Package psidev.psi.mi.jami.tab.extension

Class MitabComplex

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultInteractor

psidev.psi.mi.jami.model.impl.DefaultComplex

psidev.psi.mi.jami.tab.extension.MitabComplex

All Implemented Interfaces:

FileSourceContext, Complex, Interaction<ModelledParticipant>, Interactor, ModelledInteraction, NamedInteraction<ModelledParticipant>

public class MitabComplex
extends DefaultComplex
implements FileSourceContext

Mitab extension for Complex. It contains a FileSourceLocator

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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
MitabComplex(String name)	Constructor for MitabComplex.
MitabComplex(String name, String fullName)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, CvTerm interactorType)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, CvTerm interactorType, Organism organism)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, CvTerm interactorType, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, Organism organism)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType, Organism organism)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, Organism organism)	Constructor for MitabComplex.
MitabComplex(String name, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, Xref uniqueId)	Constructor for MitabComplex.

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultComplex

addAllParticipants, addParticipant, assignComplexAc, assignComplexAc, clearPropertiesLinkedToAliases, clearPropertiesLinkedToAnnotations, clearPropertiesLinkedToChecksums, clearPropertiesLinkedToXrefs, getAliases, getAnnotations, getChecksums, getComplexAc, getComplexVersion, getCooperativeEffects, getCreatedDate, getEvidenceType, getIdentifiers, getInteractionEvidences, getInteractionType, getModelledConfidences, getModelledParameters, getParticipants, getPhysicalProperties, getRecommendedName, getRigid, getSource, getSystematicName, getUpdatedDate, getXrefs, initialiseAliases, initialiseAnnotations, initialiseChecksums, initialiseComponents, initialiseComponentsWith, initialiseConfidences, initialiseConfidencesWith, initialiseCooperativeEffects, initialiseCooperativeEffectsWith, initialiseInteractionEvidences, initialiseInteractionEvidencesWith, initialiseParameters, initialiseParametersWith, initialiseXrefs, processAddedAliasEvent, processAddedAnnotationEvent, processAddedChecksumEvent, processAddedXrefEvent, processRemovedAliasEvent, processRemovedAnnotationEvent, processRemovedChecksumEvent, processRemovedXrefEvent, removeAllParticipants, removeParticipant, setCreatedDate, setEvidenceType, setInteractionType, setInteractorType, setPhysicalProperties, setRecommendedName, setRigid, setSource, setSystematicName, setUpdatedDate

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultInteractor

getFullName, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, initialiseAliasesWith, initialiseAnnotationsWith, initialiseChecksumsWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseXrefsWith, setFullName, setOrganism, setShortName

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.model.Interaction

getShortName, setShortName

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

getFullName, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, setFullName, setOrganism, setShortName

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

getFullName, setFullName

Constructor Detail

MitabComplex

public MitabComplex(String name,
                    CvTerm interactorType)

Constructor for MitabComplex.

Parameters:

name - a String object.

interactorType - a CvTerm object.

MitabComplex

public MitabComplex(String name,
                    String fullName,
                    CvTerm interactorType)

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

interactorType - a CvTerm object.

MitabComplex

public MitabComplex(String name,
                    CvTerm interactorType,
                    Organism organism)

Constructor for MitabComplex.

Parameters:

name - a String object.

interactorType - a CvTerm object.

organism - a Organism object.

MitabComplex

public MitabComplex(String name,
                    String fullName,
                    CvTerm interactorType,
                    Organism organism)

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

interactorType - a CvTerm object.

organism - a Organism object.

MitabComplex

public MitabComplex(String name,
                    CvTerm interactorType,
                    Xref uniqueId)

Constructor for MitabComplex.

Parameters:

name - a String object.

interactorType - a CvTerm object.

uniqueId - a Xref object.

MitabComplex

public MitabComplex(String name,
                    String fullName,
                    CvTerm interactorType,
                    Xref uniqueId)

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

interactorType - a CvTerm object.

uniqueId - a Xref object.

MitabComplex

public MitabComplex(String name,
                    CvTerm interactorType,
                    Organism organism,
                    Xref uniqueId)

Constructor for MitabComplex.

Parameters:

name - a String object.

interactorType - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabComplex

public MitabComplex(String name,
                    String fullName,
                    CvTerm interactorType,
                    Organism organism,
                    Xref uniqueId)

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

interactorType - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabComplex

public MitabComplex(String name)

Constructor for MitabComplex.

Parameters:

name - a String object.

MitabComplex

public MitabComplex(String name,
                    String fullName)

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

MitabComplex

public MitabComplex(String name,
                    Organism organism)

Constructor for MitabComplex.

Parameters:

name - a String object.

organism - a Organism object.

MitabComplex

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

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

MitabComplex

public MitabComplex(String name,
                    Xref uniqueId)

Constructor for MitabComplex.

Parameters:

name - a String object.

uniqueId - a Xref object.

MitabComplex

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

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

MitabComplex

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

Constructor for MitabComplex.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabComplex

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

Constructor for MitabComplex.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultComplex

Returns:

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