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

Class DefaultProtein

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.DefaultProtein

All Implemented Interfaces:

Interactor, Molecule, Polymer, Protein

Direct Known Subclasses:

CsvProtein, MitabProtein, XmlProtein, XmlProtein, XmlProtein

public class DefaultProtein
extends DefaultPolymer
implements Protein

Default implementation for proteins and peptides Notes: The equals and hashcode methods have NOT been overridden because the Protein object is a complex object. To compare Protein objects, you can use some comparators provided by default: - DefaultProteinComparator - UnambiguousProteinComparator - DefaultExactProteinComparator - UnambiguousExactProteinComparator - AvbstractProteinComparator

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.Polymer

POLYMER, POLYMER_MI

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

PEPTIDE, PEPTIDE_MI, PROTEIN, PROTEIN_MI

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToAliases()	clearPropertiesLinkedToAliases
protected void	clearPropertiesLinkedToChecksums()	clearPropertiesLinkedToChecksums
protected void	clearPropertiesLinkedToIdentifiers()	clearPropertiesLinkedToIdentifiers
String	getGeneName()	Getter for the field geneName.
Xref	getPreferredIdentifier()	getPreferredIdentifier
String	getPreferredName()	The preferred name is the name by which we want to refer the interactor on our web site.
String	getRefseq()	Getter for the field refseq.
String	getRogid()	Getter for the field rogid.
String	getUniprotkb()	Getter for the field uniprotkb.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseChecksums()	initialiseChecksums
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	processAddedAliasEvent(Alias added)	processAddedAliasEvent
protected void	processAddedChecksumEvent(Checksum added)	processAddedChecksumEvent
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processRemovedAliasEvent(Alias removed)	processRemovedAliasEvent
protected void	processRemovedChecksumEvent(Checksum removed)	processRemovedChecksumEvent
protected void	processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
void	setGeneName(String name)	Sets the gene name.
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	setRefseq(String ac)	Sets the unique refseq identifier for this protein.
void	setRogid(String rogid)	Sets the rogid.
void	setUniprotkb(String ac)	Sets the uniprot accession for this protein.
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, getShortName, getXrefs, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, 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, getShortName, getXrefs, setFullName, setOrganism, setShortName

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

getSequence, setSequence

Constructor Detail

DefaultProtein

public DefaultProtein(String name,
                      CvTerm type)

Constructor for DefaultProtein.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultProtein

public DefaultProtein(String name)

Constructor for DefaultProtein.

Parameters:

name - a String object.

DefaultProtein

public DefaultProtein(String name,
                      String fullName)

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

DefaultProtein

public DefaultProtein(String name,
                      Organism organism)

Constructor for DefaultProtein.

Parameters:

name - a String object.

organism - a Organism object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultProtein

public DefaultProtein(String name,
                      Xref uniqueId)

Constructor for DefaultProtein.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultProtein

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

Constructor for DefaultProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

Overrides:

initialiseIdentifiers in class DefaultInteractor

initialiseChecksums

protected void initialiseChecksums()

initialiseChecksums

Overrides:

initialiseChecksums in class DefaultInteractor

initialiseAliases

protected void initialiseAliases()

initialiseAliases

Overrides:

initialiseAliases in class DefaultInteractor

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

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

Overrides:

getPreferredName in class DefaultInteractor

Returns:

the preferred name

getUniprotkb

public String getUniprotkb()

Getter for the field uniprotkb.

Specified by:

getUniprotkb in interface Protein

Returns:

a String object.

setUniprotkb

public void setUniprotkb(String ac)

Sets the uniprot accession for this protein. It will remove the old uniprotkb identifier from the collection of identifiers and replace it with the new uniprokb identifier. If the new uniprotkb identifier is null, all the existing uniprotkb identifiers will be removed from the collection of identifiers

Specified by:

setUniprotkb in interface Protein

Parameters:

ac - : the uniprot accession

getRefseq

public String getRefseq()

Getter for the field refseq.

Specified by:

getRefseq in interface Protein

Returns:

a String object.

setRefseq

public void setRefseq(String ac)

Sets the unique refseq identifier for this protein. 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 Protein

Parameters:

ac - : refseq identifier

getGeneName

public String getGeneName()

Getter for the field geneName.

Specified by:

getGeneName in interface Protein

Returns:

a String object.

setGeneName

public void setGeneName(String name)

Sets the gene name. It will remove the old gene name from the collection of aliases and replace it with the new gene name. If the new gene name is null, all the existing gene names will be removed from the collection of aliases

Specified by:

setGeneName in interface Protein

Parameters:

name - : gene name

getRogid

public String getRogid()

Getter for the field rogid.

Specified by:

getRogid in interface Protein

Returns:

a String object.

setRogid

public void setRogid(String rogid)

Sets the rogid. It will remove the old rogid from the collection of checksums and replace it with the new rogid. If the new rogid is null, all the existing rogid will be removed from the collection of checksums

Specified by:

setRogid in interface Protein

Parameters:

rogid - : rogid

processAddedAliasEvent

protected void processAddedAliasEvent(Alias added)

processAddedAliasEvent

Parameters:

added - a Alias object.

processRemovedAliasEvent

protected void processRemovedAliasEvent(Alias removed)

processRemovedAliasEvent

Parameters:

removed - a Alias object.

clearPropertiesLinkedToAliases

protected void clearPropertiesLinkedToAliases()

clearPropertiesLinkedToAliases

processAddedChecksumEvent

protected void processAddedChecksumEvent(Checksum added)

processAddedChecksumEvent

Parameters:

added - a Checksum object.

processRemovedChecksumEvent

protected void processRemovedChecksumEvent(Checksum removed)

processRemovedChecksumEvent

Parameters:

removed - a Checksum object.

clearPropertiesLinkedToChecksums

protected void clearPropertiesLinkedToChecksums()

clearPropertiesLinkedToChecksums

processAddedIdentifierEvent

protected void processAddedIdentifierEvent(Xref added)

processAddedIdentifierEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

clearPropertiesLinkedToIdentifiers

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) Sets the interactor type of this polymer. If the given interactorType is null, it sets the interactorType to 'biopolymer'(MI:0383) Sets the interactor type of this protein. If the given interactorType is null, it will set the interactor type to 'protein' (MI:0326)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultPolymer

Parameters:

interactorType - : molecule type

toString

public String toString()

Overrides:

toString in class DefaultInteractor