Package psidev.psi.mi.jami.xml.model.extension.xml253

Class AbstractXmlModelledInteraction

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteraction<T>

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractPsiXmlInteraction<ModelledParticipant>

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlModelledInteraction

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Interaction<ModelledParticipant>, ModelledInteraction, NamedInteraction<ModelledParticipant>, ExtendedPsiXmlInteraction<ModelledParticipant>, ExtendedPsiXmlModelledInteraction, PsiXmlInteraction<ModelledParticipant>

Direct Known Subclasses:

AbstractXmlComplex, DefaultXmlModelledInteraction, XmlModelledInteraction

public abstract class AbstractXmlModelledInteraction
extends AbstractPsiXmlInteraction<ModelledParticipant>
implements ExtendedPsiXmlModelledInteraction

Xml implementation of ModelledInteraction

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	AbstractXmlModelledInteraction.JAXBConfidenceWrapper
static class	AbstractXmlModelledInteraction.JAXBExperimentWrapper
static class	AbstractXmlModelledInteraction.JAXBParameterWrapper
static class	AbstractXmlModelledInteraction.JAXBParticipantWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractPsiXmlInteraction

AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteraction

AbstractXmlInteraction.JAXBAttributeWrapper

Field Summary

Fields

Modifier and Type	Field	Description
protected Locator	locator

Fields inherited from interface psidev.psi.mi.jami.model.ModelledInteraction

ECO, ECO_MI

Constructor Summary

Constructors

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

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.
List<CvTerm>	getInteractionTypes()	Gets the value of the interactionTypeList property.
Collection<ModelledConfidence>	getModelledConfidences()	getModelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	getModelledParameters.
Source	getSource()	Getter for the field source.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
protected void	initialiseCooperativeEffects()	initialiseCooperativeEffects.
protected void	initialiseInteractionEvidences()	initialiseInteractionEvidences.
protected void	initialiseModelledConfidenceWrapper()	initialiseModelledConfidenceWrapper.
protected void	initialiseModelledParameterWrapper()	initialiseModelledParameterWrapper.
protected void	initialiseParticipantWrapper()	initialiseParticipantWrapper.
void	setEvidenceType(CvTerm evidenceType)	Sets the evidence type
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	setJAXBConfidenceWrapper(AbstractXmlModelledInteraction.JAXBConfidenceWrapper wrapper)	setJAXBConfidenceWrapper.
void	setJAXBExperimentWrapper(AbstractXmlModelledInteraction.JAXBExperimentWrapper value)	setJAXBExperimentWrapper.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBInferredInteractionWrapper(AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper jaxbInferredWrapper)	setJAXBInferredInteractionWrapper.
void	setJAXBIntraMolecular(boolean intra)	setJAXBIntraMolecular.
void	setJAXBParameterWrapper(AbstractXmlModelledInteraction.JAXBParameterWrapper wrapper)	setJAXBParameterWrapper.
void	setJAXBParticipantWrapper(AbstractXmlModelledInteraction.JAXBParticipantWrapper jaxbParticipantWrapper)	setJAXBParticipantWrapper.
void	setSource(Source source)	Sets the source reporting the interaction.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractPsiXmlInteraction

getInferredInteractions, getInteractionType, setInteractionType

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteraction

addAllParticipants, addParticipant, assignComplexAc, assignImexId, getAliases, getAnnotations, getAttributeWrapper, getChecksums, getComplexAc, getComplexVersion, getCreatedDate, getEntry, getFullName, getId, getIdentifiers, getImexId, getInteractionNamesContainer, getInteractionXrefContainer, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotationWrapper, initialiseNamesContainer, isIntraMolecular, processAddedParticipant, 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.ExtendedPsiXmlModelledInteraction

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

AbstractXmlModelledInteraction

public AbstractXmlModelledInteraction()

Constructor for AbstractXmlModelledInteraction.

AbstractXmlModelledInteraction

public AbstractXmlModelledInteraction(String shortName)

Constructor for AbstractXmlModelledInteraction.

Parameters:

shortName - a String object.

AbstractXmlModelledInteraction

public AbstractXmlModelledInteraction(String shortName,
                                      CvTerm type)

Constructor for AbstractXmlModelledInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

initialiseInteractionEvidences

protected void initialiseInteractionEvidences()

initialiseInteractionEvidences.

initialiseCooperativeEffects

protected void initialiseCooperativeEffects()

initialiseCooperativeEffects.

initialiseModelledConfidenceWrapper

protected void initialiseModelledConfidenceWrapper()

initialiseModelledConfidenceWrapper.

initialiseModelledParameterWrapper

protected void initialiseModelledParameterWrapper()

initialiseModelledParameterWrapper.

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()

getModelledConfidences.

Specified by:

getModelledConfidences in interface ModelledInteraction

Returns:

a Collection object.

getModelledParameters

public Collection<ModelledParameter> getModelledParameters()

getModelledParameters.

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.

setInteractionNamesContainer

public void setInteractionNamesContainer(NamesContainer value)

Sets the value of the names property.

Overrides:

setInteractionNamesContainer in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

value - allowed object is NamesContainer

setInteractionXrefContainer

public void setInteractionXrefContainer(InteractionXrefContainer value)

Sets the value of the interactionXrefContainer property.

Overrides:

setInteractionXrefContainer in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

value - allowed object is InteractionXrefContainer

setJAXBIntraMolecular

public void setJAXBIntraMolecular(boolean intra)

setJAXBIntraMolecular.

Parameters:

intra - a boolean.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Overrides:

setJAXBAttributeWrapper in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

jaxbAttributeWrapper - a AbstractXmlInteraction.JAXBAttributeWrapper object.

setJAXBId

public void setJAXBId(int value)

setJAXBId.

Parameters:

value - a int.

setJAXBParticipantWrapper

public void setJAXBParticipantWrapper(AbstractXmlModelledInteraction.JAXBParticipantWrapper jaxbParticipantWrapper)

setJAXBParticipantWrapper.

Parameters:

jaxbParticipantWrapper - a AbstractXmlModelledInteraction.JAXBParticipantWrapper object.

setJAXBConfidenceWrapper

public void setJAXBConfidenceWrapper(AbstractXmlModelledInteraction.JAXBConfidenceWrapper wrapper)

setJAXBConfidenceWrapper.

Parameters:

wrapper - a AbstractXmlModelledInteraction.JAXBConfidenceWrapper object.

setJAXBParameterWrapper

public void setJAXBParameterWrapper(AbstractXmlModelledInteraction.JAXBParameterWrapper wrapper)

setJAXBParameterWrapper.

Parameters:

wrapper - a AbstractXmlModelledInteraction.JAXBParameterWrapper object.

setJAXBExperimentWrapper

public void setJAXBExperimentWrapper(AbstractXmlModelledInteraction.JAXBExperimentWrapper value)

setJAXBExperimentWrapper.

Parameters:

value - a AbstractXmlModelledInteraction.JAXBExperimentWrapper 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

setJAXBInferredInteractionWrapper

public void setJAXBInferredInteractionWrapper(AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper jaxbInferredWrapper)

setJAXBInferredInteractionWrapper.

Overrides:

setJAXBInferredInteractionWrapper in class AbstractPsiXmlInteraction<ModelledParticipant>

Parameters:

jaxbInferredWrapper - a AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper object.

getInteractionTypes

public List<CvTerm> getInteractionTypes()

Gets the value of the interactionTypeList property.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Overrides:

getInteractionTypes in class AbstractPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Overrides:

getSourceLocator in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a FileSourceLocator object.

initialiseParticipantWrapper

protected void initialiseParticipantWrapper()

initialiseParticipantWrapper.

Overrides:

initialiseParticipantWrapper in class AbstractXmlInteraction<ModelledParticipant>

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.