Package psidev.psi.mi.jami.xml.model.extension.binary

Class AbstractXmlBinaryInteractionEvidence

java.lang.Object

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

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

psidev.psi.mi.jami.xml.model.extension.binary.AbstractExtendedXmlBinaryInteraction<ParticipantEvidence>

psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteractionEvidence

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>, ExtendedPsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence, PsiXmlInteraction<ParticipantEvidence>

Direct Known Subclasses:

XmlBinaryInteractionEvidence, XmlBinaryInteractionEvidence, XmlBinaryInteractionEvidence

public abstract class AbstractXmlBinaryInteractionEvidence
extends AbstractExtendedXmlBinaryInteraction<ParticipantEvidence>
implements BinaryInteractionEvidence, ExtendedPsiXmlInteractionEvidence

Abstract class for Xml BinaryInteractionEvidence

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	AbstractXmlBinaryInteractionEvidence.ExperimentalBinaryInteractionXrefList	Experimental interaction Xref list

Constructor Summary

Constructors

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

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()	getExperiment.
List<Experiment>	getExperiments()	getExperiments.
String	getImexId()	Getter for the field imexId.
List<ExtendedPsiXmlExperiment>	getOriginalExperiments()	getOriginalExperiments.
Collection<Parameter>	getParameters()	Getter for the field parameters.
Collection<VariableParameterValueSet>	getVariableParameterValues()	getVariableParameterValues.
AbstractAvailability	getXmlAvailability()	getXmlAvailability.
protected void	initialiseExperimentalConfidences()	initialiseExperimentalConfidences.
protected void	initialiseExperimentalParameters()	initialiseExperimentalParameters.
protected void	initialiseVariableParameterValueSets()	initialiseVariableParameterValueSets.
protected void	initialiseXrefs()	initialiseXrefs
boolean	isInferred()	isInferred.
boolean	isModelled()	isModelled.
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
protected abstract void	setImexId(CvTerm database, String id, CvTerm qualifier)
void	setImexId(Xref imexId)
void	setInferred(boolean inferred)	Sets the inferred boolean value
void	setModelled(boolean modelled)	setModelled.
void	setNegative(boolean negative)	Sets the negative boolean value.
void	setXmlAvailability(AbstractAvailability availability)	setXmlAvailability.
String	toString()

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.binary.AbstractExtendedXmlBinaryInteraction

getAliases, getEntry, getFullName, getId, getInferredInteractions, getInteractionType, getInteractionTypes, getSourceLocator, isIntraMolecular, setEntry, setFullName, setId, setInteractionType, setIntraMolecular, setSourceLocator

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, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, 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.xml.model.extension.ExtendedPsiXmlInteraction

getInferredInteractions, getInteractionTypes

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.ExtendedPsiXmlInteractionEvidence

getAliases

Methods inherited from interface psidev.psi.mi.jami.datasource.FileSourceContext

getSourceLocator, setSourceLocator

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

Methods inherited from interface psidev.psi.mi.jami.model.NamedInteraction

getFullName, setFullName

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.PsiXmlInteraction

getEntry, getId, isIntraMolecular, setEntry, setId, setIntraMolecular

Constructor Detail

AbstractXmlBinaryInteractionEvidence

public AbstractXmlBinaryInteractionEvidence()

Constructor for AbstractXmlBinaryInteractionEvidence.

AbstractXmlBinaryInteractionEvidence

public AbstractXmlBinaryInteractionEvidence(String shortName)

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

AbstractXmlBinaryInteractionEvidence

public AbstractXmlBinaryInteractionEvidence(String shortName,
                                            CvTerm type)

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

AbstractXmlBinaryInteractionEvidence

public AbstractXmlBinaryInteractionEvidence(ParticipantEvidence participantA,
                                            ParticipantEvidence participantB)

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

AbstractXmlBinaryInteractionEvidence

public AbstractXmlBinaryInteractionEvidence(CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

Parameters:

shortName - a String object.

participantA - a ParticipantEvidence object.

participantB - a ParticipantEvidence object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteractionEvidence

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

Constructor for AbstractXmlBinaryInteractionEvidence.

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.

initialiseVariableParameterValueSets

protected void initialiseVariableParameterValueSets()

initialiseVariableParameterValueSets.

initialiseExperimentalParameters

protected void initialiseExperimentalParameters()

initialiseExperimentalParameters.

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.

setImexId

public void setImexId(Xref imexId)

setImexId

protected abstract void setImexId(CvTerm database,
                                  String id,
                                  CvTerm qualifier)

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.

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()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractExtendedXmlBinaryInteraction<ParticipantEvidence>

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

getXmlAvailability

public AbstractAvailability getXmlAvailability()

getXmlAvailability.

Specified by:

getXmlAvailability in interface ExtendedPsiXmlInteractionEvidence

Returns:

a AbstractAvailability object.

setXmlAvailability

public void setXmlAvailability(AbstractAvailability availability)

setXmlAvailability.

Specified by:

setXmlAvailability in interface ExtendedPsiXmlInteractionEvidence

Parameters:

availability - a AbstractAvailability object.

isModelled

public boolean isModelled()

isModelled.

Specified by:

isModelled in interface ExtendedPsiXmlInteractionEvidence

Returns:

a boolean.

setModelled

public void setModelled(boolean modelled)

setModelled.

Specified by:

setModelled in interface ExtendedPsiXmlInteractionEvidence

Parameters:

modelled - a boolean.

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

getOriginalExperiments

public List<ExtendedPsiXmlExperiment> getOriginalExperiments()

getOriginalExperiments.

Specified by:

getOriginalExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.