Package ubic.gemma.core.association.phenotype

Class PhenotypeAssoOntologyHelperImpl

java.lang.Object

ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl

All Implemented Interfaces:

PhenotypeAssoOntologyHelper

@Component
@Deprecated
public class PhenotypeAssoOntologyHelperImpl
extends Object
implements PhenotypeAssoOntologyHelper

Deprecated.

Author:

nicolas

Constructor Summary

Constructors

Constructor	Description
PhenotypeAssoOntologyHelperImpl(OntologyService ontologyService, MondoOntologyService diseaseOntologyService, MammalianPhenotypeOntologyService mammalianPhenotypeOntologyService, HumanPhenotypeOntologyService humanPhenotypeOntologyService)	Deprecated.

Method Summary

Modifier and Type	Method	Description
Characteristic	characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)	Deprecated. CharacteristicValueObject to Characteristic with no valueUri given
OntologyTerm	findOntologyTermByUri(String valueUri)	Deprecated. For a valueUri return the OntologyTerm found
Set<CharacteristicValueObject>	findPhenotypesInOntology(String searchQuery)	Deprecated. search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
Collection<OntologyTerm>	findValueUriInOntology(String searchQuery)	Deprecated. search the disease, hp and mp ontology for OntologyTerm
Collection<OntologyService>	getOntologyServices()	Deprecated. Returns the ontology services this helper is using.
Characteristic	valueUri2Characteristic(String valueUri)	Deprecated. Helper method.

Methods inherited from class java.lang.Object

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

Constructor Detail

PhenotypeAssoOntologyHelperImpl

@Autowired
public PhenotypeAssoOntologyHelperImpl(OntologyService ontologyService,
                                       MondoOntologyService diseaseOntologyService,
                                       MammalianPhenotypeOntologyService mammalianPhenotypeOntologyService,
                                       HumanPhenotypeOntologyService humanPhenotypeOntologyService)

Deprecated.

Method Detail

getOntologyServices

public Collection<OntologyService> getOntologyServices()

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

Returns the ontology services this helper is using.

Specified by:

getOntologyServices in interface PhenotypeAssoOntologyHelper

characteristicValueObject2Characteristic

public Characteristic characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

CharacteristicValueObject to Characteristic with no valueUri given

Specified by:

characteristicValueObject2Characteristic in interface PhenotypeAssoOntologyHelper

Parameters:

characteristicValueObject - characteristic VO

Returns:

vocab characteristic

findOntologyTermByUri

public OntologyTerm findOntologyTermByUri(String valueUri)

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

For a valueUri return the OntologyTerm found

Specified by:

findOntologyTermByUri in interface PhenotypeAssoOntologyHelper

Parameters:

valueUri - value uri

Returns:

ontology term

findPhenotypesInOntology

public Set<CharacteristicValueObject> findPhenotypesInOntology(String searchQuery)
                                                        throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO

Specified by:

findPhenotypesInOntology in interface PhenotypeAssoOntologyHelper

Parameters:

searchQuery - query

Returns:

characteristic VOs

Throws:

SearchException

findValueUriInOntology

public Collection<OntologyTerm> findValueUriInOntology(String searchQuery)
                                                throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

search the disease, hp and mp ontology for OntologyTerm

Specified by:

findValueUriInOntology in interface PhenotypeAssoOntologyHelper

Parameters:

searchQuery - free text query?

Returns:

terms

Throws:

SearchException

valueUri2Characteristic

public Characteristic valueUri2Characteristic(String valueUri)

Deprecated.

Description copied from interface: PhenotypeAssoOntologyHelper

Helper method. For a valueUri return the Characteristic (represents a phenotype)

Specified by:

valueUri2Characteristic in interface PhenotypeAssoOntologyHelper

Parameters:

valueUri - value uri

Returns:

Characteristic