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

Class XmlComplex

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

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

All Implemented Interfaces:

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

public class XmlComplex
extends AbstractXmlComplex

Xml implementation of ModelledInteraction

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

Method Summary

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

assignComplexAc, assignComplexAc, getAliases, getAnnotations, getChecksums, getComplexAc, getComplexVersion, getIdentifiers, getInteractorType, getOrganism, getPhysicalProperties, getPreferredIdentifier, getPreferredName, getRecommendedName, getSystematicName, getXrefs, setId, setInteractionXrefContainer, setInteractorType, setOrganism, setPhysicalProperties, setRecommendedName, setSystematicName, 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

XmlComplex

public XmlComplex()

Constructor for XmlComplex.

XmlComplex

public XmlComplex(String name,
                  CvTerm type)

Constructor for XmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlComplex

public XmlComplex(String name,
                  Xref uniqueId)

Constructor for XmlComplex.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlComplex

public XmlComplex(String name,
                  Organism organism)

Constructor for XmlComplex.

Parameters:

name - a String object.

organism - a Organism object.

XmlComplex

public XmlComplex(String name,
                  String fullName)

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

XmlComplex

public XmlComplex(String name)

Constructor for XmlComplex.

Parameters:

name - a String object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlComplex

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

Constructor for XmlComplex.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.