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

Class AbstractXmlComplex

java.lang.Object

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

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

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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

DefaultXmlComplex, XmlComplex

public abstract class AbstractXmlComplex
extends AbstractXmlModelledInteraction
implements Complex, ExtendedPsiXmlInteractor

Xml implementation for complex

Since:

08/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

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

AbstractXmlModelledInteraction.JAXBConfidenceWrapper, AbstractXmlModelledInteraction.JAXBExperimentWrapper, AbstractXmlModelledInteraction.JAXBParameterWrapper, AbstractXmlModelledInteraction.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.AbstractXmlModelledInteraction

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
AbstractXmlComplex()	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Organism organism)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Organism organism)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Organism organism)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Xref uniqueId)	Constructor for AbstractXmlComplex.

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.
Collection<Checksum>	getChecksums()	getChecksums.
String	getComplexAc()	Gets the value of the complexAc property.
String	getComplexVersion()	Gets the value of the complexVersion property.
Collection<Xref>	getIdentifiers()	getIdentifiers.
CvTerm	getInteractorType()	The molecule type of this interactor.
Organism	getOrganism()	The original source organism for this interactor.
String	getPhysicalProperties()	The physical properties for this complex.
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()	The recommended name of a complex.
String	getSystematicName()	The systematic name of a complex.
Collection<Xref>	getXrefs()	getXrefs.
void	setId(int value)	Sets the value of the id property.
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	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	setSystematicName(String name)	Sets the systematic name of this complex.
String	toString()	toString

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

getCooperativeEffects, getEvidenceType, getExperiments, getInteractionEvidences, getInteractionTypes, getModelledConfidences, getModelledParameters, getSource, getSourceLocator, initialiseCooperativeEffects, initialiseInteractionEvidences, initialiseModelledConfidenceWrapper, initialiseModelledParameterWrapper, initialiseParticipantWrapper, setEvidenceType, setInteractionNamesContainer, setJAXBAttributeWrapper, setJAXBConfidenceWrapper, setJAXBExperimentWrapper, setJAXBId, setJAXBInferredInteractionWrapper, setJAXBIntraMolecular, setJAXBParameterWrapper, setJAXBParticipantWrapper, setSource

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, assignImexId, getAttributeWrapper, getCreatedDate, getEntry, getFullName, getId, getImexId, getInteractionNamesContainer, getInteractionXrefContainer, getParticipants, getRigid, getShortName, getUpdatedDate, initialiseAnnotationWrapper, initialiseNamesContainer, isIntraMolecular, processAddedParticipant, removeAllParticipants, removeParticipant, setCreatedDate, setEntry, setFullName, setIntraMolecular, setParticipantWrapper, setRigid, setShortName, setSourceLocator, setUpdatedDate, sourceLocation

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.xml.model.extension.ExtendedPsiXmlInteraction

getInferredInteractions

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

getId

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

setSourceLocator

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

addAllParticipants, addParticipant, getCreatedDate, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, 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.ModelledInteraction

getCooperativeEffects, getEvidenceType, getInteractionEvidences, getModelledConfidences, getModelledParameters, getSource, setEvidenceType, setSource

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, setIntraMolecular

Constructor Detail

AbstractXmlComplex

public AbstractXmlComplex()

Constructor for AbstractXmlComplex.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          CvTerm type)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          CvTerm type)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          CvTerm type,
                          Organism organism)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          CvTerm type,
                          Organism organism)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          CvTerm type,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          CvTerm type,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          CvTerm type,
                          Organism organism,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          CvTerm type,
                          Organism organism,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          Organism organism)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

organism - a Organism object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          Organism organism)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          Organism organism,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractXmlComplex

public AbstractXmlComplex(String name,
                          String fullName,
                          Organism organism,
                          Xref uniqueId)

Constructor for AbstractXmlComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

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

setId

public void setId(int value)

Sets the value of the id property. Sets the value of the id property.

Specified by:

setId in interface ExtendedPsiXmlInteractor

Specified by:

setId in interface PsiXmlInteraction<ModelledParticipant>

Overrides:

setId in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

value - a int.

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)

Sets the value of the complexAc property

Specified by:

assignComplexAc in interface Complex

Overrides:

assignComplexAc in class AbstractXmlInteraction<ModelledParticipant>

Parameters:

accession - 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

getPhysicalProperties

public String getPhysicalProperties()

The physical properties for this complex. It is a shortcut which should point to the first complex-properties annotation in the collection of annotations. Example: Molecular mass = 154 kDa

Specified by:

getPhysicalProperties in interface Complex

Returns:

the properties

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()

The recommended name of a complex. It is a shortcut which should point to the first complex recommended name alias in the collection of aliases.

Specified by:

getRecommendedName in interface Complex

Returns:

the recommended name

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()

The systematic name of a complex. It is a shortcut which should point to the first complex systematic name alias in the collection of aliases.

Specified by:

getSystematicName in interface Complex

Returns:

the systematic name

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()

The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: protein, gene, small molecule, ...

Specified by:

getInteractorType in interface Interactor

Returns:

interactor type

setInteractionXrefContainer

public void setInteractionXrefContainer(InteractionXrefContainer value)

Sets the value of the interactionXrefContainer property.

Overrides:

setInteractionXrefContainer in class AbstractXmlModelledInteraction

Parameters:

value - allowed object is InteractionXrefContainer

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractXmlInteraction<ModelledParticipant>

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

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 ExtendedPsiXmlInteraction<ModelledParticipant>

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

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.

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.

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.

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.