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

Class BinaryInteractionEvidenceWrapper

java.lang.Object

psidev.psi.mi.jami.binary.impl.AbstractBinaryInteractionWrapper<InteractionEvidence,ParticipantEvidence>

psidev.psi.mi.jami.binary.impl.BinaryInteractionEvidenceWrapper

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, Interaction<ParticipantEvidence>, InteractionEvidence

public class BinaryInteractionEvidenceWrapper
extends AbstractBinaryInteractionWrapper<InteractionEvidence,ParticipantEvidence>
implements BinaryInteractionEvidence

A wrapper for InteractionEvidence which contains two participants

Since:

05/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
BinaryInteractionEvidenceWrapper(InteractionEvidence interaction)	Constructor for BinaryInteractionEvidenceWrapper.
BinaryInteractionEvidenceWrapper(InteractionEvidence interaction, CvTerm complexExpansion)	Constructor for BinaryInteractionEvidenceWrapper.

Method Summary

Modifier and Type	Method	Description
void	assignImexId(String identifier)	Assign an IMEx id to an interaction.
String	getAvailability()	getAvailability
Collection<Confidence>	getConfidences()	getConfidences
Experiment	getExperiment()	getExperiment
String	getImexId()	getImexId
Collection<Parameter>	getParameters()	getParameters
Collection<VariableParameterValueSet>	getVariableParameterValues()	getVariableParameterValues
boolean	isInferred()	isInferred
boolean	isNegative()	isNegative
void	setAvailability(String availability)	Sets the availability.
void	setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	setInferred(boolean inferred)	Sets the inferred boolean value
void	setNegative(boolean negative)	Sets the negative boolean value.

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

addAllParticipants, addParticipant, getAnnotations, getCausalRegulatoryMechanism, getChecksums, getComplexExpansion, getCreatedDate, getIdentifiers, getInteractionType, getParticipantA, getParticipantB, getParticipants, getRigid, getShortName, getUpdatedDate, getWrappedInteraction, getXrefs, removeAllParticipants, removeParticipant, setCausalRegulatoryMechanism, setComplexExpansion, setCreatedDate, setInteractionType, setParticipantA, setParticipantB, 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.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

BinaryInteractionEvidenceWrapper

public BinaryInteractionEvidenceWrapper(InteractionEvidence interaction)

Constructor for BinaryInteractionEvidenceWrapper.

Parameters:

interaction - a InteractionEvidence object.

BinaryInteractionEvidenceWrapper

public BinaryInteractionEvidenceWrapper(InteractionEvidence interaction,
                                        CvTerm complexExpansion)

Constructor for BinaryInteractionEvidenceWrapper.

Parameters:

interaction - a InteractionEvidence object.

complexExpansion - a CvTerm object.

Method Detail

getImexId

public String getImexId()

getImexId

Specified by:

getImexId in interface InteractionEvidence

Returns:

a String object.

assignImexId

public void assignImexId(String identifier)

Assign an IMEx id to an interaction. It will add the new imex-primary ref to the collection of xrefs

Specified by:

assignImexId in interface InteractionEvidence

Parameters:

identifier - : the IMEx id from IMEx central

getExperiment

public Experiment getExperiment()

getExperiment

Specified by:

getExperiment in interface InteractionEvidence

Returns:

a Experiment object.

setExperiment

public void setExperiment(Experiment experiment)

Sets the experiment for this interaction.

Specified by:

setExperiment in interface InteractionEvidence

Parameters:

experiment - : experiment

setExperimentAndAddInteractionEvidence

public void setExperimentAndAddInteractionEvidence(Experiment experiment)

Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction

Specified by:

setExperimentAndAddInteractionEvidence in interface InteractionEvidence

Parameters:

experiment - : experiment

getVariableParameterValues

public Collection<VariableParameterValueSet> getVariableParameterValues()

getVariableParameterValues

Specified by:

getVariableParameterValues in interface InteractionEvidence

Returns:

a Collection object.

getAvailability

public String getAvailability()

getAvailability

Specified by:

getAvailability in interface InteractionEvidence

Returns:

a String object.

setAvailability

public void setAvailability(String availability)

Sets the availability.

Specified by:

setAvailability in interface InteractionEvidence

Parameters:

availability - : availability

getParameters

public Collection<Parameter> getParameters()

getParameters

Specified by:

getParameters in interface InteractionEvidence

Returns:

a Collection object.

isInferred

public boolean isInferred()

isInferred

Specified by:

isInferred in interface InteractionEvidence

Returns:

a boolean.

setInferred

public void setInferred(boolean inferred)

Sets the inferred boolean value

Specified by:

setInferred in interface InteractionEvidence

Parameters:

inferred - : inferred boolean value

getConfidences

public Collection<Confidence> getConfidences()

getConfidences

Specified by:

getConfidences in interface InteractionEvidence

Returns:

a Collection object.

isNegative

public boolean isNegative()

isNegative

Specified by:

isNegative in interface InteractionEvidence

Returns:

a boolean.

setNegative

public void setNegative(boolean negative)

Sets the negative boolean value.

Specified by:

setNegative in interface InteractionEvidence

Parameters:

negative - : negative value