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

Class DefaultNamedModelledBinaryInteraction

java.lang.Object

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

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

psidev.psi.mi.jami.binary.impl.DefaultModelledBinaryInteraction

psidev.psi.mi.jami.binary.impl.DefaultNamedModelledBinaryInteraction

All Implemented Interfaces:

BinaryInteraction<ModelledParticipant>, ModelledBinaryInteraction, Interaction<ModelledParticipant>, ModelledInteraction, NamedInteraction<ModelledParticipant>

public class DefaultNamedModelledBinaryInteraction
extends DefaultModelledBinaryInteraction
implements NamedInteraction<ModelledParticipant>

Default implementation for Named modelled binary interaction

Since:

13/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.ModelledInteraction

ECO, ECO_MI

Constructor Summary

Constructors

Constructor	Description
DefaultNamedModelledBinaryInteraction()	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.

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.DefaultModelledBinaryInteraction

getCooperativeEffects, getEvidenceType, getInteractionEvidences, getModelledConfidences, getModelledParameters, getSource, initialiseCooperativeEffects, initialiseCooperativeEffectsWith, initialiseInteractionEvidences, initialiseInteractionEvidencesWith, initialiseModelledConfidences, initialiseModelledConfidencesWith, initialiseModelledParameters, initialiseModelledParametersWith, setEvidenceType, setSource

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

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

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, initialiseXrefs, 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

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction()

Constructor for DefaultNamedModelledBinaryInteraction.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName,
                                             CvTerm type)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA,
                                             ModelledParticipant participantB)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName,
                                             ModelledParticipant participantA,
                                             ModelledParticipant participantB)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName,
                                             CvTerm type,
                                             ModelledParticipant participantA,
                                             ModelledParticipant participantB)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(CvTerm complexExpansion)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

DefaultNamedModelledBinaryInteraction

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

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA,
                                             ModelledParticipant participantB,
                                             CvTerm complexExpansion)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName,
                                             ModelledParticipant participantA,
                                             ModelledParticipant participantB,
                                             CvTerm complexExpansion)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

DefaultNamedModelledBinaryInteraction

public DefaultNamedModelledBinaryInteraction(String shortName,
                                             CvTerm type,
                                             ModelledParticipant participantA,
                                             ModelledParticipant participantB,
                                             CvTerm complexExpansion)

Constructor for DefaultNamedModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant 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<ModelledParticipant>

Returns:

a String object.

setFullName

public void setFullName(String fullName)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<ModelledParticipant>

Parameters:

fullName - : full name

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

getAliases in interface NamedInteraction<ModelledParticipant>

Returns:

a Collection object.