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

Class XmlModelledBinaryInteraction

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<ModelledParticipant>

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

All Implemented Interfaces:

BinaryInteraction<ModelledParticipant>, ModelledBinaryInteraction, FileSourceContext, Interaction<ModelledParticipant>, ModelledInteraction, NamedInteraction<ModelledParticipant>, ExtendedPsiXmlInteraction<ModelledParticipant>, ExtendedPsiXmlModelledInteraction, PsiXmlInteraction<ModelledParticipant>

public class XmlModelledBinaryInteraction
extends AbstractExtendedXmlBinaryInteraction<ModelledParticipant>
implements ModelledBinaryInteraction, ExtendedPsiXmlModelledInteraction

Xml implementation of ModelledInteraction

Since:

16/10/13

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
XmlModelledBinaryInteraction()	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.

Method Summary

Modifier and Type	Method	Description
Collection<CooperativeEffect>	getCooperativeEffects()	Getter for the field cooperativeEffects.
CvTerm	getEvidenceType()	Getter for the field evidenceType.
List<Experiment>	getExperiments()	getExperiments.
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	initialiseInteractionEvidences()	initialiseInteractionEvidences.
protected void	initialiseModelledConfidences()	initialiseModelledConfidences.
protected void	initialiseModelledParameters()	initialiseModelledParameters.
void	setEvidenceType(CvTerm evidenceType)	Sets the evidence type
void	setSource(Source source)	Sets the source reporting the interaction.

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, 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, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefs, 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.ExtendedPsiXmlModelledInteraction

getAliases

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

getSourceLocator, setSourceLocator, toString

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

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction()

Constructor for XmlModelledBinaryInteraction.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

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

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

Method Detail

initialiseInteractionEvidences

protected void initialiseInteractionEvidences()

initialiseInteractionEvidences.

initialiseCooperativeEffects

protected void initialiseCooperativeEffects()

initialiseCooperativeEffects.

initialiseModelledConfidences

protected void initialiseModelledConfidences()

initialiseModelledConfidences.

initialiseModelledParameters

protected void initialiseModelledParameters()

initialiseModelledParameters.

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 evidenceType)

Sets the evidence type

Specified by:

setEvidenceType in interface ModelledInteraction

Parameters:

evidenceType - : the evidence type

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.