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

Class DefaultBinaryInteractionEvidence

java.lang.Object

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

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

psidev.psi.mi.jami.binary.impl.DefaultBinaryInteractionEvidence

All Implemented Interfaces:

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

Direct Known Subclasses:

CsvBinaryInteractionEvidence, DefaultNamedBinaryInteractionEvidence, MitabBinaryInteractionEvidence

public class DefaultBinaryInteractionEvidence
extends AbstractBinaryInteraction<ParticipantEvidence>
implements BinaryInteractionEvidence

Default implementation for BinaryInteractionEvidence

Since:

04/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
DefaultBinaryInteractionEvidence()	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, CvTerm type)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(CvTerm complexExpansion)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB)	Constructor for DefaultBinaryInteractionEvidence.
DefaultBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)	Constructor for DefaultBinaryInteractionEvidence.

Method Summary

Modifier and Type	Method	Description
void	assignImexId(String identifier)	Assign an IMEx id to an interaction.
protected void	clearPropertiesLinkedToXrefs()	clearPropertiesLinkedToXrefs
String	getAvailability()	Getter for the field availability.
Collection<Confidence>	getConfidences()	Getter for the field confidences.
Experiment	getExperiment()	Getter for the field experiment.
String	getImexId()	Getter for the field imexId.
Collection<Parameter>	getParameters()	Getter for the field parameters.
Collection<VariableParameterValueSet>	getVariableParameterValues()	getVariableParameterValues
protected void	initialiseExperimentalConfidences()	initialiseExperimentalConfidences
protected void	initialiseExperimentalConfidencesWith(Collection<Confidence> confidences)	initialiseExperimentalConfidencesWith
protected void	initialiseExperimentalParameters()	initialiseExperimentalParameters
protected void	initialiseExperimentalParametersWith(Collection<Parameter> parameters)	initialiseExperimentalParametersWith
protected void	initialiseVariableParameterValueSets()	initialiseVariableParameterValueSets
protected void	initialiseVariableParameterValueSetsWith(Collection<VariableParameterValueSet> variableValues)	initialiseVariableParameterValueSetsWith
protected void	initialiseXrefs()	initialiseXrefs
boolean	isInferred()	isInferred
boolean	isNegative()	isNegative
protected void	processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent
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.
String	toString()

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

addAllParticipants, addParticipant, getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, getParticipants, removeAllParticipants, removeParticipant, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

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, 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.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

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence()

Constructor for DefaultBinaryInteractionEvidence.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName,
                                        CvTerm type)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(ParticipantEvidence participantA,
                                        ParticipantEvidence participantB)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName,
                                        ParticipantEvidence participantA,
                                        ParticipantEvidence participantB)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName,
                                        CvTerm type,
                                        ParticipantEvidence participantA,
                                        ParticipantEvidence participantB)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(CvTerm complexExpansion)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

complexExpansion - a CvTerm object.

DefaultBinaryInteractionEvidence

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

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(ParticipantEvidence participantA,
                                        ParticipantEvidence participantB,
                                        CvTerm complexExpansion)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName,
                                        ParticipantEvidence participantA,
                                        ParticipantEvidence participantB,
                                        CvTerm complexExpansion)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

DefaultBinaryInteractionEvidence

public DefaultBinaryInteractionEvidence(String shortName,
                                        CvTerm type,
                                        ParticipantEvidence participantA,
                                        ParticipantEvidence participantB,
                                        CvTerm complexExpansion)

Constructor for DefaultBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

Method Detail

initialiseExperimentalConfidences

protected void initialiseExperimentalConfidences()

initialiseExperimentalConfidences

initialiseExperimentalConfidencesWith

protected void initialiseExperimentalConfidencesWith(Collection<Confidence> confidences)

initialiseExperimentalConfidencesWith

Parameters:

confidences - a Collection object.

initialiseVariableParameterValueSets

protected void initialiseVariableParameterValueSets()

initialiseVariableParameterValueSets

initialiseVariableParameterValueSetsWith

protected void initialiseVariableParameterValueSetsWith(Collection<VariableParameterValueSet> variableValues)

initialiseVariableParameterValueSetsWith

Parameters:

variableValues - a Collection object.

initialiseExperimentalParameters

protected void initialiseExperimentalParameters()

initialiseExperimentalParameters

initialiseExperimentalParametersWith

protected void initialiseExperimentalParametersWith(Collection<Parameter> parameters)

initialiseExperimentalParametersWith

Parameters:

parameters - a Collection object.

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

Overrides:

initialiseXrefs in class AbstractInteraction<ParticipantEvidence>

getImexId

public String getImexId()

Getter for the field imexId.

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()

Getter for the field experiment.

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.

getConfidences

public Collection<Confidence> getConfidences()

Getter for the field confidences.

Specified by:

getConfidences in interface InteractionEvidence

Returns:

a Collection object.

getAvailability

public String getAvailability()

Getter for the field availability.

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

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

getParameters

public Collection<Parameter> getParameters()

Getter for the field parameters.

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

processAddedXrefEvent

protected void processAddedXrefEvent(Xref added)

processAddedXrefEvent

Parameters:

added - a Xref object.

processRemovedXrefEvent

protected void processRemovedXrefEvent(Xref removed)

processRemovedXrefEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToXrefs

protected void clearPropertiesLinkedToXrefs()

clearPropertiesLinkedToXrefs

toString

public String toString()

Overrides:

toString in class AbstractBinaryInteraction<ParticipantEvidence>