.mi.jami.xml.model.extension.binary.xml30

Class XmlBinaryInteractionEvidence

java.lang.Object

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

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

psidev.psi.mi.jami.xml.model.extension.binary.AbstractExtendedXmlBinaryInteraction<ParticipantEvidence>

psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteractionEvidence

psidev.psi.mi.jami.xml.model.extension.binary.xml30.XmlBinaryInteractionEvidence

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>, ExtendedPsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence, PsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence

public class XmlBinaryInteractionEvidence
extends AbstractXmlBinaryInteractionEvidence
implements ExtendedPsiXmlInteractionEvidence

Xml implementation of BinaryInteractionEvidence

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteractionEvidence

AbstractXmlBinaryInteractionEvidence.ExperimentalBinaryInteractionXrefList

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
List<ExtendedPsiXmlCausalRelationship>	getCausalRelationships()	getCausalRelationships.
void	setImexId(CvTerm database, String id, CvTerm qualifier)

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteractionEvidence

assignImexId, clearPropertiesLinkedToXrefs, getAvailability, getConfidences, getExperiment, getExperiments, getImexId, getOriginalExperiments, getParameters, getVariableParameterValues, getXmlAvailability, initialiseExperimentalConfidences, initialiseExperimentalParameters, initialiseVariableParameterValueSets, initialiseXrefs, isInferred, isModelled, isNegative, processAddedXrefEvent, processRemovedXrefEvent, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setImexId, setInferred, setModelled, setNegative, setXmlAvailability, toString

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.binary.AbstractExtendedXmlBinaryInteraction

getAliases, getEntry, getFullName, getId, getInferredInteractions, getInteractionType, getInteractionTypes, getSourceLocator, isIntraMolecular, setEntry, setFullName, setId, setInteractionType, setIntraMolecular, setSourceLocator

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, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, 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.xml.model.extension.ExtendedPsiXmlInteraction

getInferredInteractions, getInteractionTypes

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.ExtendedPsiXmlInteractionEvidence

getAliases, getExperiments, getOriginalExperiments, getXmlAvailability, isModelled, setModelled, setXmlAvailability

Methods inherited from interface psidev.psi.mi.jami.datasource.FileSourceContext

getSourceLocator, setSourceLocator, toString

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

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

getFullName, setFullName

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.PsiXmlInteraction

getEntry, getId, isIntraMolecular, setEntry, setId, setIntraMolecular

Constructor Detail

XmlBinaryInteractionEvidence

public XmlBinaryInteractionEvidence()

Constructor for XmlBinaryInteractionEvidence.

XmlBinaryInteractionEvidence

public XmlBinaryInteractionEvidence(String shortName)

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

XmlBinaryInteractionEvidence

public XmlBinaryInteractionEvidence(String shortName,
                                    CvTerm type)

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

XmlBinaryInteractionEvidence

public XmlBinaryInteractionEvidence(ParticipantEvidence participantA,
                                    ParticipantEvidence participantB)

Constructor for XmlBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

XmlBinaryInteractionEvidence

public XmlBinaryInteractionEvidence(CvTerm complexExpansion)

Constructor for XmlBinaryInteractionEvidence.

Parameters:

complexExpansion - a CvTerm object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

XmlBinaryInteractionEvidence

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

Constructor for XmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

Method Detail

setImexId

public void setImexId(CvTerm database,
                      String id,
                      CvTerm qualifier)

Specified by:

setImexId in class AbstractXmlBinaryInteractionEvidence

getCausalRelationships

public List<ExtendedPsiXmlCausalRelationship> getCausalRelationships()

getCausalRelationships.

Specified by:

getCausalRelationships in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.