Package psidev.psi.mi.jami.model.impl

Class DefaultInteractor

java.lang.Object

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

All Implemented Interfaces:

Interactor

Direct Known Subclasses:

DefaultComplex, DefaultInteractorPool, DefaultMolecule, MitabInteractor

public class DefaultInteractor
extends Object
implements Interactor

Default implementation for Interactor Notes: The equals and hashcode methods have NOT been overridden because the Interactor object is a complex object. To compare Interactor objects, you can use some comparators provided by default: - DefaultInteractorBaseComparator - UnambiguousInteractorBaseComparator - DefaultExactInteractorBaseComparator - UnambiguousExactInteractorBaseComparator - DefaultInteractorComparator - UnambiguousInteractorComparator - DefaultExactInteractorComparator - UnambiguousExactInteractorComparator - AbstractInteractorBaseComparator

Since:

22/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	Getter for the field aliases.
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
Collection<Checksum>	getChecksums()	Getter for the field checksums.
String	getFullName()	Getter for the field fullName.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
CvTerm	getInteractorType()	Getter for the field interactorType.
Organism	getOrganism()	Getter for the field organism.
Xref	getPreferredIdentifier()	getPreferredIdentifier
String	getPreferredName()	The preferred name is the name by which we want to refer the interactor on our web site.
String	getShortName()	Getter for the field shortName.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseChecksums()	initialiseChecksums
protected void	initialiseChecksumsWith(Collection<Checksum> checksums)	initialiseChecksumsWith
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
void	setFullName(String name)	Sets the full name of the interactor
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	setShortName(String name)	Sets the short name of an interactor
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DefaultInteractor

public DefaultInteractor(String name,
                         CvTerm type)

Constructor for DefaultInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultInteractor

public DefaultInteractor(String name)

Constructor for DefaultInteractor.

Parameters:

name - a String object.

DefaultInteractor

public DefaultInteractor(String name,
                         String fullName)

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

DefaultInteractor

public DefaultInteractor(String name,
                         Organism organism)

Constructor for DefaultInteractor.

Parameters:

name - a String object.

organism - a Organism object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultInteractor

public DefaultInteractor(String name,
                         Xref uniqueId)

Constructor for DefaultInteractor.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultInteractor

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

Constructor for DefaultInteractor.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

initialiseChecksums

protected void initialiseChecksums()

initialiseChecksums

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

initialiseIdentifiersWith

protected void initialiseIdentifiersWith(Collection<Xref> identifiers)

initialiseIdentifiersWith

Parameters:

identifiers - a Collection object.

initialiseChecksumsWith

protected void initialiseChecksumsWith(Collection<Checksum> checksums)

initialiseChecksumsWith

Parameters:

checksums - a Collection object.

getShortName

public String getShortName()

Getter for the field shortName.

Specified by:

getShortName in interface Interactor

Returns:

a String object.

setShortName

public void setShortName(String name)

Sets the short name of an interactor

Specified by:

setShortName in interface Interactor

Parameters:

name - : short name

getFullName

public String getFullName()

Getter for the field fullName.

Specified by:

getFullName in interface Interactor

Returns:

a String object.

setFullName

public void setFullName(String name)

Sets the full name of the interactor

Specified by:

setFullName in interface Interactor

Parameters:

name - : full name

getIdentifiers

public Collection<Xref> getIdentifiers()

Getter for the field identifiers.

Specified by:

getIdentifiers in interface Interactor

Returns:

a Collection object.

getPreferredIdentifier

public Xref getPreferredIdentifier()

getPreferredIdentifier

Specified by:

getPreferredIdentifier in interface Interactor

Returns:

the first identifier in the list of identifiers or null if the list is empty

getPreferredName

public String getPreferredName()

Description copied from interface: Interactor

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

getChecksums

public Collection<Checksum> getChecksums()

Getter for the field checksums.

Specified by:

getChecksums in interface Interactor

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

getXrefs in interface Interactor

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface Interactor

Returns:

a Collection object.

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

getAliases in interface Interactor

Returns:

a Collection object.

getOrganism

public Organism getOrganism()

Getter for the field organism.

Specified by:

getOrganism in interface Interactor

Returns:

a Organism object.

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

toString

public String toString()

Overrides:

toString in class Object