Package psidev.psi.mi.jami.xml.model.extension.xml254

Class AbstractXmlInteractionEvidence

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml254.AbstractXmlInteraction<T>

psidev.psi.mi.jami.xml.model.extension.xml254.AbstractPsiXmlInteraction<ParticipantEvidence>

psidev.psi.mi.jami.xml.model.extension.xml254.AbstractXmlInteractionEvidence

All Implemented Interfaces:

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

Direct Known Subclasses:

DefaultXmlInteractionEvidence, XmlInteractionEvidence

public abstract class AbstractXmlInteractionEvidence
extends AbstractPsiXmlInteraction<ParticipantEvidence>
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	AbstractXmlInteractionEvidence.JAXBConfidenceWrapper
static class	AbstractXmlInteractionEvidence.JAXBExperimentWrapper
static class	AbstractXmlInteractionEvidence.JAXBParameterWrapper
static class	AbstractXmlInteractionEvidence.JAXBParticipantWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml254.AbstractPsiXmlInteraction

AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml254.AbstractXmlInteraction

AbstractXmlInteraction.JAXBAttributeWrapper

Field Summary

Fields

Modifier and Type	Field	Description
protected Locator	locator

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	assignImexId(String identifier)	Sets the value of the imexId property
String	getAvailability()	Getter for the field availability.
Collection<Confidence>	getConfidences()	getConfidences.
Experiment	getExperiment()	getExperiment.
List<Experiment>	getExperiments()	getExperiments.
String	getImexId()	getImexId.
List<CvTerm>	getInteractionTypes()	Gets the value of the interactionTypeList property.
AbstractXmlInteractionEvidence.JAXBConfidenceWrapper	getJAXBConfidenceWrapper()	getJAXBConfidenceWrapper.
AbstractXmlInteractionEvidence.JAXBExperimentWrapper	getJAXBExperimentWrapper()	getJAXBExperimentWrapper.
AbstractXmlInteractionEvidence.JAXBParameterWrapper	getJAXBParameterWrapper()	getJAXBParameterWrapper.
List<ExtendedPsiXmlExperiment>	getOriginalExperiments()	getOriginalExperiments.
Collection<Parameter>	getParameters()	getParameters.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
Collection<VariableParameterValueSet>	getVariableParameterValues()	getVariableParameterValues.
AbstractAvailability	getXmlAvailability()	getXmlAvailability.
protected void	initialiseConfidenceWrapper()	initialiseConfidenceWrapper.
protected void	initialiseParameterWrapper()	initialiseParameterWrapper.
protected void	initialiseParticipantWrapper()	initialiseParticipantWrapper.
protected void	initialiseVariableParameterValueSets()	initialiseVariableParameterValueSets.
boolean	isInferred()	isInferred.
boolean	isModelled()	Gets the value of the modelled property.
boolean	isNegative()	isNegative.
void	processAddedParticipant(ParticipantEvidence participant)	processAddedParticipant.
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	setInteractionNamesContainer(NamesContainer value)	Sets the value of the names property.
void	setInteractionXrefContainer(InteractionXrefContainer value)	Sets the value of the interactionXrefContainer property.
void	setJAXBAttributeWrapper(AbstractXmlInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBAvailability(DefaultAvailability value)	Sets the value of the availability property.
void	setJAXBAvailabilityRef(Integer value)	Sets the value of the availabilityRef property.
void	setJAXBConfidenceWrapper(AbstractXmlInteractionEvidence.JAXBConfidenceWrapper wrapper)	Gets the value of the confidenceList property.
void	setJAXBExperimentWrapper(AbstractXmlInteractionEvidence.JAXBExperimentWrapper value)	Sets the value of the experimentList property.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBImexId(String identifier)	setJAXBImexId.
void	setJAXBInferredInteractionWrapper(AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper jaxbInferredWrapper)	setJAXBInferredInteractionWrapper.
void	setJAXBIntraMolecular(Boolean intra)	setJAXBIntraMolecular.
void	setJAXBModelled(Boolean value)	setJAXBModelled.
void	setJAXBNegative(Boolean value)	Sets the value of the negative property.
void	setJAXBParameterWrapper(AbstractXmlInteractionEvidence.JAXBParameterWrapper wrapper)	Gets the value of the parameterList property.
void	setJAXBParticipantWrapper(AbstractXmlInteractionEvidence.JAXBParticipantWrapper jaxbParticipantWrapper)	setJAXBParticipantWrapper.
void	setModelled(boolean value)	setModelled.
void	setNegative(boolean negative)	Sets the negative boolean value.
void	setXmlAvailability(AbstractAvailability availability)	setXmlAvailability.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml254.AbstractPsiXmlInteraction

getInferredInteractions, getInteractionType, setInteractionType

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml254.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

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

getAliases

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

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

Field Detail

locator

protected Locator locator

Constructor Detail

AbstractXmlInteractionEvidence

public AbstractXmlInteractionEvidence()

Constructor for AbstractXmlInteractionEvidence.

AbstractXmlInteractionEvidence

public AbstractXmlInteractionEvidence(String shortName)

Constructor for AbstractXmlInteractionEvidence.

Parameters:

shortName - a String object.

AbstractXmlInteractionEvidence

public AbstractXmlInteractionEvidence(String shortName,
                                      CvTerm type)

Constructor for AbstractXmlInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

setInteractionNamesContainer

public void setInteractionNamesContainer(NamesContainer value)

Sets the value of the names property.

Overrides:

setInteractionNamesContainer in class AbstractXmlInteraction<ParticipantEvidence>

Parameters:

value - allowed object is NamesContainer

setInteractionXrefContainer

public void setInteractionXrefContainer(InteractionXrefContainer value)

Sets the value of the interactionXrefContainer property.

Overrides:

setInteractionXrefContainer in class AbstractXmlInteraction<ParticipantEvidence>

Parameters:

value - allowed object is InteractionXrefContainer

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Overrides:

setJAXBAttributeWrapper in class AbstractXmlInteraction<ParticipantEvidence>

Parameters:

jaxbAttributeWrapper - a AbstractXmlInteraction.JAXBAttributeWrapper object.

setJAXBInferredInteractionWrapper

public void setJAXBInferredInteractionWrapper(AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper jaxbInferredWrapper)

setJAXBInferredInteractionWrapper.

Overrides:

setJAXBInferredInteractionWrapper in class AbstractPsiXmlInteraction<ParticipantEvidence>

Parameters:

jaxbInferredWrapper - a AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper object.

getInteractionTypes

public List<CvTerm> getInteractionTypes()

Gets the value of the interactionTypeList property.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ParticipantEvidence>

Overrides:

getInteractionTypes in class AbstractPsiXmlInteraction<ParticipantEvidence>

Returns:

a List object.

getImexId

public String getImexId()

getImexId.

Specified by:

getImexId in interface InteractionEvidence

Overrides:

getImexId in class AbstractXmlInteraction<ParticipantEvidence>

Returns:

a String object.

assignImexId

public void assignImexId(String identifier)

Sets the value of the imexId property

Specified by:

assignImexId in interface InteractionEvidence

Overrides:

assignImexId in class AbstractXmlInteraction<ParticipantEvidence>

Parameters:

identifier - a String object.

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

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

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()

getConfidences.

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()

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

setJAXBIntraMolecular

public void setJAXBIntraMolecular(Boolean intra)

setJAXBIntraMolecular.

Parameters:

intra - a Boolean object.

setJAXBId

public void setJAXBId(int value)

setJAXBId.

Parameters:

value - a int.

setJAXBImexId

public void setJAXBImexId(String identifier)

setJAXBImexId.

Parameters:

identifier - a String object.

setJAXBParticipantWrapper

public void setJAXBParticipantWrapper(AbstractXmlInteractionEvidence.JAXBParticipantWrapper jaxbParticipantWrapper)

setJAXBParticipantWrapper.

Parameters:

jaxbParticipantWrapper - a AbstractXmlInteractionEvidence.JAXBParticipantWrapper object.

setJAXBConfidenceWrapper

public void setJAXBConfidenceWrapper(AbstractXmlInteractionEvidence.JAXBConfidenceWrapper wrapper)

Gets the value of the confidenceList property.

Parameters:

wrapper - a AbstractXmlInteractionEvidence.JAXBConfidenceWrapper object.

setJAXBParameterWrapper

public void setJAXBParameterWrapper(AbstractXmlInteractionEvidence.JAXBParameterWrapper wrapper)

Gets the value of the parameterList property.

Parameters:

wrapper - a AbstractXmlInteractionEvidence.JAXBParameterWrapper object.

setJAXBAvailability

public void setJAXBAvailability(DefaultAvailability value)

Sets the value of the availability property.

Parameters:

value - allowed object is DefaultAvailability

setJAXBAvailabilityRef

public void setJAXBAvailabilityRef(Integer value)

Sets the value of the availabilityRef property.

Parameters:

value - allowed object is Integer

setJAXBExperimentWrapper

public void setJAXBExperimentWrapper(AbstractXmlInteractionEvidence.JAXBExperimentWrapper value)

Sets the value of the experimentList property.

Parameters:

value - allowed object is AbstractXmlInteractionEvidence.JAXBExperimentWrapper

isModelled

public boolean isModelled()

Gets the value of the modelled property.

Specified by:

isModelled in interface ExtendedPsiXmlInteractionEvidence

Returns:

a boolean.

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.

setModelled

public void setModelled(boolean value)

setModelled.

Sets the value of the modelled property.

Specified by:

setModelled in interface ExtendedPsiXmlInteractionEvidence

Parameters:

value - a boolean.

setJAXBModelled

public void setJAXBModelled(Boolean value)

setJAXBModelled.

Parameters:

value - a Boolean object.

setJAXBNegative

public void setJAXBNegative(Boolean value)

Sets the value of the negative property.

Parameters:

value - allowed object is Boolean

getJAXBConfidenceWrapper

public AbstractXmlInteractionEvidence.JAXBConfidenceWrapper getJAXBConfidenceWrapper()

getJAXBConfidenceWrapper.

Returns:

a AbstractXmlInteractionEvidence.JAXBConfidenceWrapper object.

getJAXBParameterWrapper

public AbstractXmlInteractionEvidence.JAXBParameterWrapper getJAXBParameterWrapper()

getJAXBParameterWrapper.

Returns:

a AbstractXmlInteractionEvidence.JAXBParameterWrapper object.

getJAXBExperimentWrapper

public AbstractXmlInteractionEvidence.JAXBExperimentWrapper getJAXBExperimentWrapper()

getJAXBExperimentWrapper.

Returns:

a AbstractXmlInteractionEvidence.JAXBExperimentWrapper object.

getOriginalExperiments

public List<ExtendedPsiXmlExperiment> getOriginalExperiments()

getOriginalExperiments.

Specified by:

getOriginalExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

initialiseConfidenceWrapper

protected void initialiseConfidenceWrapper()

initialiseConfidenceWrapper.

initialiseVariableParameterValueSets

protected void initialiseVariableParameterValueSets()

initialiseVariableParameterValueSets.

initialiseParameterWrapper

protected void initialiseParameterWrapper()

initialiseParameterWrapper.

processAddedParticipant

public void processAddedParticipant(ParticipantEvidence participant)

processAddedParticipant.

Overrides:

processAddedParticipant in class AbstractXmlInteraction<ParticipantEvidence>

Parameters:

participant - a T object.

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Overrides:

getSourceLocator in class AbstractXmlInteraction<ParticipantEvidence>

Returns:

a FileSourceLocator object.

initialiseParticipantWrapper

protected void initialiseParticipantWrapper()

initialiseParticipantWrapper.

Overrides:

initialiseParticipantWrapper in class AbstractXmlInteraction<ParticipantEvidence>