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

Class XmlModelledInteraction

java.lang.Object

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

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

All Implemented Interfaces:

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

public class XmlModelledInteraction
extends AbstractXmlInteraction<ModelledParticipant>
implements ExtendedPsiXmlModelledInteraction

Xml 3.0.0 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	XmlModelledInteraction.JAXBAttributeWrapper
static class	XmlModelledInteraction.JAXBBindingFeaturesWrapper
static class	XmlModelledInteraction.JAXBCausalRelationshipWrapper
static class	XmlModelledInteraction.JAXBConfidenceWrapper
static class	XmlModelledInteraction.JAXBCooperativeEffectWrapper
static class	XmlModelledInteraction.JAXBParameterWrapper
static class	XmlModelledInteraction.JAXBParticipantWrapper

Field Summary

Fields

Modifier and Type	Field	Description
protected Locator	locator

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

COMPLEX, COMPLEX_MI

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

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

ECO, ECO_MI

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	assignComplexAc(String accession)	Sets the value of the complexAc property
void	assignComplexAc(String accession, String version)	Assign a complex accession to a complex.
List<Alias>	getAliases()	Collection of aliases for an interaction.
Collection<Annotation>	getAnnotations()	getAnnotations.
protected XmlModelledInteraction.JAXBAttributeWrapper	getAttributeWrapper()	getAttributeWrapper.
List<BindingFeatures>	getBindingFeatures()	getBindingFeatures.
List<ExtendedPsiXmlCausalRelationship>	getCausalRelationships()	getCausalRelationships.
Collection<Checksum>	getChecksums()	getChecksums.
String	getComplexAc()	Gets the value of the complexAc property.
String	getComplexVersion()	Gets the value of the complexVersion property.
Collection<CooperativeEffect>	getCooperativeEffects()	getCooperativeEffects.
CvTerm	getEvidenceType()	Getter for the field evidenceType.
Collection<Xref>	getIdentifiers()	getIdentifiers.
Collection<InteractionEvidence>	getInteractionEvidences()	Getter for the field interactionEvidences.
protected ComplexNamesContainer	getInteractionNamesContainer()	Getter for the field interactionNamesContainer.
CvTerm	getInteractionType()	getInteractionType.
CvTerm	getInteractorType()	Getter for the field interactorType.
Collection<ModelledConfidence>	getModelledConfidences()	getModelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	getModelledParameters.
Organism	getOrganism()	The original source organism for this interactor.
String	getPhysicalProperties()	getPhysicalProperties.
Xref	getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
String	getPreferredName()	The preferred name is the name by which we want to refer the interactor on our web site.
String	getRecommendedName()	getRecommendedName.
Source	getSource()	Getter for the field source.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
String	getSystematicName()	getSystematicName.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	initialiseCooperativeEffects()	initialiseCooperativeEffects.
protected void	initialiseInteractionEvidences()	initialiseInteractionEvidences.
protected void	initialiseModelledConfidenceWrapper()	initialiseModelledConfidenceWrapper.
protected void	initialiseModelledParameterWrapper()	initialiseModelledParameterWrapper.
protected void	initialiseNamesContainer()	initialiseNamesContainer.
protected void	initialiseParticipantWrapper()	initialiseParticipantWrapper.
void	setEvidenceType(CvTerm evidenceType)	Sets the evidence type
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setInteractionXrefContainer(InteractionXrefContainer value)	Sets the value of the interactionXrefContainer property.
void	setInteractorType(CvTerm interactorType)	Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
void	setJAXBAttributeWrapper(XmlModelledInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBBindingFeaturesWrapper(XmlModelledInteraction.JAXBBindingFeaturesWrapper jaxbInferredWrapper)	setJAXBBindingFeaturesWrapper.
void	setJAXBCausalRelationshipWrapper(XmlModelledInteraction.JAXBCausalRelationshipWrapper jaxbCausalRelationshipWrapper)	setJAXBCausalRelationshipWrapper.
void	setJAXBConfidenceWrapper(XmlModelledInteraction.JAXBConfidenceWrapper wrapper)	setJAXBConfidenceWrapper.
void	setJAXBCooperativeEffectWrapper(XmlModelledInteraction.JAXBCooperativeEffectWrapper jaxbEffectWrapper)	setJAXBCooperativeEffectWrapper.
void	setJAXBEvidenceType(XmlCvTerm evidenceType)	setJAXBEvidenceType.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBInteractionType(XmlCvTerm term)	setJAXBInteractionType.
void	setJAXBInteractorType(XmlCvTerm interactorType)	setJAXBInteractorType.
void	setJAXBIntraMolecular(boolean intra)	setJAXBIntraMolecular.
void	setJAXBNames(ComplexNamesContainer value)	setJAXBNames.
void	setJAXBOrganism(XmlOrganism organism)	setJAXBOrganism.
void	setJAXBParameterWrapper(XmlModelledInteraction.JAXBParameterWrapper wrapper)	setJAXBParameterWrapper.
void	setJAXBParticipantWrapper(XmlModelledInteraction.JAXBParticipantWrapper jaxbParticipantWrapper)	setJAXBParticipantWrapper.
void	setOrganism(Organism organism)	Sets the source organism of this interactor
void	setPhysicalProperties(String properties)	Sets the physical properties of this complex.
void	setRecommendedName(String name)	Sets the recommended name of this complex.
void	setSource(Source source)	Sets the source reporting the interaction.
void	setSystematicName(String name)	Sets the systematic name of this complex.

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

addAllParticipants, addParticipant, assignImexId, getCreatedDate, getEntry, getFullName, getId, getImexId, getInteractionXrefContainer, getParticipants, getRigid, getShortName, getUpdatedDate, isIntraMolecular, processAddedParticipant, removeAllParticipants, removeParticipant, setCreatedDate, setEntry, setFullName, setId, setInteractionNamesContainer, setIntraMolecular, setJAXBAttributeWrapper, 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.model.Complex

getComparableParticipants

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

setSourceLocator, toString

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

addAllParticipants, addParticipant, getCreatedDate, getParticipants, getRigid, getShortName, getUpdatedDate, removeAllParticipants, removeParticipant, setCreatedDate, setRigid, setShortName, setUpdatedDate

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

getFullName, getShortName, setFullName, setShortName

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

XmlModelledInteraction

public XmlModelledInteraction()

Constructor for XmlModelledInteraction.

XmlModelledInteraction

public XmlModelledInteraction(String shortName)

Constructor for XmlModelledInteraction.

Parameters:

shortName - a String object.

XmlModelledInteraction

public XmlModelledInteraction(String shortName,
                              CvTerm type)

Constructor for XmlModelledInteraction.

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()

getCooperativeEffects.

Specified by:

getCooperativeEffects in interface ModelledInteraction

Returns:

a Collection object.

getComplexAc

public String getComplexAc()

Gets the value of the complexAc property.

Specified by:

getComplexAc in interface Complex

Overrides:

getComplexAc in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a String object.

getComplexVersion

public String getComplexVersion()

Gets the value of the complexVersion property.

Specified by:

getComplexVersion in interface Complex

Overrides:

getComplexVersion in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a String object.

assignComplexAc

public void assignComplexAc(String accession,
                            String version)

Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs

Specified by:

assignComplexAc in interface Complex

Parameters:

accession - : the complex accession

version - : the version of the complex if it is provided. If version is null it will create the complex with version 1

assignComplexAc

public void assignComplexAc(String accession)

Sets the value of the complexAc property

Specified by:

assignComplexAc in interface Complex

Overrides:

assignComplexAc in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

accession - a String object.

getPhysicalProperties

public String getPhysicalProperties()

getPhysicalProperties.

Specified by:

getPhysicalProperties in interface Complex

Returns:

a String object.

setPhysicalProperties

public void setPhysicalProperties(String properties)

Sets the physical properties of this complex. It will remove the old complex-properties annotation from the collection of annotations and replace it with the new complex-properties annotation. If the new complex-properties is null, all the existing complex-properties annotations will be removed from the collection of annotations

Specified by:

setPhysicalProperties in interface Complex

Parameters:

properties - : complex properties

getRecommendedName

public String getRecommendedName()

getRecommendedName.

Specified by:

getRecommendedName in interface Complex

Returns:

a String object.

setRecommendedName

public void setRecommendedName(String name)

Sets the recommended name of this complex. It will remove the old recommended name from the collection of aliases and replace it with the new recommended name. If the new recommended name is null, all the existing recommended names will be removed from the collection of aliases

Specified by:

setRecommendedName in interface Complex

Parameters:

name - : the recommended name

getSystematicName

public String getSystematicName()

getSystematicName.

Specified by:

getSystematicName in interface Complex

Returns:

a String object.

setSystematicName

public void setSystematicName(String name)

Sets the systematic name of this complex. It will remove the old systematic name from the collection of aliases and replace it with the new systematic name. If the new systematic name is null, all the existing systematic names will be removed from the collection of aliases

Specified by:

setSystematicName in interface Complex

Parameters:

name - : the systematic name

getPreferredIdentifier

public Xref getPreferredIdentifier()

The identifier in the list of identifiers which is the preferred identifier. If no identifiers is preferred, it should return the first identifier of the list of identifiers, null if the list of identifiers is empty.

Specified by:

getPreferredIdentifier in interface Interactor

Returns:

the preferred identifier in the list of identifiers, null if the list of identifiers is empty

getPreferredName

public String getPreferredName()

The preferred name is the name by which we want to refer the interactor on our web site.

Specified by:

getPreferredName in interface Interactor

Returns:

the preferred name

getOrganism

public Organism getOrganism()

The original source organism for this interactor. It can be null in case of chemical compounds/synthetic peptides

Specified by:

getOrganism in interface Interactor

Returns:

the organism

setOrganism

public void setOrganism(Organism organism)

Sets the source organism of this interactor

Specified by:

setOrganism in interface Interactor

Parameters:

organism - : source organism

getInteractorType

public CvTerm getInteractorType()

Getter for the field interactorType.

Specified by:

getInteractorType in interface Interactor

Returns:

a CvTerm object.

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)

Specified by:

setInteractorType in interface Interactor

Parameters:

interactorType - : molecule type

getAliases

public List<Alias> getAliases()

Collection of aliases for an interaction. The Collection cannot be null and if the interaction does not have any aliases, the method should return an empty Collection.

Specified by:

getAliases in interface ExtendedPsiXmlModelledInteraction

Specified by:

getAliases in interface Interactor

Specified by:

getAliases in interface NamedInteraction<ModelledParticipant>

Specified by:

getAliases in interface PsiXmlInteraction<ModelledParticipant>

Overrides:

getAliases in class AbstractXmlInteraction<ModelledParticipant>

Returns:

the aliases

getChecksums

public Collection<Checksum> getChecksums()

getChecksums.

Specified by:

getChecksums in interface Interaction<ModelledParticipant>

Specified by:

getChecksums in interface Interactor

Overrides:

getChecksums in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Interaction<ModelledParticipant>

Specified by:

getXrefs in interface Interactor

Overrides:

getXrefs in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a Collection object.

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface Interaction<ModelledParticipant>

Specified by:

getIdentifiers in interface Interactor

Overrides:

getIdentifiers in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Interaction<ModelledParticipant>

Specified by:

getAnnotations in interface Interactor

Overrides:

getAnnotations in class AbstractXmlInteraction<ModelledParticipant>

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

getInteractionType

public CvTerm getInteractionType()

getInteractionType.

Specified by:

getInteractionType in interface Interaction<ModelledParticipant>

Specified by:

getInteractionType in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a CvTerm object.

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<ModelledParticipant>

Specified by:

setInteractionType in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

term - : interaction type

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.

getBindingFeatures

public List<BindingFeatures> getBindingFeatures()

getBindingFeatures.

Specified by:

getBindingFeatures in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.

getCausalRelationships

public List<ExtendedPsiXmlCausalRelationship> getCausalRelationships()

getCausalRelationships.

Specified by:

getCausalRelationships in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.

setJAXBNames

public void setJAXBNames(ComplexNamesContainer value)

setJAXBNames.

Parameters:

value - a ComplexNamesContainer object.

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(XmlModelledInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Parameters:

jaxbAttributeWrapper - a XmlModelledInteraction.JAXBAttributeWrapper object.

setJAXBId

public void setJAXBId(int value)

setJAXBId.

Parameters:

value - a int.

setJAXBParticipantWrapper

public void setJAXBParticipantWrapper(XmlModelledInteraction.JAXBParticipantWrapper jaxbParticipantWrapper)

setJAXBParticipantWrapper.

Parameters:

jaxbParticipantWrapper - a XmlModelledInteraction.JAXBParticipantWrapper object.

setJAXBConfidenceWrapper

public void setJAXBConfidenceWrapper(XmlModelledInteraction.JAXBConfidenceWrapper wrapper)

setJAXBConfidenceWrapper.

Parameters:

wrapper - a XmlModelledInteraction.JAXBConfidenceWrapper object.

setJAXBParameterWrapper

public void setJAXBParameterWrapper(XmlModelledInteraction.JAXBParameterWrapper wrapper)

setJAXBParameterWrapper.

Parameters:

wrapper - a XmlModelledInteraction.JAXBParameterWrapper object.

setJAXBOrganism

public void setJAXBOrganism(XmlOrganism organism)

setJAXBOrganism.

Parameters:

organism - a XmlOrganism object.

setJAXBInteractorType

public void setJAXBInteractorType(XmlCvTerm interactorType)

setJAXBInteractorType.

Parameters:

interactorType - a XmlCvTerm object.

setJAXBInteractionType

public void setJAXBInteractionType(XmlCvTerm term)

setJAXBInteractionType.

Parameters:

term - a XmlCvTerm object.

setJAXBBindingFeaturesWrapper

public void setJAXBBindingFeaturesWrapper(XmlModelledInteraction.JAXBBindingFeaturesWrapper jaxbInferredWrapper)

setJAXBBindingFeaturesWrapper.

Parameters:

jaxbInferredWrapper - a XmlModelledInteraction.JAXBBindingFeaturesWrapper object.

setJAXBCooperativeEffectWrapper

public void setJAXBCooperativeEffectWrapper(XmlModelledInteraction.JAXBCooperativeEffectWrapper jaxbEffectWrapper)

setJAXBCooperativeEffectWrapper.

Parameters:

jaxbEffectWrapper - a XmlModelledInteraction.JAXBCooperativeEffectWrapper object.

setJAXBCausalRelationshipWrapper

public void setJAXBCausalRelationshipWrapper(XmlModelledInteraction.JAXBCausalRelationshipWrapper jaxbCausalRelationshipWrapper)

setJAXBCausalRelationshipWrapper.

Parameters:

jaxbCausalRelationshipWrapper - a XmlModelledInteraction.JAXBCausalRelationshipWrapper object.

setJAXBEvidenceType

public void setJAXBEvidenceType(XmlCvTerm evidenceType)

setJAXBEvidenceType.

Parameters:

evidenceType - a XmlCvTerm object.

initialiseParticipantWrapper

protected void initialiseParticipantWrapper()

initialiseParticipantWrapper.

Overrides:

initialiseParticipantWrapper in class AbstractXmlInteraction<ModelledParticipant>

initialiseNamesContainer

protected void initialiseNamesContainer()

initialiseNamesContainer.

Overrides:

initialiseNamesContainer in class AbstractXmlInteraction<ModelledParticipant>

getInteractionNamesContainer

protected ComplexNamesContainer getInteractionNamesContainer()

Getter for the field interactionNamesContainer.

Overrides:

getInteractionNamesContainer in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a NamesContainer object.

getAttributeWrapper

protected XmlModelledInteraction.JAXBAttributeWrapper getAttributeWrapper()

getAttributeWrapper.

Overrides:

getAttributeWrapper in class AbstractXmlInteraction<ModelledParticipant>

Returns:

a XmlModelledInteraction.JAXBAttributeWrapper object.

initialiseAnnotationWrapper

protected void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.

Overrides:

initialiseAnnotationWrapper in class AbstractXmlInteraction<ModelledParticipant>