Package psidev.psi.mi.jami.xml.model.extension.xml300

Class XmlInteractionEvidence

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteraction<T>

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractPsiXmlInteraction<ParticipantEvidence>

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteractionEvidence

psidev.psi.mi.jami.xml.model.extension.xml300.XmlInteractionEvidence

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>, ExtendedPsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence, PsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence

public class XmlInteractionEvidence
extends AbstractXmlInteractionEvidence
implements ExtendedPsiXmlInteractionEvidence

Xml implementation of InteractionEvidence

Since:

08/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	XmlInteractionEvidence.JAXBCausalRelationshipWrapper
static class	XmlInteractionEvidence.JAXBExperimentWrapper
static class	XmlInteractionEvidence.JAXBVariableParameterValueSetWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteractionEvidence

AbstractXmlInteractionEvidence.JAXBConfidenceWrapper, AbstractXmlInteractionEvidence.JAXBParameterWrapper, AbstractXmlInteractionEvidence.JAXBParticipantWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractPsiXmlInteraction

AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteraction

AbstractXmlInteraction.JAXBAttributeWrapper

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteractionEvidence

locator

Constructor Summary

Constructors

Constructor	Description
XmlInteractionEvidence()	Constructor for XmlInteractionEvidence.
XmlInteractionEvidence(String shortName)	Constructor for XmlInteractionEvidence.
XmlInteractionEvidence(String shortName, CvTerm type)	Constructor for XmlInteractionEvidence.

Method Summary

Modifier and Type	Method	Description
List<ExtendedPsiXmlCausalRelationship>	getCausalRelationships()	getCausalRelationships.
Collection<VariableParameterValueSet>	getVariableParameterValues()	getVariableParameterValues.
void	setJAXBCausalRelationshipWrapper(XmlInteractionEvidence.JAXBCausalRelationshipWrapper jaxbCausalRelationshipWrapper)	setJAXBCausalRelationshipWrapper.
void	setJAXBVariableParameterValueSetWrapper(XmlInteractionEvidence.JAXBVariableParameterValueSetWrapper jaxbVariableValueList)	setJAXBVariableParameterValueSetWrapper.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteractionEvidence

assignImexId, getAvailability, getConfidences, getExperiment, getExperiments, getImexId, getInteractionTypes, getJAXBConfidenceWrapper, getJAXBExperimentWrapper, getJAXBParameterWrapper, getOriginalExperiments, getParameters, getSourceLocator, getXmlAvailability, initialiseConfidenceWrapper, initialiseParameterWrapper, initialiseParticipantWrapper, initialiseVariableParameterValueSets, isInferred, isModelled, isNegative, processAddedParticipant, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setInteractionNamesContainer, setInteractionXrefContainer, setJAXBAttributeWrapper, setJAXBAvailability, setJAXBAvailabilityRef, setJAXBConfidenceWrapper, setJAXBExperimentWrapper, setJAXBId, setJAXBImexId, setJAXBInferredInteractionWrapper, setJAXBIntraMolecular, setJAXBModelled, setJAXBNegative, setJAXBParameterWrapper, setJAXBParticipantWrapper, setModelled, setNegative, setXmlAvailability

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractPsiXmlInteraction

getInferredInteractions, getInteractionType, setInteractionType

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlInteraction

addAllParticipants, addParticipant, assignComplexAc, getAliases, getAnnotations, getAttributeWrapper, getChecksums, getComplexAc, getComplexVersion, getCreatedDate, getEntry, getFullName, getId, getIdentifiers, getInteractionNamesContainer, getInteractionXrefContainer, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotationWrapper, initialiseNamesContainer, isIntraMolecular, removeAllParticipants, removeParticipant, setCreatedDate, setEntry, setFullName, setId, setIntraMolecular, setParticipantWrapper, setRigid, setShortName, setSourceLocator, setUpdatedDate, sourceLocation, 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.xml.model.extension.ExtendedPsiXmlInteraction

getInferredInteractions, getInteractionTypes

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

getAliases, getExperiments, getOriginalExperiments, getXmlAvailability, isModelled, setModelled, setXmlAvailability

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.InteractionEvidence

assignImexId, getAvailability, getConfidences, getExperiment, getImexId, getParameters, isInferred, isNegative, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setNegative

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

XmlInteractionEvidence

public XmlInteractionEvidence()

Constructor for XmlInteractionEvidence.

XmlInteractionEvidence

public XmlInteractionEvidence(String shortName)

Constructor for XmlInteractionEvidence.

Parameters:

shortName - a String object.

XmlInteractionEvidence

public XmlInteractionEvidence(String shortName,
                              CvTerm type)

Constructor for XmlInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

getVariableParameterValues

public Collection<VariableParameterValueSet> getVariableParameterValues()

getVariableParameterValues.

Specified by:

getVariableParameterValues in interface InteractionEvidence

Overrides:

getVariableParameterValues in class AbstractXmlInteractionEvidence

Returns:

a Collection object.

getCausalRelationships

public List<ExtendedPsiXmlCausalRelationship> getCausalRelationships()

getCausalRelationships.

Specified by:

getCausalRelationships in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

setJAXBVariableParameterValueSetWrapper

public void setJAXBVariableParameterValueSetWrapper(XmlInteractionEvidence.JAXBVariableParameterValueSetWrapper jaxbVariableValueList)

setJAXBVariableParameterValueSetWrapper.

Parameters:

jaxbVariableValueList - a XmlInteractionEvidence.JAXBVariableParameterValueSetWrapper object.

setJAXBCausalRelationshipWrapper

public void setJAXBCausalRelationshipWrapper(XmlInteractionEvidence.JAXBCausalRelationshipWrapper jaxbCausalRelationshipWrapper)

setJAXBCausalRelationshipWrapper.

Parameters:

jaxbCausalRelationshipWrapper - a XmlInteractionEvidence.JAXBCausalRelationshipWrapper object.