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

Class AbstractBinaryInteraction<T extends Participant>

java.lang.Object

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

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

All Implemented Interfaces:

BinaryInteraction<T>, Interaction<T>

Direct Known Subclasses:

AbstractExtendedXmlBinaryInteraction, AbstractXmlBinaryInteraction, DefaultBinaryInteraction, DefaultBinaryInteractionEvidence, DefaultModelledBinaryInteraction

public abstract class AbstractBinaryInteraction<T extends Participant>
extends AbstractInteraction<T>
implements BinaryInteraction<T>

Abstract class for BinaryInteraction. A binary interaction is an interaction but will not allow to add more than two participants. As a consequence, the method getParticipants return a Unmodifiable collection and to add/remove participants, we must use the setParticipantA/B methods or the add/removeParticipant methods provided by the Interaction interface

Since:

09/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractBinaryInteraction()	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, CvTerm type)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB, CvTerm complexExpansion)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB, CvTerm complexExpansion, CvTerm causalRegulatoryMechanism)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, T participantA, T participantB)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(String shortName, T participantA, T participantB, CvTerm complexExpansion)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(CvTerm complexExpansion)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(T participantA, T participantB)	Constructor for AbstractBinaryInteraction.
AbstractBinaryInteraction(T participantA, T participantB, CvTerm complexExpansion)	Constructor for AbstractBinaryInteraction.

Method Summary

Modifier and Type	Method	Description
boolean	addAllParticipants(Collection<? extends T> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	addParticipant(T part)	addParticipant
CvTerm	getCausalRegulatoryMechanism()	Getter for the field causalRegulatoryMechanism.
CvTerm	getComplexExpansion()	Getter for the field complexExpansion.
T	getParticipantA()	Getter for the field participantA.
T	getParticipantB()	Getter for the field participantB.
Collection<T>	getParticipants()	Getter for the field participants.
boolean	removeAllParticipants(Collection<? extends T> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	removeParticipant(T part)	removeParticipant
void	setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)	Setter for the field causalRegulatoryMechanism.
void	setComplexExpansion(CvTerm expansion)	Sets the complex expansion of this binary interaction
void	setParticipantA(T participantA)	Setter for the field participantA.
void	setParticipantB(T participantB)	Setter for the field participantB.
String	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.model.Interaction

getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getRigid, getShortName, getUpdatedDate, getXrefs, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Constructor Detail

AbstractBinaryInteraction

public AbstractBinaryInteraction()

Constructor for AbstractBinaryInteraction.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 CvTerm type)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(T participantA,
                                 T participantB)

Constructor for AbstractBinaryInteraction.

Parameters:

participantA - a T object.

participantB - a T object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 T participantA,
                                 T participantB)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a T object.

participantB - a T object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 CvTerm type,
                                 T participantA,
                                 T participantB)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a T object.

participantB - a T object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(CvTerm complexExpansion)

Constructor for AbstractBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

AbstractBinaryInteraction

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

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(T participantA,
                                 T participantB,
                                 CvTerm complexExpansion)

Constructor for AbstractBinaryInteraction.

Parameters:

participantA - a T object.

participantB - a T object.

complexExpansion - a CvTerm object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 T participantA,
                                 T participantB,
                                 CvTerm complexExpansion)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a T object.

participantB - a T object.

complexExpansion - a CvTerm object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 CvTerm type,
                                 T participantA,
                                 T participantB,
                                 CvTerm complexExpansion)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a T object.

participantB - a T object.

complexExpansion - a CvTerm object.

AbstractBinaryInteraction

public AbstractBinaryInteraction(String shortName,
                                 CvTerm type,
                                 T participantA,
                                 T participantB,
                                 CvTerm complexExpansion,
                                 CvTerm causalRegulatoryMechanism)

Constructor for AbstractBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a T object.

participantB - a T object.

complexExpansion - a CvTerm object.

causalRegulatoryMechanism - a CvTerm object.

Method Detail

getParticipantA

public T getParticipantA()

Getter for the field participantA.

Specified by:

getParticipantA in interface BinaryInteraction<T extends Participant>

Returns:

a T object.

getParticipantB

public T getParticipantB()

Getter for the field participantB.

Specified by:

getParticipantB in interface BinaryInteraction<T extends Participant>

Returns:

a T object.

setParticipantA

public void setParticipantA(T participantA)

Setter for the field participantA.

Specified by:

setParticipantA in interface BinaryInteraction<T extends Participant>

Parameters:

participantA - a T object.

setParticipantB

public void setParticipantB(T participantB)

Setter for the field participantB.

Specified by:

setParticipantB in interface BinaryInteraction<T extends Participant>

Parameters:

participantB - a T object.

getComplexExpansion

public CvTerm getComplexExpansion()

Getter for the field complexExpansion.

Specified by:

getComplexExpansion in interface BinaryInteraction<T extends Participant>

Returns:

a CvTerm object.

setComplexExpansion

public void setComplexExpansion(CvTerm expansion)

Sets the complex expansion of this binary interaction

Specified by:

setComplexExpansion in interface BinaryInteraction<T extends Participant>

Parameters:

expansion - : the complex expansion

getCausalRegulatoryMechanism

public CvTerm getCausalRegulatoryMechanism()

Getter for the field causalRegulatoryMechanism.

Specified by:

getCausalRegulatoryMechanism in interface BinaryInteraction<T extends Participant>

Returns:

a CvTerm object.

setCausalRegulatoryMechanism

public void setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)

Setter for the field causalRegulatoryMechanism.

Specified by:

setCausalRegulatoryMechanism in interface BinaryInteraction<T extends Participant>

Parameters:

causalRegulatoryMechanism - a CvTerm object.

getParticipants

public Collection<T> getParticipants()

Getter for the field participants.

The collection of participants for this binary interaction. It cannot be changed.

Specified by:

getParticipants in interface Interaction<T extends Participant>

Overrides:

getParticipants in class AbstractInteraction<T extends Participant>

Returns:

a Collection object.

addParticipant

public boolean addParticipant(T part)

addParticipant

Adds a new Participant and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB

Specified by:

addParticipant in interface Interaction<T extends Participant>

Overrides:

addParticipant in class AbstractInteraction<T extends Participant>

Parameters:

part - a T object.

Returns:

a boolean.

removeParticipant

public boolean removeParticipant(T part)

removeParticipant

Removes the Participant from this binary interaction

Specified by:

removeParticipant in interface Interaction<T extends Participant>

Overrides:

removeParticipant in class AbstractInteraction<T extends Participant>

Parameters:

part - a T object.

Returns:

a boolean.

addAllParticipants

public boolean addAllParticipants(Collection<? extends T> participants)

This method will add all the participant and set the interaction of the new participant to this current interaction Adds the participants and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB

Specified by:

addAllParticipants in interface Interaction<T extends Participant>

Overrides:

addAllParticipants in class AbstractInteraction<T extends Participant>

Parameters:

participants - : participants to add

Returns:

true if participant are added to the list of participants

removeAllParticipants

public boolean removeAllParticipants(Collection<? extends T> participants)

This method will remove the participant and set the interaction of the removed participant to null.

Specified by:

removeAllParticipants in interface Interaction<T extends Participant>

Overrides:

removeAllParticipants in class AbstractInteraction<T extends Participant>

Parameters:

participants - : participants to remove

Returns:

true if participant are removed from the list of participants

toString

public String toString()

Overrides:

toString in class AbstractInteraction<T extends Participant>