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

Class DefaultModelledInteraction

java.lang.Object

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

psidev.psi.mi.jami.model.impl.DefaultModelledInteraction

All Implemented Interfaces:

Interaction<ModelledParticipant>, ModelledInteraction

Direct Known Subclasses:

DefaultNamedModelledInteraction, MitabModelledInteraction

public class DefaultModelledInteraction
extends AbstractInteraction<ModelledParticipant>
implements ModelledInteraction

Default implemntation for ModelledInteraction Notes: The equals and hashcode methods have NOT been overridden because the ModelledInteraction object is a complex object. To compare ModelledInteraction objects, you can use some comparators provided by default: - DefaultModelledInteractionComparator - UnambiguousModelledInteractionComparator - DefaultCuratedModelledInteractionComparator - UnambiguousCuratedModelledInteractionComparator - DefaultCuratedExactModelledInteractionComparator - UnambiguousCuratedExactModelledInteractionComparator - DefaultExactModelledInteractionComparator - UnambiguousExactModelledInteractionComparator - ModelledInteractionComparator - CuratedModelledInteractionComparator

Since:

05/02/13

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
DefaultModelledInteraction()	Constructor for DefaultModelledInteraction.
DefaultModelledInteraction(String shortName)	Constructor for DefaultModelledInteraction.
DefaultModelledInteraction(String shortName, CvTerm type)	Constructor for DefaultModelledInteraction.
DefaultModelledInteraction(String shortName, Source source)	Constructor for DefaultModelledInteraction.
DefaultModelledInteraction(String shortName, Source source, CvTerm type)	Constructor for DefaultModelledInteraction.

Method Summary

Modifier and Type	Method	Description
Collection<CooperativeEffect>	getCooperativeEffects()	Getter for the field cooperativeEffects.
CvTerm	getEvidenceType()	Getter for the field evidenceType.
Collection<InteractionEvidence>	getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<ModelledConfidence>	getModelledConfidences()	Getter for the field modelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	Getter for the field modelledParameters.
Source	getSource()	Getter for the field source.
protected void	initialiseCooperativeEffects()	initialiseCooperativeEffects
protected void	initialiseCooperativeEffectsWith(Collection<CooperativeEffect> cooperativeEffects)	initialiseCooperativeEffectsWith
protected void	initialiseInteractionEvidences()	initialiseInteractionEvidences
protected void	initialiseInteractionEvidencesWith(Collection<InteractionEvidence> evidences)	initialiseInteractionEvidencesWith
protected void	initialiseModelledConfidences()	initialiseModelledConfidences
protected void	initialiseModelledConfidencesWith(Collection<ModelledConfidence> confidences)	initialiseModelledConfidencesWith
protected void	initialiseModelledParameters()	initialiseModelledParameters
protected void	initialiseModelledParametersWith(Collection<ModelledParameter> parameters)	initialiseModelledParametersWith
void	setEvidenceType(CvTerm eco)	Sets the evidence type
void	setSource(Source source)	Sets the source reporting the interaction.

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

addAllParticipants, addParticipant, clearPropertiesLinkedToChecksums, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefs, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate, toString

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

addAllParticipants, addParticipant, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Constructor Detail

DefaultModelledInteraction

public DefaultModelledInteraction()

Constructor for DefaultModelledInteraction.

DefaultModelledInteraction

public DefaultModelledInteraction(String shortName)

Constructor for DefaultModelledInteraction.

Parameters:

shortName - a String object.

DefaultModelledInteraction

public DefaultModelledInteraction(String shortName,
                                  Source source)

Constructor for DefaultModelledInteraction.

Parameters:

shortName - a String object.

source - a Source object.

DefaultModelledInteraction

public DefaultModelledInteraction(String shortName,
                                  CvTerm type)

Constructor for DefaultModelledInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

DefaultModelledInteraction

public DefaultModelledInteraction(String shortName,
                                  Source source,
                                  CvTerm type)

Constructor for DefaultModelledInteraction.

Parameters:

shortName - a String object.

source - a Source object.

type - a CvTerm object.

Method Detail

initialiseInteractionEvidences

protected void initialiseInteractionEvidences()

initialiseInteractionEvidences

initialiseCooperativeEffects

protected void initialiseCooperativeEffects()

initialiseCooperativeEffects

initialiseCooperativeEffectsWith

protected void initialiseCooperativeEffectsWith(Collection<CooperativeEffect> cooperativeEffects)

initialiseCooperativeEffectsWith

Parameters:

cooperativeEffects - a Collection object.

initialiseModelledConfidences

protected void initialiseModelledConfidences()

initialiseModelledConfidences

initialiseModelledConfidencesWith

protected void initialiseModelledConfidencesWith(Collection<ModelledConfidence> confidences)

initialiseModelledConfidencesWith

Parameters:

confidences - a Collection object.

initialiseInteractionEvidencesWith

protected void initialiseInteractionEvidencesWith(Collection<InteractionEvidence> evidences)

initialiseInteractionEvidencesWith

Parameters:

evidences - a Collection object.

initialiseModelledParameters

protected void initialiseModelledParameters()

initialiseModelledParameters

initialiseModelledParametersWith

protected void initialiseModelledParametersWith(Collection<ModelledParameter> parameters)

initialiseModelledParametersWith

Parameters:

parameters - a Collection object.

getInteractionEvidences

public Collection<InteractionEvidence> getInteractionEvidences()

Getter for the field interactionEvidences.

Specified by:

getInteractionEvidences in interface ModelledInteraction

Returns:

a Collection object.

getSource

public Source getSource()

Getter for the field source.

Specified by:

getSource in interface ModelledInteraction

Returns:

a Source object.

setSource

public void setSource(Source source)

Sets the source reporting the interaction.

Specified by:

setSource in interface ModelledInteraction

Parameters:

source - : source for this interaction

getModelledConfidences

public Collection<ModelledConfidence> getModelledConfidences()

Getter for the field modelledConfidences.

Specified by:

getModelledConfidences in interface ModelledInteraction

Returns:

a Collection object.

getModelledParameters

public Collection<ModelledParameter> getModelledParameters()

Getter for the field modelledParameters.

Specified by:

getModelledParameters in interface ModelledInteraction

Returns:

a Collection object.

getCooperativeEffects

public Collection<CooperativeEffect> getCooperativeEffects()

Getter for the field cooperativeEffects.

Specified by:

getCooperativeEffects in interface ModelledInteraction

Returns:

a Collection object.

getEvidenceType

public CvTerm getEvidenceType()

Getter for the field evidenceType.

Specified by:

getEvidenceType in interface ModelledInteraction

Returns:

a CvTerm object.

setEvidenceType

public void setEvidenceType(CvTerm eco)

Sets the evidence type

Specified by:

setEvidenceType in interface ModelledInteraction

Parameters:

eco - : the evidence type