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

Class DefaultNucleicAcid

java.lang.Object

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

psidev.psi.mi.jami.model.impl.DefaultMolecule

psidev.psi.mi.jami.model.impl.DefaultPolymer

psidev.psi.mi.jami.model.impl.DefaultNucleicAcid

All Implemented Interfaces:

Interactor, Molecule, NucleicAcid, Polymer

Direct Known Subclasses:

MitabNucleicAcid, XmlNucleicAcid, XmlNucleicAcid, XmlNucleicAcid

public class DefaultNucleicAcid
extends DefaultPolymer
implements NucleicAcid

Default implementation for NucleicAcid.

Notes: The equals and hashcode methods have NOT been overridden because the NucleicAcid object is a complex object. To compare NucleicAcid objects, you can use some comparators provided by default: - DefaultNucleicAcidComparator - UnambiguousNucleicAcidComparator - DefaultExactNucleicAcidComparator - UnambiguousExactNucleicAcidComparator - NucleicAcidComparator

Since:

01/02/13

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

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

NULCEIC_ACID, NULCEIC_ACID_MI

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

POLYMER, POLYMER_MI

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToIdentifiers()
String	getDdbjEmblGenbank()	Getter for the field ddbjEmblGenbank.
Xref	getPreferredIdentifier()	getPreferredIdentifier
String	getRefseq()	Getter for the field refseq.
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	processAddedIdentifiersEvent(Xref added)	processAddedIdentifiersEvent
protected void	processRemovedIdentifierEvent(Xref removed)
void	setDdbjEmblGenbank(String id)	Sets the DDBJ/EMBL/GemBank identifier.
void	setInteractorType(CvTerm interactorType)	Sets the interactor type of this NucleicAcid.
void	setRefseq(String id)	Sets the Refseq identifier.
String	toString()

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

getSequence, setSequence

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

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumsWith, initialiseIdentifiersWith, initialiseXrefs, 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.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

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

getSequence, setSequence

Constructor Detail

DefaultNucleicAcid

public DefaultNucleicAcid(String name,
                          CvTerm type)

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultNucleicAcid

public DefaultNucleicAcid(String name)

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

DefaultNucleicAcid

public DefaultNucleicAcid(String name,
                          String fullName)

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

DefaultNucleicAcid

public DefaultNucleicAcid(String name,
                          Organism organism)

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultNucleicAcid

public DefaultNucleicAcid(String name,
                          Xref uniqueId)

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultNucleicAcid

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

Constructor for DefaultNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

getPreferredIdentifier

public Xref getPreferredIdentifier()

getPreferredIdentifier

Specified by:

getPreferredIdentifier in interface Interactor

Overrides:

getPreferredIdentifier in class DefaultInteractor

Returns:

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

getDdbjEmblGenbank

public String getDdbjEmblGenbank()

Getter for the field ddbjEmblGenbank.

Specified by:

getDdbjEmblGenbank in interface NucleicAcid

Returns:

a String object.

setDdbjEmblGenbank

public void setDdbjEmblGenbank(String id)

Sets the DDBJ/EMBL/GemBank identifier. It will remove the old DDBJ/EMBL/GemBank identifier from the collection of identifiers and replace it with the new DDBJ/EMBL/GemBank identifier. If the new DDBJ/EMBL/GemBank identifier is null, all the existing DDBJ/EMBL/GemBank identifiers will be removed from the collection of identifiers

Specified by:

setDdbjEmblGenbank in interface NucleicAcid

Parameters:

id - : DDBJ/EMBL/GemBank identifier

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

Overrides:

initialiseIdentifiers in class DefaultInteractor

getRefseq

public String getRefseq()

Getter for the field refseq.

Specified by:

getRefseq in interface NucleicAcid

Returns:

a String object.

setRefseq

public void setRefseq(String id)

Sets the Refseq identifier. It will remove the old refseq identifier from the collection of identifiers and replace it with the new refseq identifier. If the new refseq identifier is null, all the existing refseq identifiers will be removed from the collection of identifiers

Specified by:

setRefseq in interface NucleicAcid

Parameters:

id - : Refseq identifier

processAddedIdentifiersEvent

protected void processAddedIdentifiersEvent(Xref added)

processAddedIdentifiersEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the interactor type of this NucleicAcid. If the interactor type is null, it will set the interactor type to nucleic acid (MI:0318)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultPolymer

Parameters:

interactorType - : molecule type

toString

public String toString()

Overrides:

toString in class DefaultInteractor