Package ubic.gemma.web.controller

Class PhenotypeController

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.PhenotypeController

@Controller
public class PhenotypeController
extends BaseController

Controller for phenotype

Author:

frances

Field Summary

Fields inherited from class ubic.gemma.web.controller.BaseController

log

Constructor Summary

Constructors

Constructor	Description
PhenotypeController()

Method Summary

Modifier and Type	Method	Description
Collection<ExternalDatabaseStatisticsValueObject>	calculateExternalDatabasesStatistics()
Collection<BibliographicReferenceValueObject>	findBibliographicReference(String pubMedId, Long evidenceId)	Finds bibliographic reference with the given pubmed id.
Collection<GeneEvidenceValueObject>	findCandidateGenes(Long taxonId, boolean showOnlyEditable, Collection<Long> databaseIds, String[] phenotypes)
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	findEvidenceByFilters(Long taxonId, Integer limit, String userName)
Collection<UserValueObject>	findEvidenceOwners()	Returns a collection of users who own evidence.
Collection<CharacteristicValueObject>	findExperimentCategory()	Returns available efo category terms.
Collection<CharacteristicValueObject>	findExperimentOntologyValue(String givenQueryString, String categoryUri, Long taxonId)
Collection<ExternalDatabaseValueObject>	findExternalDatabaseName()
Collection<SimpleTreeValueObject>	loadAllPhenotypesByTree(Long taxonId, boolean showOnlyEditable, Collection<Long> databaseIds)
ValidateEvidenceValueObject	makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, SortedSet<CharacteristicValueObject> phenotypes, Double selectionThreshold)
ValidateEvidenceValueObject	processPhenotypeAssociationForm(EvidenceValueObject<?> evidenceValueObject)
ValidateEvidenceValueObject	removeAllEvidenceFromMetaAnalysis(Long metaAnalysisId)
ValidateEvidenceValueObject	removePhenotypeAssociation(Long evidenceId)
Collection<CharacteristicValueObject>	searchOntologyForPhenotypes(String query, Long geneId)	Returns all phenotypes satisfied the given search criteria.
ModelAndView	showAllPhenotypes(javax.servlet.http.HttpServletRequest request)
ModelAndView	showNeurocartaStatistics()
ModelAndView	showPhenotypeAssociationManager()
ValidateEvidenceValueObject	validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation> evidenceValueObject)

Methods inherited from class ubic.gemma.web.controller.BaseController

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMailEngine, setMessageSource, setMessageUtil

Methods inherited from class java.lang.Object

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

Constructor Detail

PhenotypeController

public PhenotypeController()

Method Detail

calculateExternalDatabasesStatistics

public Collection<ExternalDatabaseStatisticsValueObject> calculateExternalDatabasesStatistics()

findBibliographicReference

public Collection<BibliographicReferenceValueObject> findBibliographicReference(String pubMedId,
                                                                                Long evidenceId)

Finds bibliographic reference with the given pubmed id.

Returns:

bibliographic reference with the given pubmed id

findCandidateGenes

public Collection<GeneEvidenceValueObject> findCandidateGenes(Long taxonId,
                                                              boolean showOnlyEditable,
                                                              Collection<Long> databaseIds,
                                                              String[] phenotypes)

Parameters:

showOnlyEditable - show only editable

taxonId - taxon id

databaseIds - db ids

phenotypes - phenotypes

Returns:

all genes that have given phenotypes.

findEvidenceByFilters

public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByFilters(Long taxonId,
                                                                                             Integer limit,
                                                                                             String userName)

findEvidenceOwners

public Collection<UserValueObject> findEvidenceOwners()

Returns a collection of users who own evidence. Note that a collection of value objects instead of strings is returned for front end convenience.

Returns:

a collection of users who own evidence

findExperimentCategory

public Collection<CharacteristicValueObject> findExperimentCategory()

Returns available efo category terms.

Returns:

Collection

findExperimentOntologyValue

public Collection<CharacteristicValueObject> findExperimentOntologyValue(String givenQueryString,
                                                                         String categoryUri,
                                                                         Long taxonId)
                                                                  throws SearchException

Throws:

SearchException

findExternalDatabaseName

public Collection<ExternalDatabaseValueObject> findExternalDatabaseName()

loadAllPhenotypesByTree

public Collection<SimpleTreeValueObject> loadAllPhenotypesByTree(Long taxonId,
                                                                 boolean showOnlyEditable,
                                                                 Collection<Long> databaseIds)

Parameters:

showOnlyEditable - show only editable

taxonId - taxon id

databaseIds - db ids

Returns:

the big 'tree' data structure shown in phenocarta's page.

makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis

public ValidateEvidenceValueObject makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId,
                                                                                                     SortedSet<CharacteristicValueObject> phenotypes,
                                                                                                     Double selectionThreshold)

processPhenotypeAssociationForm

public ValidateEvidenceValueObject processPhenotypeAssociationForm(EvidenceValueObject<?> evidenceValueObject)

removeAllEvidenceFromMetaAnalysis

public ValidateEvidenceValueObject removeAllEvidenceFromMetaAnalysis(Long metaAnalysisId)

removePhenotypeAssociation

public ValidateEvidenceValueObject removePhenotypeAssociation(Long evidenceId)

searchOntologyForPhenotypes

public Collection<CharacteristicValueObject> searchOntologyForPhenotypes(String query,
                                                                         Long geneId)
                                                                  throws SearchException

Returns all phenotypes satisfied the given search criteria.

Returns:

Collection of phenotypes

Throws:

SearchException

showAllPhenotypes

public ModelAndView showAllPhenotypes(javax.servlet.http.HttpServletRequest request)

showNeurocartaStatistics

public ModelAndView showNeurocartaStatistics()

showPhenotypeAssociationManager

public ModelAndView showPhenotypeAssociationManager()

validatePhenotypeAssociationForm

public ValidateEvidenceValueObject validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation> evidenceValueObject)