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

Class DefaultCvTerm

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultCvTerm

All Implemented Interfaces:

CvTerm

Direct Known Subclasses:

DefaultOntologyTerm, DefaultSource, LazyCvTerm, MitabCvTerm

public class DefaultCvTerm
extends Object
implements CvTerm

Default implementation for CvTerm Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparator

Since:

21/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

PSI_MI, PSI_MI_MI, PSI_MOD, PSI_MOD_MI, PSI_PAR

Constructor Summary

Constructors

Constructor	Description
DefaultCvTerm(String shortName)	Constructor for DefaultCvTerm.
DefaultCvTerm(String shortName, String miIdentifier)	Constructor for DefaultCvTerm.
DefaultCvTerm(String shortName, String fullName, String miIdentifier)	Constructor for DefaultCvTerm.
DefaultCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultCvTerm.
DefaultCvTerm(String shortName, Xref ontologyId)	Constructor for DefaultCvTerm.

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToIdentifiers()	clearPropertiesLinkedToIdentifiers
boolean	equals(Object o)
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
String	getFullName()	Getter for the field fullName.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
String	getMIIdentifier()	getMIIdentifier
String	getMODIdentifier()	getMODIdentifier
String	getPARIdentifier()	getPARIdentifier
String	getShortName()	Getter for the field shortName.
Collection<Alias>	getSynonyms()	Getter for the field synonyms.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
int	hashCode()
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	initialiseSynonyms()	initialiseSynonyms
protected void	initialiseSynonymsWith(Collection<Alias> aliases)	initialiseSynonymsWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
void	setFullName(String name)	Set the full name
void	setMIIdentifier(String mi)	Sets the PSI-MI identifier.
void	setMODIdentifier(String mod)	Sets the PSI-MOD identifier.
void	setPARIdentifier(String par)	Sets the PSI-PAR identifier.
void	setShortName(String name)	Set the short name
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

DefaultCvTerm

public DefaultCvTerm(String shortName)

Constructor for DefaultCvTerm.

Parameters:

shortName - a String object.

DefaultCvTerm

public DefaultCvTerm(String shortName,
                     String miIdentifier)

Constructor for DefaultCvTerm.

Parameters:

shortName - a String object.

miIdentifier - a String object.

DefaultCvTerm

public DefaultCvTerm(String shortName,
                     String fullName,
                     String miIdentifier)

Constructor for DefaultCvTerm.

Parameters:

shortName - a String object.

fullName - a String object.

miIdentifier - a String object.

DefaultCvTerm

public DefaultCvTerm(String shortName,
                     Xref ontologyId)

Constructor for DefaultCvTerm.

Parameters:

shortName - a String object.

ontologyId - a Xref object.

DefaultCvTerm

public DefaultCvTerm(String shortName,
                     String fullName,
                     Xref ontologyId)

Constructor for DefaultCvTerm.

Parameters:

shortName - a String object.

fullName - a String object.

ontologyId - a Xref object.

Method Detail

getShortName

public String getShortName()

Getter for the field shortName.

Specified by:

getShortName in interface CvTerm

Returns:

a String object.

setShortName

public void setShortName(String name)

Set the short name

Specified by:

setShortName in interface CvTerm

Parameters:

name - : short name

getFullName

public String getFullName()

Getter for the field fullName.

Specified by:

getFullName in interface CvTerm

Returns:

a String object.

setFullName

public void setFullName(String name)

Set the full name

Specified by:

setFullName in interface CvTerm

Parameters:

name - : full name

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseSynonyms

protected void initialiseSynonyms()

initialiseSynonyms

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

initialiseSynonymsWith

protected void initialiseSynonymsWith(Collection<Alias> aliases)

initialiseSynonymsWith

Parameters:

aliases - a Collection object.

initialiseIdentifiersWith

protected void initialiseIdentifiersWith(Collection<Xref> identifiers)

initialiseIdentifiersWith

Parameters:

identifiers - a Collection object.

getIdentifiers

public Collection<Xref> getIdentifiers()

Getter for the field identifiers.

Specified by:

getIdentifiers in interface CvTerm

Returns:

a Collection object.

getMIIdentifier

public String getMIIdentifier()

getMIIdentifier

Specified by:

getMIIdentifier in interface CvTerm

Returns:

a String object.

getMODIdentifier

public String getMODIdentifier()

getMODIdentifier

Specified by:

getMODIdentifier in interface CvTerm

Returns:

a String object.

getPARIdentifier

public String getPARIdentifier()

getPARIdentifier

Specified by:

getPARIdentifier in interface CvTerm

Returns:

a String object.

setMIIdentifier

public void setMIIdentifier(String mi)

Sets the PSI-MI identifier. It will remove the previous PSI-MI identifier from the collection of identifiers, and add the new one in the collection of identifiers with qualifier identity. If mi is null, it will remove all the psi-mi identifiers from the collection of identifiers.

Specified by:

setMIIdentifier in interface CvTerm

Parameters:

mi - : mi identifier

setMODIdentifier

public void setMODIdentifier(String mod)

Sets the PSI-MOD identifier. It will remove the previous PSI-MOD identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If mod is null, it will remove all the psi-mod identifiers from the collection of identifiers.

Specified by:

setMODIdentifier in interface CvTerm

Parameters:

mod - : mod identifier

setPARIdentifier

public void setPARIdentifier(String par)

Sets the PSI-PAR identifier. It will remove the previous PSI-PAR identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If par is null, it will remove all the psi-par identifiers from the collection of identifiers.

Specified by:

setPARIdentifier in interface CvTerm

Parameters:

par - : par identifier

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

getXrefs in interface CvTerm

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface CvTerm

Returns:

a Collection object.

getSynonyms

public Collection<Alias> getSynonyms()

Getter for the field synonyms.

Specified by:

getSynonyms in interface CvTerm

Returns:

a Collection object.

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

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object