Package psidev.psi.mi.jami.bridges.ols

Class LazyCvTerm

java.lang.Object

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

psidev.psi.mi.jami.bridges.ols.LazyCvTerm

All Implemented Interfaces:

CvTerm

Direct Known Subclasses:

LazyOntologyTerm, LazySource

public class LazyCvTerm
extends DefaultCvTerm

A lazy cvTerm which will only fetch metadata when required.

Since:

14/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
protected Logger	log

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
LazyCvTerm(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient olsClient, String fullName, Xref identityRef, String ontologyName)	Constructor for LazyCvTerm.

Method Summary

Modifier and Type	Method	Description
Collection<Annotation>	getAnnotations()	getAnnotations.
protected uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient	getOlsClient()	Getter for the field olsClient.
protected String	getOntologyName()	Getter for the field ontologyName.
protected Xref	getOriginalXref()	Getter for the field originalXref.
String	getShortName()	Getter for the field shortName.
Collection<Alias>	getSynonyms()	getSynonyms.
Collection<Xref>	getXrefs()	getXrefs.
protected boolean	hasLoadedMetadata()	hasLoadedMetadata.
protected boolean	hasLoadedXrefs()	hasLoadedXrefs.
protected void	initialiseDefinition(String description)	initialiseDefinition.
protected void	initialiseMetaData(Xref xref)	Retrieve the metadata for an entry.
void	setShortName(String name)	Set the short name
String	toString()

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

clearPropertiesLinkedToIdentifiers, equals, getFullName, getIdentifiers, getMIIdentifier, getMODIdentifier, getPARIdentifier, hashCode, initialiseAnnotations, initialiseAnnotationsWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseSynonyms, initialiseSynonymsWith, initialiseXrefs, initialiseXrefsWith, processAddedIdentifierEvent, processRemovedIdentifierEvent, setFullName, setMIIdentifier, setMODIdentifier, setPARIdentifier

Methods inherited from class java.lang.Object

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

Field Detail

log

protected final Logger log

Constructor Detail

LazyCvTerm

public LazyCvTerm(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient olsClient,
                  String fullName,
                  Xref identityRef,
                  String ontologyName)

Constructor for LazyCvTerm.

Parameters:

olsClient - a OLSClient object.

fullName - a String object.

identityRef - a Xref object.

ontologyName - a String object.

Method Detail

getShortName

public String getShortName()

Getter for the field shortName.

If the shortName is not yet known, a query will be made to OLS. If no shortName is found, the fullName is used instead.

Specified by:

getShortName in interface CvTerm

Overrides:

getShortName in class DefaultCvTerm

Returns:

a String object.

setShortName

public void setShortName(String name)

Set the short name

Specified by:

setShortName in interface CvTerm

Overrides:

setShortName in class DefaultCvTerm

Parameters:

name - : short name

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface CvTerm

Overrides:

getXrefs in class DefaultCvTerm

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface CvTerm

Overrides:

getAnnotations in class DefaultCvTerm

Returns:

a Collection object.

getSynonyms

public Collection<Alias> getSynonyms()

getSynonyms.

Specified by:

getSynonyms in interface CvTerm

Overrides:

getSynonyms in class DefaultCvTerm

Returns:

a Collection object.

toString

public String toString()

Overrides:

toString in class DefaultCvTerm

getOriginalXref

protected Xref getOriginalXref()

Getter for the field originalXref.

Returns:

a Xref object.

getOntologyName

protected String getOntologyName()

Getter for the field ontologyName.

Returns:

a String object.

getOlsClient

protected uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient getOlsClient()

Getter for the field olsClient.

Returns:

a OLSClient object.

initialiseMetaData

protected void initialiseMetaData(Xref xref)

Retrieve the metadata for an entry.

The identifier is used to find the metadata which can be used to find the identifier phrases for short labels and synonyms.

Parameters:

xref - The identifier that is being used.

initialiseDefinition

protected void initialiseDefinition(String description)

initialiseDefinition.

Parameters:

description - a String object.

hasLoadedMetadata

protected boolean hasLoadedMetadata()

hasLoadedMetadata.

Returns:

a boolean.

hasLoadedXrefs

protected boolean hasLoadedXrefs()

hasLoadedXrefs.

Returns:

a boolean.