Package psidev.psi.mi.jami.model.impl

Class DefaultAllostery<T extends AllostericEffector>

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultCooperativeEffect

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

All Implemented Interfaces:

Allostery<T>, CooperativeEffect

public class DefaultAllostery<T extends AllostericEffector>
extends DefaultCooperativeEffect
implements Allostery<T>

Default implementation for Allostery Notes: The equals and hashcode methods have NOT been overridden because the Allostery object is a complex object. To compare Allostery objects, you can use some comparators provided by default: - DefaultAllosteryComparator - UnambiguousAllosteryComparator - AllosteryComparator

Since:

23/05/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

AFFECTED_INTERACTION, AFFECTED_INTERACTION_ID, ALLOSTERIC_DYNAMIC_CHANGE, ALLOSTERIC_DYNAMIC_CHANGE_ID, ALLOSTERIC_EFFECTOR, ALLOSTERIC_EFFECTOR_ID, ALLOSTERIC_K_RESPONSE, ALLOSTERIC_K_RESPONSE_ID, ALLOSTERIC_MOLECULE, ALLOSTERIC_MOLECULE_ID, ALLOSTERIC_PTM, ALLOSTERIC_PTM_ID, ALLOSTERIC_STRUCTURE_CHANE, ALLOSTERIC_STRUCTURE_CHANE_ID, ALLOSTERIC_V_RESPONSE, ALLOSTERIC_V_RESPONSE_ID, ALLOSTERY, ALLOSTERY_ID, ALTERED_PHYSICO_COMPATIBILITY, ALTERED_PHYSICO_COMPATIBILITY_ID, BINDING_HIDING, BINDING_HIDING_ID, COMPOSITE_BINDING, COMPOSITE_BINDING_ID, COOPERATIVE_EFFECT_VALUE, COOPERATIVE_EFFECT_VALUE_ID, EFFECT_OUTCOME, EFFECT_OUTCOME_MI, HETEROTROPIC_ALLOSTERY, HETEROTROPIC_ALLOSTERY_ID, HOMOTROPIC_ALLOSTERY, HOMOTROPIC_ALLOSTERY_ID, NEGATIVE_EFFECT, NEGATIVE_EFFECT_ID, PARTICIPANT_REF, PARTICIPANT_REF_ID, POSITIVE_EFFECT, POSITIVE_EFFECT_ID, PRE_ORGANIZATION, PRE_ORGANIZATION_ID, PREASSEMBLY, PREASSEMBLY_ID

Constructor Summary

Constructors

Constructor	Description
DefaultAllostery(CvTerm outcome, CvTerm response, ModelledParticipant allostericMolecule, T allostericEffector)	Constructor for DefaultAllostery.
DefaultAllostery(CvTerm outcome, ModelledParticipant allostericMolecule, T allostericEffector)	Constructor for DefaultAllostery.

Method Summary

Modifier and Type	Method	Description
T	getAllostericEffector()	Getter for the field allostericEffector.
CvTerm	getAllostericMechanism()	Getter for the field allostericMechanism.
ModelledEntity	getAllostericMolecule()	Getter for the field allostericMolecule.
CvTerm	getAllosteryType()	Getter for the field allosteryType.
void	setAllostericEffector(T effector)	Setter for the field allostericEffector.
void	setAllostericMechanism(CvTerm mechanism)	Sets the allosteric mechanism.
void	setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	setAllosteryType(CvTerm type)	Sets the allostery type.
String	toString()

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

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, initialiseAffectedInteractions, initialiseAffectedInteractionsWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseCooperativityEvidences, initialiseCooperativityEvidencesWith, setOutCome, setResponse

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.CooperativeEffect

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, setOutCome, setResponse

Constructor Detail

DefaultAllostery

public DefaultAllostery(CvTerm outcome,
                        ModelledParticipant allostericMolecule,
                        T allostericEffector)

Constructor for DefaultAllostery.

Parameters:

outcome - a CvTerm object.

allostericMolecule - a ModelledParticipant object.

allostericEffector - a T object.

DefaultAllostery

public DefaultAllostery(CvTerm outcome,
                        CvTerm response,
                        ModelledParticipant allostericMolecule,
                        T allostericEffector)

Constructor for DefaultAllostery.

Parameters:

outcome - a CvTerm object.

response - a CvTerm object.

allostericMolecule - a ModelledParticipant object.

allostericEffector - a T object.

Method Detail

getAllostericMechanism

public CvTerm getAllostericMechanism()

Getter for the field allostericMechanism.

Specified by:

getAllostericMechanism in interface Allostery<T extends AllostericEffector>

Returns:

a CvTerm object.

setAllostericMechanism

public void setAllostericMechanism(CvTerm mechanism)

Sets the allosteric mechanism.

Specified by:

setAllostericMechanism in interface Allostery<T extends AllostericEffector>

Parameters:

mechanism - : allosteric mechanism

getAllosteryType

public CvTerm getAllosteryType()

Getter for the field allosteryType.

Specified by:

getAllosteryType in interface Allostery<T extends AllostericEffector>

Returns:

a CvTerm object.

setAllosteryType

public void setAllosteryType(CvTerm type)

Sets the allostery type.

Specified by:

setAllosteryType in interface Allostery<T extends AllostericEffector>

Parameters:

type - : allostery type

getAllostericMolecule

public ModelledEntity getAllostericMolecule()

Getter for the field allostericMolecule.

Specified by:

getAllostericMolecule in interface Allostery<T extends AllostericEffector>

Returns:

a ModelledEntity object.

setAllostericMolecule

public void setAllostericMolecule(ModelledEntity participant)

Sets the allosteric molecule.

Specified by:

setAllostericMolecule in interface Allostery<T extends AllostericEffector>

Parameters:

participant - : allosteric molecule (can refer to any participating entity)

getAllostericEffector

public T getAllostericEffector()

Getter for the field allostericEffector.

Specified by:

getAllostericEffector in interface Allostery<T extends AllostericEffector>

Returns:

a T object.

setAllostericEffector

public void setAllostericEffector(T effector)

Setter for the field allostericEffector.

Specified by:

setAllostericEffector in interface Allostery<T extends AllostericEffector>

Parameters:

effector - a T object.

toString

public String toString()

Overrides:

toString in class DefaultCooperativeEffect