Package psidev.psi.mi.jami.binary.impl

Class DefaultNamedBinaryInteractionEvidence

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.binary.impl.DefaultNamedBinaryInteractionEvidence

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>

public class DefaultNamedBinaryInteractionEvidence
extends DefaultBinaryInteractionEvidence
implements NamedInteraction<ParticipantEvidence>

Default implementation of a Named binary interaction evidence

Since:

13/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	Getter for the field aliases.
String	getFullName()	Getter for the field fullName.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
void	setFullName(String fullName)	Sets the full name of the interaction

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, toString

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

Constructor Detail

DefaultNamedBinaryInteractionEvidence

public DefaultNamedBinaryInteractionEvidence()

Constructor for DefaultNamedBinaryInteractionEvidence.

DefaultNamedBinaryInteractionEvidence

public DefaultNamedBinaryInteractionEvidence(String shortName)

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

DefaultNamedBinaryInteractionEvidence

public DefaultNamedBinaryInteractionEvidence(String shortName,
                                             CvTerm type)

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

DefaultNamedBinaryInteractionEvidence

public DefaultNamedBinaryInteractionEvidence(ParticipantEvidence participantA,
                                             ParticipantEvidence participantB)

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultNamedBinaryInteractionEvidence

public DefaultNamedBinaryInteractionEvidence(CvTerm complexExpansion)

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

complexExpansion - a CvTerm object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

DefaultNamedBinaryInteractionEvidence

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

Constructor for DefaultNamedBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

Method Detail

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

getFullName

public String getFullName()

Getter for the field fullName.

Specified by:

getFullName in interface NamedInteraction<ParticipantEvidence>

Returns:

a String object.

setFullName

public void setFullName(String fullName)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<ParticipantEvidence>

Parameters:

fullName - : full name

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

getAliases in interface NamedInteraction<ParticipantEvidence>

Returns:

a Collection object.