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

Class DefaultCooperativeEffect

java.lang.Object

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

All Implemented Interfaces:

CooperativeEffect

Direct Known Subclasses:

DefaultAllostery, DefaultPreassemby, XmlAllostery, XmlAllostery

public class DefaultCooperativeEffect
extends Object
implements CooperativeEffect

Default implementation for CooperativeEffect Notes: The equals and hashcode methods have NOT been overridden because the CooperativeEffect object is a complex object. To compare CooperativeEffect objects, you can use some comparators provided by default: - DefaultCooperativeEffectComparator - UnambiguousCooperativeEffectComparator - DefaultExactCooperativeEffectComparator - UnambiguousExactCooperativeEffectComparator - CooperativeEffectComparator

Since:

22/05/13

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
DefaultCooperativeEffect(CvTerm outcome)	Constructor for DefaultCooperativeEffect.
DefaultCooperativeEffect(CvTerm outcome, CvTerm response)	Constructor for DefaultCooperativeEffect.

Method Summary

Modifier and Type	Method	Description
Collection<ModelledInteraction>	getAffectedInteractions()	Getter for the field affectedInteractions.
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
Collection<CooperativityEvidence>	getCooperativityEvidences()	Getter for the field cooperativityEvidences.
CvTerm	getOutCome()	getOutCome
CvTerm	getResponse()	Getter for the field response.
protected void	initialiseAffectedInteractions()	initialiseAffectedInteractions
protected void	initialiseAffectedInteractionsWith(Collection<ModelledInteraction> affected)	initialiseAffectedInteractionsWith
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseCooperativityEvidences()	initialiseCooperativityEvidences
protected void	initialiseCooperativityEvidencesWith(Collection<CooperativityEvidence> evidences)	initialiseCooperativityEvidencesWith
void	setOutCome(CvTerm effect)	Sets the cooperative effect outcome
void	setResponse(CvTerm response)	Sets the response.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DefaultCooperativeEffect

public DefaultCooperativeEffect(CvTerm outcome)

Constructor for DefaultCooperativeEffect.

Parameters:

outcome - a CvTerm object.

DefaultCooperativeEffect

public DefaultCooperativeEffect(CvTerm outcome,
                                CvTerm response)

Constructor for DefaultCooperativeEffect.

Parameters:

outcome - a CvTerm object.

response - a CvTerm object.

Method Detail

initialiseCooperativityEvidences

protected void initialiseCooperativityEvidences()

initialiseCooperativityEvidences

initialiseCooperativityEvidencesWith

protected void initialiseCooperativityEvidencesWith(Collection<CooperativityEvidence> evidences)

initialiseCooperativityEvidencesWith

Parameters:

evidences - a Collection object.

initialiseAffectedInteractions

protected void initialiseAffectedInteractions()

initialiseAffectedInteractions

initialiseAffectedInteractionsWith

protected void initialiseAffectedInteractionsWith(Collection<ModelledInteraction> affected)

initialiseAffectedInteractionsWith

Parameters:

affected - a Collection object.

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

getCooperativityEvidences

public Collection<CooperativityEvidence> getCooperativityEvidences()

Getter for the field cooperativityEvidences.

Specified by:

getCooperativityEvidences in interface CooperativeEffect

Returns:

a Collection object.

getAffectedInteractions

public Collection<ModelledInteraction> getAffectedInteractions()

Getter for the field affectedInteractions.

Specified by:

getAffectedInteractions in interface CooperativeEffect

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface CooperativeEffect

Returns:

a Collection object.

getOutCome

public CvTerm getOutCome()

getOutCome

Specified by:

getOutCome in interface CooperativeEffect

Returns:

a CvTerm object.

setOutCome

public void setOutCome(CvTerm effect)

Sets the cooperative effect outcome

Specified by:

setOutCome in interface CooperativeEffect

Parameters:

effect - : cooperative effect outcome

getResponse

public CvTerm getResponse()

Getter for the field response.

Specified by:

getResponse in interface CooperativeEffect

Returns:

a CvTerm object.

setResponse

public void setResponse(CvTerm response)

Sets the response.

Specified by:

setResponse in interface CooperativeEffect

Parameters:

response - : the allosteric or pre-assembly response

toString

public String toString()

Overrides:

toString in class Object