Deprecated API

Contents

• Interfaces
• Classes
• Fields
• Methods
• Enum Constants

Interfaces

Interface	Description
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao	as Person is deprecated

Classes

Class	Description
ubic.gemma.apps.ArrayDesignProbeRenamerCli	renaming probes is not a good idea in general
ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli	use DifferentialExpressionAnalysisWriterCli instead.
ubic.gemma.apps.FactorValueMigratorCLI	this will be removed as soon as all the old-style characteristics are migrated
ubic.gemma.apps.MeshTermFetcherCli	should not be part of Gemma main code
ubic.gemma.apps.RNASeqBatchInfoCli	this should not be necessary and the regular batch population tool can be used instead.
ubic.gemma.core.config.PropertySourcesConfiguration	This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
ubic.gemma.core.config.Settings	This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent	this event type was used by the auto-tagger, which has been removed. This event type has been kept so that the audit-trails can still properly display these events, but creation new events of this type should not occur.
ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent	use BatchInformationMissingEvent
ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent
ubic.gemma.model.common.auditAndSecurity.Person	not needed
ubic.gemma.model.expression.experiment.FactorValueValueObject	aim towards using the FactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl	as Person is deprecated
ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl
ubic.gemma.rest.serializers.FactorValueValueObjectSerializer
ubic.gemma.rest.util.args.FactorValueValueArg
ubic.gemma.web.controller.util.upload.CommonsMultipartFile

Fields

Field	Description
ubic.gemma.rest.util.args.FilterArgLexer.tokenNames	Use FilterArgLexer.VOCABULARY instead.
ubic.gemma.rest.util.args.FilterArgParser.tokenNames	Use FilterArgParser.VOCABULARY instead.

Methods

Method	Description
ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject.trim()	because this is too ad hoc and messy
ubic.gemma.core.context.SpringContextUtils.getApplicationContext(boolean, boolean, String[])	this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtils.getApplicationContext(String[], String...) instead.
ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix.set(int, int, Double)
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix.getRowElement(int)	use ExpressionDataMatrix.getDesignElementForRow(int) instead
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix.getRowElements()	use ExpressionDataMatrix.getDesignElements() instead
ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix.getRowElement(int)
ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix.getRowElements()
ubic.gemma.core.ontology.OntologyConfig.humanDevelopmentOntologyServiceOntologyService(TaskExecutor)
ubic.gemma.core.ontology.OntologyService.findExperimentsCharacteristicTags(String, int, boolean, long, TimeUnit)
ubic.gemma.core.search.SearchSource.searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>)	use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
ubic.gemma.core.search.SearchSource.searchCompositeSequenceAndGene(SearchSettings)	use SearchSource.searchCompositeSequence(SearchSettings) instead
ubic.gemma.core.search.source.CompositeSearchSource.searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>)
ubic.gemma.core.search.source.CompositeSearchSource.searchCompositeSequenceAndGene(SearchSettings)
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getBioAssaySetId()	use #getExperimentAnalyzedId() instead
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getFactorValuesUsed()	This was renamed for clarity.
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getSourceExperiment()	use #getSourceExperimentId() instead
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getDownregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getUpregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isEditable()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isOwnedByCurrentUser()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isPublic()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isShared()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setEditable(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setOwnedByCurrentUser(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setPublic(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setShared(boolean)
ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject.getActionName()
ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType.getId()	you should never use this property, rely instead on the actual type via Object.getClass().
ubic.gemma.model.common.description.BibliographicReference.getAnnotatedAbstract()
ubic.gemma.model.common.description.BibliographicReference.getAnnotations()
ubic.gemma.model.common.description.BibliographicReference.setAnnotatedAbstract(String)
ubic.gemma.model.common.description.BibliographicReference.setAnnotations(Set<Characteristic>)
ubic.gemma.model.common.description.Characteristic.isMigratedToStatement()
ubic.gemma.model.common.description.Characteristic.setMigratedToStatement(boolean)
ubic.gemma.model.common.description.DatabaseEntry.getUri()
ubic.gemma.model.common.description.DatabaseEntry.setUri(String)
ubic.gemma.model.common.quantitationtype.QuantitationType.getIsMaskedPreferred()
ubic.gemma.model.common.quantitationtype.QuantitationType.setIsMaskedPreferred(boolean)
ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject.getIsMaskedPreferred()
ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject.setIsMaskedPreferred(boolean)
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getExpressionExperimentCount()	use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getTaxonID()	use #getTaxonObject() instead
ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject.getDescription()
ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject.getName()
ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject.setDescription(String)
ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject.setName(String)
ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.getCharacteristics()	Use #getCellTypes() instead.
ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.getIndices()	Use #getCellTypeIndices() instead.
ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.getNumberOfCharacteristics()	Use #getNumberOfCellTypes() instead.
ubic.gemma.model.expression.biomaterial.BioMaterialValueObject.getFactorValueObjects()	use BioMaterialValueObject.getFactorValues()
ubic.gemma.model.expression.experiment.ExperimentalFactor.getAnnotations()
ubic.gemma.model.expression.experiment.ExperimentalFactor.setAnnotations(Set<Characteristic>)
ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject.getSourceExperiment()	use #getSourceExperimentId() instead
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getBioAssayCount()	use BioAssaySetValueObject.getNumberOfBioAssays() instead.
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getTaxonId()	use #getTaxonObject() instead
ubic.gemma.model.expression.experiment.FactorValue.getOldStyleCharacteristics()
ubic.gemma.model.expression.experiment.FactorValue.getValue()	use FactorValue.getMeasurement() or FactorValue.getCharacteristics() to retrieve the value.
ubic.gemma.model.expression.experiment.FactorValue.setOldStyleCharacteristics(Set<Characteristic>)
ubic.gemma.model.expression.experiment.FactorValue.setValue(String)
ubic.gemma.model.expression.experiment.FactorValueValueObject.getDescription()
ubic.gemma.model.expression.experiment.FactorValueValueObject.getFactorValue()
ubic.gemma.model.expression.experiment.Statement.getValue()	use Statement.getSubject() instead
ubic.gemma.model.expression.experiment.Statement.getValueUri()	use Statement.getSubjectUri() instead
ubic.gemma.model.expression.experiment.Statement.setValue(String)	use Statement.setSubject(String) instead
ubic.gemma.model.expression.experiment.Statement.setValueUri(String)	use Statement.setSubjectUri(String) instead
ubic.gemma.model.genome.gene.GeneProductValueObject.getNucleotideEnd()
ubic.gemma.model.genome.gene.GeneProductValueObject.setNucleotideEnd(Long)
ubic.gemma.persistence.hibernate.TypedResultTransformer.transformList(List)	Use TypedResultTransformer.transformListTyped(List) instead.
ubic.gemma.persistence.service.AbstractService.ensureInSession(O)	avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl.thaw(Collection<BulkExpressionDataVector>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.updateIgnoreAcl(FactorValue)	do not use this, it is only a workaround to make FV migration faster
ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)	do not use, this is only for migrating old-style characteristics to statements and will be removed
ubic.gemma.persistence.service.expression.experiment.FactorValueService.loadWithOldStyleCharacteristics(Long, boolean)	do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
ubic.gemma.persistence.service.expression.experiment.FactorValueService.saveStatementIgnoreAcl(FactorValue, Statement)	do not use this, it is meant for FactorValue migration only
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.genome.GeneDao.findByPhysicalLocation(PhysicalLocation)
ubic.gemma.persistence.util.Slice.add(O)
ubic.gemma.persistence.util.Slice.remove(Object)
ubic.gemma.rest.RootWebService.ApiInfoValueObject.getDocs()
ubic.gemma.rest.util.args.FilterArgLexer.getTokenNames()
ubic.gemma.rest.util.args.FilterArgParser.getTokenNames()
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getCurrentGroup()	use UserValueObject.getGroups() instead
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getRole()	use UserValueObject.getGroups() instead
ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController.addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean)
ubic.gemma.web.controller.genome.gene.GeneSetController.addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean)
ubic.gemma.web.controller.genome.gene.GeneSetController.removeSessionGroups(Collection<SessionBoundGeneSetValueObject>)
ubic.gemma.web.controller.genome.gene.GeneSetController.updateSessionGroups(Collection<SessionBoundGeneSetValueObject>)

Enum Constants

Enum Constant	Description
ubic.gemma.model.common.quantitationtype.ScaleType.FOLDCHANGE