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AbaGene - Class in ubic.gemma.core.image.aba
 
AbaGene() - Constructor for class ubic.gemma.core.image.aba.AbaGene
 
AbaGene(Integer, String, String, String, String, Collection<ImageSeries>) - Constructor for class ubic.gemma.core.image.aba.AbaGene
 
ABALinkOutValueObject - Class in ubic.gemma.core.image
Value Object for transporting details needed from other websites to provide convenient links to them in gemma
ABALinkOutValueObject() - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
 
ABALinkOutValueObject(Collection<String>, String, String) - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
 
ABSOLUTE - Static variable in class ubic.gemma.model.common.measurement.MeasurementType
 
AbstractAnalyzer - Class in ubic.gemma.core.analysis.expression.diff
Analyzer base class.
AbstractAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
 
AbstractAuditable - Class in ubic.gemma.model.common
An entity which can have an audit trail attached to it.
AbstractAuditable() - Constructor for class ubic.gemma.model.common.AbstractAuditable
No-arg constructor added to satisfy javabean contract
AbstractCLI - Class in ubic.gemma.core.util
Base Command Line Interface.
AbstractCLI() - Constructor for class ubic.gemma.core.util.AbstractCLI
 
AbstractCLIContextCLI - Class in ubic.gemma.core.util
Spring configuration for CLI.
AbstractCLIContextCLI() - Constructor for class ubic.gemma.core.util.AbstractCLIContextCLI
 
AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation
Created by tesarst on 07/03/17.
AbstractCuratableDao(Class<C>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
 
AbstractCuratableValueObject<C extends Curatable> - Class in ubic.gemma.model.common.auditAndSecurity.curation
Created by tesarst on 07/03/17.
AbstractCuratableValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
Required when using the implementing classes as a spring beans.
AbstractCuratableValueObject(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
 
AbstractCuratableValueObject(C) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
 
AbstractCuratableValueObject(Long, Date, Boolean, AuditEventValueObject, Boolean, AuditEventValueObject, String, AuditEventValueObject) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
 
AbstractCuratableValueObject(Long, Date, Boolean, AuditEvent, Boolean, AuditEvent, String, AuditEvent, Integer) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
Creates a VO with the given curatable properties Note that the events can still be null, as the value-change events they represent might have not occurred since the curatable object was created, and they are not initialised with a creation event.
AbstractDao<T extends Identifiable> - Class in ubic.gemma.persistence.service
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
AbstractDao(Class<T>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractDao
 
AbstractDifferentialExpressionAnalyzer - Class in ubic.gemma.core.analysis.expression.diff
An abstract differential expression analyzer to be extended
AbstractDifferentialExpressionAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer
 
AbstractFetcher - Class in ubic.gemma.core.loader.util.fetcher
 
AbstractFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
 
AbstractGemmaEndpoint - Class in ubic.gemma.web.services
Abstracts out the security and a few constants.
AbstractGemmaEndpoint() - Constructor for class ubic.gemma.web.services.AbstractGemmaEndpoint
 
AbstractGeoService - Class in ubic.gemma.core.loader.expression.geo.service
 
AbstractGeoService() - Constructor for class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
 
AbstractMatrixRowPairAnalysis - Class in ubic.gemma.core.analysis.expression.coexpression.links
 
AbstractMatrixRowPairAnalysis() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
 
AbstractPersister - Class in ubic.gemma.persistence.persister
Base class for persisters.
AbstractPersister() - Constructor for class ubic.gemma.persistence.persister.AbstractPersister
 
AbstractService<O extends Identifiable> - Class in ubic.gemma.persistence.service
Base for all services handling DAO access.
AbstractService(BaseDao<O>) - Constructor for class ubic.gemma.persistence.service.AbstractService
 
AbstractSetListContainer - Class in ubic.gemma.web.persistence
 
AbstractSetListContainer() - Constructor for class ubic.gemma.web.persistence.AbstractSetListContainer
 
AbstractSpringAwareCLI - Class in ubic.gemma.core.util
Subclass this to create command line interface (CLI) tools that need a Spring context.
AbstractSpringAwareCLI() - Constructor for class ubic.gemma.core.util.AbstractSpringAwareCLI
 
AbstractTask<T extends TaskResult,C extends TaskCommand> - Class in ubic.gemma.core.tasks
 
AbstractTask() - Constructor for class ubic.gemma.core.tasks.AbstractTask
 
AbstractTask(C) - Constructor for class ubic.gemma.core.tasks.AbstractTask
 
AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service
Created by tesarst on 01/06/17.
AbstractVoEnabledDao(Class<O>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledDao
 
AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service
Created by tesarst on 01/06/17.
AbstractVoEnabledService(BaseVoEnabledDao<O, VO>) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledService
 
AclAdvice - Class in ubic.gemma.core.security.authorization.acl
For permissions modification to be triggered, the method name must match certain patterns, which include "create", or "remove".
AclAdvice() - Constructor for class ubic.gemma.core.security.authorization.acl.AclAdvice
 
AclAfterCollectionCompSeqByArrayDesignFilter - Class in ubic.gemma.core.security.authorization.acl
For this particular AfterInvocationProvider, composite sequence authorization is determined based on the secured array design acl.
AclAfterCollectionCompSeqByArrayDesignFilter(AclService, List<Permission>) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
 
AclAfterCollectionDataVectorByExpressionExperimentFilter - Class in ubic.gemma.core.security.authorization.acl
Filter collections of DesignElementDataVectors or DataVectorValueObjects based on the permissions of the associated ExpressionExperiment(s).
AclAfterCollectionDataVectorByExpressionExperimentFilter(AclService, List<Permission>) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
 
add(ArrayDesign) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
 
add(ArrayDesign, Map<CompositeSequence, BioSequence>) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
 
add(ArrayDesign, Set<CompositeSequence>) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
 
add(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
 
add(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
 
addAccession(NCBIGene2Accession) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
 
addAffyDataFromAPTOutput(ExpressionExperiment, String) - Method in class ubic.gemma.core.loader.expression.DataUpdater
Affymetrix: Use when we want to avoid downloading the CEL files etc.
addAlternateName(Long, String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
 
addAlternateName(Long, String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
 
addAuditEvent(EntityDelegator, String, String, String) - Method in class ubic.gemma.web.remote.AuditController
 
addAuthority(UserGroup, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
 
addAuthority(UserGroup, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
 
addAutoOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI
You must implement the handling for this option.
addBinToQuery(String, Long, Long) - Static method in class ubic.gemma.persistence.util.SequenceBinUtils
Directly ported from jksrc binRange.c and hdb.c From the binRange.c comments: There's a bin for each 128k segment, for each 1M segment, for each 8M segment, for each 64M segment, and for each chromosome (which is assumed to be less than 512M.) A range goes into the smallest bin it will fit in.
addBioAssays(List<BioAssayValueObject>) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
 
addBioMaterialAssociation(BioAssay, BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
Associates a bioMaterial with a specified bioAssay.
addBioMaterialAssociation(BioAssay, BioMaterial) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
 
addBlackCell(Long, String, double, double, int, int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
addCell(Long, String, Double, Double, Integer, Integer, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
addChannel() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addCharacteristic(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addCoexpCorrelationDistribution(ExpressionExperiment, CoexpCorrelationDistribution) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
For backfilling of the coexpression distributions from flat files - remove when no longer needed.
addCoexpCorrelationDistribution(ExpressionExperiment, CoexpCorrelationDistribution) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
 
addColumnName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
 
addCondition(DifferentialExpressionGenesConditionsValueObject.Condition) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
Initialize the column of cells for the given Condition, treating them as missing values.
addContrast(Long, Long, Double, Double, Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
 
addContrast(Long, Long, Double, Double, Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
 
addContrastsFactorValue(long, String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
 
addContributer(GeoContact) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addCorrespondence(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
 
addCountData(ExpressionExperiment, ArrayDesign, DoubleMatrix<String, String>, DoubleMatrix<String, String>, Integer, Boolean, boolean) - Method in class ubic.gemma.core.loader.expression.DataUpdater
RNA-seq: Replaces data.
addCreateAuditEvent(Auditable, String, User) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelper
Add AuditAction.CREATE event and update Status.
addCreateAuditEvent(Auditable, String, User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelperImpl
 
addDataSet(GeoDataset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addDateOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI
 
addElements(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService
For the rare cases (Exon arrays) where we load the platform in two stages.
addElements(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
 
addEmailAlert() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
 
addEmailAlert() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskProxy
 
addEmailAlert(String) - Method in interface ubic.gemma.core.job.progress.ProgressStatusService
Set up an email alert for this job; an email will be sent when it has finished (or failed).
addEmailAlert(String) - Method in class ubic.gemma.core.job.progress.ProgressStatusServiceImpl
 
addEmailAlert() - Method in interface ubic.gemma.core.job.SubmittedTask
Add email notification of task completion.
addEmailAlertNotificationAfterCompletion() - Method in class ubic.gemma.core.job.executor.worker.SubmittedTaskRemote
 
addEmailNotification(ListenableFuture<TaskResult>, EmailNotificationContext) - Method in interface ubic.gemma.core.job.executor.common.TaskPostProcessing
 
addEmailNotification(ListenableFuture<TaskResult>, EmailNotificationContext) - Method in class ubic.gemma.core.job.executor.common.TaskPostProcessingImpl
 
addEntities(Collection<Long>) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
 
addEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
 
addEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
Add the data set to the list of those which are in the array.
addErrorObject(Object, String, Throwable) - Method in class ubic.gemma.core.util.AbstractCLI
Add an error object with a stacktrace to indicate failure in a batch processing.
addErrorObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI
Add an error object to indicate failure in a batch processing.
addErrorsField(String, String) - Method in class ubic.gemma.web.services.rest.util.WellComposedErrorBody
Adds a new field into the errors array property.
addEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
Add an event to the AuditTrail
addEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrailImpl
 
addEvent(Auditable, AuditEvent) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao
Add the given event to the audit trail of the given AbstractAuditable entity.
addEvent(Auditable, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl
 
addEventsToMap(Map<Long, Collection<AuditEvent>>, Long, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
 
addExceptionFields(WellComposedErrorBody, Throwable) - Static method in class ubic.gemma.web.services.rest.util.WellComposedErrorBody
Adds descriptive values from the throwable object to the instance of WellComposedErrorBody.
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
 
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager
 
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
 
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
 
addExpressionExperimentStatement(Characteristic, ExpressionExperiment) - Method in interface ubic.gemma.core.ontology.OntologyService
Will add the give vocab characteristic to the expression experiment.
addExpressionExperimentStatement(Characteristic, ExpressionExperiment) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
 
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
addFactorValue(ExpressionExperiment, FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
addFactorValue(ExpressionExperiment, FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
addFactorValueTo(Collection<Long>, EntityDelegator) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
AJAX
addGene(GeneProductValueObject, GeneValueObject) - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
 
addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
addGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
 
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager
 
addGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
 
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
 
addGroupAndUserNameRestriction(boolean, boolean) - Static method in class ubic.gemma.persistence.util.EntityUtils
Have to add 'and' to start of this if it's a later clause Author: nicolas with fixes to generalize by paul, same code appears in the PhenotypeAssociationDaoImpl
addGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
addGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
addHostAndPortOptions(Options, boolean, boolean) - Method in class ubic.gemma.core.util.AbstractCLI
Convenience method to add a standard pair of options to intake a host name and port number.
addImage(Image) - Method in class ubic.gemma.core.image.aba.ImageSeries
 
addImageSeries(ImageSeries) - Method in class ubic.gemma.core.image.aba.AbaGene
 
addInteractionToInclude(Collection<ExperimentalFactor>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
 
addInteractionToInclude(ExperimentalFactor...) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
 
addMatrices(ExpressionDataDoubleMatrix, ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil
Add two matrices.
addMessage(HttpServletRequest, String, Object[]) - Method in class ubic.gemma.web.controller.BaseController
 
addNewObjects(Auditable) - Method in class ubic.gemma.core.analysis.report.WhatsNew
adds a single auditable to the new object list
addNewObjects(Collection<Auditable>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
adds a collection of auditables to the new object list
addNumPublications(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
 
addOtherIssues(String) - Method in class ubic.gemma.model.expression.experiment.Geeq
 
addPlatform(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
 
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
addProgressUpdate(String) - Method in interface ubic.gemma.core.job.executor.common.ProgressUpdateCallback
 
addProgressUpdate(String) - Method in class ubic.gemma.core.job.executor.worker.SubmittedTaskRemote
 
addProperty(String, Object) - Method in class ubic.gemma.web.util.ConfigurationCookie
 
addQuantitationType(GeoPlatform, String, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
 
addRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
Used when we want to add data for a quantitation type.
addRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
addReplication(GeoReplication) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addRestrictionParameters(Query, List<ObjectFilter[]>) - Static method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
Adds all parameters contained in the filters argument to the Query by calling query.setParameter as needed.
addRestrictions(Criteria, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, BioMaterial) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
Note: The finder has to do the additional checking for equality of sequence and/or database entry - we don't know until we get the sequences.
addRestrictions(Criteria, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, Gene, boolean) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, QuantitationType) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(Criteria, Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addRestrictions(DetachedCriteria, DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
addResult(Gene2GOAssociation) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
 
addResult(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
Deprecated.
 
addResult(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
 
addResult(BlatResult) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
 
addResult(Object) - Method in class ubic.gemma.core.loader.genome.FastaParser
 
addResult(NCBIGene2Accession) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
 
addResult(Object) - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParser
 
addResult(T) - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
 
addResult(Object) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
Add an object to the results collection.
addResults(DifferentialExpressionAnalysis, Collection<ExpressionAnalysisResultSet>) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
 
addResults(DifferentialExpressionAnalysis, Collection<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl
 
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
 
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
Only call this to add a sample for which there are no data.
addSamples(Collection<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
Add a group of samples to this series.
addSeries(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
 
addSeriesAppearsIn(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addSessionGroup(SessionBoundExpressionExperimentSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
AJAX adds the Expression Experiment group to the session
addSessionGroup(SessionBoundGeneSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
* AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.
addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
Deprecated. 
addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
Deprecated. 
addSet(GemmaSessionBackedValueObject, boolean) - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
Sets the reference (generates an id and assumes this group was made as a result of a modification for the type value) for the group then adds it to the session-bound list(s) for session-bound groups
addSubclasses(List<String>, SingleTableEntityPersister) - Static method in class ubic.gemma.persistence.util.CommonQueries
 
addSubSeries(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addSubset(GeoSubset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
 
addSuccessObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI
Add a success object to indicate success in a batch processing.
addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
 
addTestAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.util.test.PersistentDummyObjectHelper
 
addThreadsOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI
Convenience method to add an option for parallel processing option.
addToCache(DiffExprGeneSearchResult) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
addToCache(Collection<DiffExprGeneSearchResult>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
addToCache(DiffExprGeneSearchResult) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
addToCache(Collection<DiffExprGeneSearchResult>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
addToCache(Long, Long, Collection<DoubleVectorValueObject>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
 
addToCache(Long, Long, Collection<DoubleVectorValueObject>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
 
addToCache(CompositeSequence) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
 
addToColumnData(String, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
Add a value to a column.
addToDataProcessing(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToDbXRefs(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
 
addToExtractProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addToGrowthProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addToHybProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToKeyWords(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToOrganisms(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
addToPubmedIds(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToRepeatsSampleList(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
 
addToScanProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToSeriesTypes(GeoSeries.SeriesType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToSummary(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToSynonyms(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
 
addToTopHitsCache(ExpressionAnalysisResultSet, List<DifferentialExpressionValueObject>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
addToTopHitsCache(ExpressionAnalysisResultSet, List<DifferentialExpressionValueObject>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
addToTreatmentProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addToVariables(Integer, GeoVariable) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToVariableSampleList(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
 
addUpdateAuditEvent(Auditable, String, User) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelper
Add AuditAction.UPDATE event and update Status.
addUpdateAuditEvent(Auditable, String, User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelperImpl
 
addUpdatedObjects(Auditable) - Method in class ubic.gemma.core.analysis.report.WhatsNew
adds a single auditable to the updated object list
addUpdatedObjects(Collection<Auditable>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
adds a collection of auditables to the updated object list
addUpdateEvent(Auditable, AuditEventType, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
 
addUpdateEvent(Auditable, AuditEventType, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
 
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
 
addUpdateEvent(Auditable, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
Add an update event defined by the given parameters, to the given auditable.
addUpdateEvent(Auditable, AuditEventType, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
 
addUpdateEvent(Auditable, AuditEventType, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
This method creates a new event in the audit trail of the passed Auditable object.
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
 
addUpdateEvent(Auditable, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
 
addUserAndGroupParameters(SQLQuery, SessionFactory) - Static method in class ubic.gemma.persistence.util.EntityUtils
Populates parameters in query created using addGroupAndUserNameRestriction(boolean, boolean).
addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
AJAX adds the experiment group to the session
addUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
AJAX adds the gene group to the session
addUserToGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
addUserToGroup(UserGroup, User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
addUserToGroup(String, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
 
addUserToGroup(String, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
 
addValue(GeoSample, Integer, String, Object) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
Store a value.
addVariable(GeoVariable) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addVectors(Long, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
 
addVectors(Long, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
 
AFFY_COLLAPSED - Static variable in class ubic.gemma.model.genome.biosequence.SequenceType
Represents Affymetrix probe sequences that have been "collapsed" or combined into a single sequence.
AFFY_PROBE - Static variable in class ubic.gemma.model.genome.biosequence.SequenceType
Represents a single probe sequence for Affymetrix reporters
AFFY_TARGET - Static variable in class ubic.gemma.model.genome.biosequence.SequenceType
Represents the target sequence provided by the manufacturer.
AffyChipTypeExtractor - Class in ubic.gemma.core.loader.expression.arrayDesign
Extract the chip type from Affymetrix CEL files.
AffyChipTypeExtractor() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
 
AffyDataFromCelCli - Class in ubic.gemma.core.apps
Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
AffyDataFromCelCli() - Constructor for class ubic.gemma.core.apps.AffyDataFromCelCli
 
AffyPowerToolsProbesetSummarize - Class in ubic.gemma.core.loader.expression
 
AffyProbeCollapseCli - Class in ubic.gemma.core.apps
Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
AffyProbeCollapseCli() - Constructor for class ubic.gemma.core.apps.AffyProbeCollapseCli
 
AffyProbeNameFilter - Class in ubic.gemma.core.analysis.preprocess.filter
 
AffyProbeNameFilter(AffyProbeNameFilter.Pattern[]) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
 
AffyProbeNameFilter.Pattern - Enum in ubic.gemma.core.analysis.preprocess.filter
 
AffyProbeReader - Class in ubic.gemma.core.loader.expression.arrayDesign
Reads Affymetrix Probe files, including exon arrays.
AffyProbeReader() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
 
AffyScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Extract the scan date from Affymetrix CEL files.
AffyScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
 
afterPropertiesSet() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
 
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
Initialize the cache; if it already exists it will not be recreated.
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
 
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
 
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
 
afterPropertiesSet() - Method in class ubic.gemma.persistence.util.ExternalCacheRegionFactory
 
afterPropertiesSet() - Method in class ubic.gemma.web.feed.FeedReader
 
afterPropertiesSet() - Method in class ubic.gemma.web.services.rest.util.RestAuthEntryPoint
 
AgilentScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Because agilent makes slides that work with any scanner, the formats are not that predictable.
AgilentScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor
 
ajaxLoginCheck(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
 
ajaxSearch(SearchSettingsValueObject) - Method in interface ubic.gemma.core.search.SearchService
The results are sorted in order of decreasing score, organized by class.
ajaxSearch(SearchSettingsValueObject) - Method in class ubic.gemma.core.search.SearchServiceImpl
 
ajaxSearch(SearchSettingsValueObject) - Method in interface ubic.gemma.web.controller.GeneralSearchController
 
ajaxSearch(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
 
AlignmentBasedGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Signifies a mapping based on sequence alignment performed by the system.
AlignmentBasedGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent
No-arg constructor added to satisfy javabean contract
AlignmentBasedGeneMappingEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
all(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.AnnotationsWebService
Placeholder for root call
all(DatasetFilterArg, IntArg, IntArg, SortArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
 
all(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.GeneWebService
Placeholder for root call
all(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.PhenotypeWebService
Placeholder for root call
all(PlatformFilterArg, IntArg, IntArg, SortArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.PlatformsWebService
 
all(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.RootWebService
Returns an object with API information.
all(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.TaxaWebService
Lists all available taxa.
all(FilterArg, IntArg, IntArg, SortArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.util.WebServiceWithFiltering
Lists all objects available in gemma.
ALL_PHENOCARTA_ANNOTATIONS_FILE_LOCATION - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
 
AllenBrainAtlasService - Interface in ubic.gemma.core.image.aba
 
AllenBrainAtlasServiceImpl - Class in ubic.gemma.core.image.aba
Acts as a convenient front end to the Allen Brain Atlas REST (web) services Used the ABAApi.java as the original template for this Service (found in ABA demo code).
AllenBrainAtlasServiceImpl() - Constructor for class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl
 
allowUseExisting - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
Whether we are allowed to use an existing file rather than downloading again, in the case where we can't connect to the remote host to check the size of the file.
AlreadyExistsInSystemException - Exception in ubic.gemma.core.loader.util
Can be thrown when an attempt is made to load data into the system that already exists.
AlreadyExistsInSystemException(String) - Constructor for exception ubic.gemma.core.loader.util.AlreadyExistsInSystemException
 
AlreadyExistsInSystemException(String, Object) - Constructor for exception ubic.gemma.core.loader.util.AlreadyExistsInSystemException
 
AlternateName - Class in ubic.gemma.model.expression.arrayDesign
 
AlternateName() - Constructor for class ubic.gemma.model.expression.arrayDesign.AlternateName
No-arg constructor added to satisfy javabean contract
AlternateName.Factory - Class in ubic.gemma.model.expression.arrayDesign
 
AlternateNameImpl - Class in ubic.gemma.model.expression.arrayDesign
 
AlternateNameImpl() - Constructor for class ubic.gemma.model.expression.arrayDesign.AlternateNameImpl
 
alternativeToProperAffyPlatform(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
AMOUNT - Static variable in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
Referring to a measured or derived "amount", indicating the relative or absolute level of something.
Analysis - Class in ubic.gemma.model.analysis
An analysis of one or more Investigations.
Analysis() - Constructor for class ubic.gemma.model.analysis.Analysis
No-arg constructor added to satisfy javabean contract
AnalysisDao<T extends Analysis> - Interface in ubic.gemma.persistence.service.analysis
 
AnalysisDaoBase<T extends Analysis> - Class in ubic.gemma.persistence.service.analysis
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.analysis.Analysis.
AnalysisDaoBase(Class<T>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.AnalysisDaoBase
 
AnalysisResultSet - Class in ubic.gemma.model.analysis
An abstract class representing a related set of generic analysis results, part of an analysis.
AnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.AnalysisResultSet
No-arg constructor added to satisfy javabean contract
analysisResultSetsToString(Collection<ExpressionAnalysisResultSet>, Map<Long, String[]>, StringBuilder) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
analysisResultSetsToString(Collection<ExpressionAnalysisResultSet>, Map<Long, String[]>, StringBuilder) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
 
analysisResultSetToString(ExpressionAnalysisResultSet, Map<Long, String[]>, StringBuilder, Map<Long, StringBuilder>, List<DifferentialExpressionAnalysisResult>) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
analysisResultSetToString(ExpressionAnalysisResultSet, Map<Long, String[]>, StringBuilder, Map<Long, StringBuilder>, List<DifferentialExpressionAnalysisResult>) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
 
AnalysisSelectionAndExecutionService - Interface in ubic.gemma.core.analysis.expression.diff
 
AnalysisSelectionAndExecutionServiceImpl - Class in ubic.gemma.core.analysis.expression.diff
A differential expression analysis tool that executes the appropriate analysis based on the number of experimental factors and factor values, as well as the block design.
AnalysisSelectionAndExecutionServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
 
AnalysisService<T extends Analysis> - Interface in ubic.gemma.persistence.service.analysis
Provides basic services for dealing with analyses
AnalysisUtilService - Interface in ubic.gemma.core.analysis.expression
 
AnalysisUtilServiceImpl - Class in ubic.gemma.core.analysis.expression
Utility methods for dealing with analyses.
AnalysisUtilServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl
 
analyze() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
Main entry point.
analyze(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
 
analyze(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
 
analyze(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
 
analyze(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
 
analyze(Collection<Long>) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
 
analyze(Collection<Long>) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
 
analyzeResultSets(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
 
AnchorTagUtil - Class in ubic.gemma.core.util
Used to generate hyperlinks to various things in Gemma.
AnchorTagUtil() - Constructor for class ubic.gemma.core.util.AnchorTagUtil
 
and(IdArray) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
 
andSet(IdArray) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
 
annot(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
 
ANNOT_DATA_DIR - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
 
ANNOTATION_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
 
AnnotationAssociation - Class in ubic.gemma.model.genome.sequenceAnalysis
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis.
AnnotationAssociation() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
 
AnnotationAssociation.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
 
AnnotationAssociationDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
AnnotationAssociationDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
AnnotationAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
 
AnnotationAssociationService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
AnnotationAssociationServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
AnnotationAssociationServiceImpl(AnnotationAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl
 
AnnotationBasedGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
To signify the array design was mapped from an external source, not by our own sequence analysis.
AnnotationBasedGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent
No-arg constructor added to satisfy javabean contract
AnnotationBasedGeneMappingEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
AnnotationController - Class in ubic.gemma.web.controller.expression.experiment
Controller for methods involving annotation of experiments (and potentially other things); delegates to OntologyService and the CharacteristicService.
AnnotationController() - Constructor for class ubic.gemma.web.controller.expression.experiment.AnnotationController
 
AnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
AnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent
No-arg constructor added to satisfy javabean contract
AnnotationsWebService - Class in ubic.gemma.web.services.rest
RESTful interface for annotations.
AnnotationsWebService() - Constructor for class ubic.gemma.web.services.rest.AnnotationsWebService
Required by spring
AnnotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, TaxonService) - Constructor for class ubic.gemma.web.services.rest.AnnotationsWebService
Constructor for service autowiring
AnnotationValueObject - Class in ubic.gemma.model.common.description
 
AnnotationValueObject() - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
 
anyDelete(HttpServletResponse, UriInfo) - Method in class ubic.gemma.web.services.rest.util.WebService
Fallback for unmapped DELETE calls
anyGet(HttpServletResponse, UriInfo) - Method in class ubic.gemma.web.services.rest.util.WebService
Fallback for unmapped GET calls
anyPost(HttpServletResponse, UriInfo) - Method in class ubic.gemma.web.services.rest.util.WebService
Fallback for unmapped POST calls
anyPut(HttpServletResponse, UriInfo) - Method in class ubic.gemma.web.services.rest.util.WebService
Fallback for unmapped PUT calls
API_VERSION - Static variable in class ubic.gemma.web.services.rest.util.WebService
 
apiVersion - Variable in class ubic.gemma.web.services.rest.util.ResponseErrorObject
Adds the apiVersion property to the final JSON object
APP_NAME - Static variable in class ubic.gemma.web.util.Constants
 
appearsInMultipleSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
append(LoggingEvent) - Method in class ubic.gemma.core.job.executor.common.LogBasedProgressAppender
 
appendBaseHeader(ExpressionExperiment, String, StringBuffer) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
Appends base header information (about the experiment) to a file.
appendBaseHeader(ExpressionExperiment, boolean, StringBuffer) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
Appends base header information (about the experiment) to a file.
ArchiveFetcher - Interface in ubic.gemma.core.loader.util.fetcher
Interface defining a class that downloads archives and unpacks them.
areOntologiesAllLoaded() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper
 
areOntologiesAllLoaded() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl
 
ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint
The local name of the expected request.
ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignUsedEndpoint
The local name of the expected request.
ArrayArg<T> - Class in ubic.gemma.web.services.rest.util.args
Class representing an API argument that should be an array.
ArrayCompositeSequenceArg - Class in ubic.gemma.web.services.rest.util.args
 
ArrayDatasetArg - Class in ubic.gemma.web.services.rest.util.args
 
ArrayDesign - Class in ubic.gemma.model.expression.arrayDesign
Represents an assembly of design elements that are assayed all at once.
ArrayDesign() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesign
No-arg constructor added to satisfy javabean contract
arrayDesign - Variable in class ubic.gemma.web.services.rest.util.args.CompositeSequenceArg
 
ArrayDesign.Factory - Class in ubic.gemma.model.expression.arrayDesign
 
ArrayDesignAddCommand - Class in ubic.gemma.web.controller.expression.arrayDesign
 
ArrayDesignAddCommand() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
 
ArrayDesignAlternativePopulateCli - Class in ubic.gemma.core.apps
This only needs to be re-run when the mappings change.
ArrayDesignAlternativePopulateCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
 
ArrayDesignAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
An event involving the analysis of an ArrayDesign
ArrayDesignAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignAnnotationFileCli - Class in ubic.gemma.core.apps
Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
ArrayDesignAnnotationFileCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
 
ArrayDesignAnnotationService - Interface in ubic.gemma.core.analysis.service
Methods to generate annotations for array designs, based on information already in the database.
ArrayDesignAnnotationService.OutputType - Enum in ubic.gemma.core.analysis.service
 
ArrayDesignAnnotationServiceImpl - Class in ubic.gemma.core.analysis.service
 
ArrayDesignAnnotationServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
 
ArrayDesignAuditTrailCleanupCli - Class in ubic.gemma.core.apps
work in progress
ArrayDesignAuditTrailCleanupCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
 
ArrayDesignBioSequenceDetachCli - Class in ubic.gemma.core.apps
Remove all associations that this array design has with BioSequences.
ArrayDesignBioSequenceDetachCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
 
ArrayDesignBlatCli - Class in ubic.gemma.core.apps
Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
ArrayDesignBlatCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBlatCli
 
ArrayDesignController - Interface in ubic.gemma.web.controller.expression.arrayDesign
Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
ArrayDesignControllerImpl - Class in ubic.gemma.web.controller.expression.arrayDesign
Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
ArrayDesignControllerImpl() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
 
ArrayDesignDao - Interface in ubic.gemma.persistence.service.expression.arrayDesign
Created by tesarst on 13/03/17.
ArrayDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign
 
ArrayDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
ArrayDesignFormController - Class in ubic.gemma.web.controller.expression.arrayDesign
Controller for editing basic information about array designs.
ArrayDesignFormController() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
 
ArrayDesignGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
The mapping of probes to genes for an ArrayDesign
ArrayDesignGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignGeneMappingEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignGroupingTag - Class in ubic.gemma.web.taglib.arrayDesign
For display of information about array designs that subsume or are subsumed.
ArrayDesignGroupingTag() - Constructor for class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
 
ArrayDesignHtmlUtil - Class in ubic.gemma.web.taglib.arrayDesign
Yes, this is used by the ArrayDesignController, but should be phased out.
ArrayDesignHtmlUtil() - Constructor for class ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil
 
ArrayDesignIdentifierByNameEndpoint - Class in ubic.gemma.web.services
array design short name -> return matching array design identifier
ArrayDesignIdentifierByNameEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint
 
ArrayDesignMapResultService - Interface in ubic.gemma.core.analysis.sequence
 
ArrayDesignMapResultServiceImpl - Class in ubic.gemma.core.analysis.sequence
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
ArrayDesignMapResultServiceImpl(BlatResultService, BlatAssociationService, ArrayDesignService, CompositeSequenceService) - Constructor for class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
 
ArrayDesignMapSummaryCli - Class in ubic.gemma.core.apps
CLI for ArrayDesignMapSummaryService
ArrayDesignMapSummaryCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
 
ArrayDesignMergeCli - Class in ubic.gemma.core.apps
make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
ArrayDesignMergeCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCli
 
ArrayDesignMergeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignMergeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignMergeEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignMergeHelperService - Interface in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignMergeHelperServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignMergeHelperServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl
 
ArrayDesignMergeService - Interface in ubic.gemma.core.loader.expression.arrayDesign
Make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees
ArrayDesignMergeServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignMergeServiceImpl(ArrayDesignService, ArrayDesignReportService, ArrayDesignMergeHelperService) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
 
ArrayDesignParser - Class in ubic.gemma.core.loader.expression.arrayDesign
Deprecated. 
ArrayDesignParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
Deprecated.
 
ArrayDesignPersister - Class in ubic.gemma.persistence.persister
This class handles persisting array designs.
ArrayDesignPersister() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignPersister
 
ArrayDesignProbeCleanupCLI - Class in ubic.gemma.core.apps
Delete design elements (probes) that are invalid for one reason or another.
ArrayDesignProbeCleanupCLI() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
 
ArrayDesignProbeMapperCli - Class in ubic.gemma.core.apps
Process the blat results for an array design to map them onto genes.
ArrayDesignProbeMapperCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
 
ArrayDesignProbeMapperController - Class in ubic.gemma.web.controller.expression.arrayDesign
A controller to run array design probe mapper either locally or in a space.
ArrayDesignProbeMapperController() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController
 
ArrayDesignProbeMapperService - Interface in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignProbeMapperServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
For an array design, generate gene product mappings for the sequences.
ArrayDesignProbeMapperServiceImpl(AnnotationAssociationService, ArrayDesignAnnotationService, ArrayDesignReportService, ArrayDesignService, ProbeMapper, BioSequenceService, BlatResultService, CompositeSequenceService, ExpressionDataFileService, GeneProductService, GeneService, Persister) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
 
ArrayDesignProbeMapperTaskImpl - Class in ubic.gemma.core.tasks.analysis.sequence
A probe mapper spaces task .
ArrayDesignProbeMapperTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
 
ArrayDesignProbeMapTaskCommand - Class in ubic.gemma.core.tasks.analysis.sequence
A command object to be used by spaces.
ArrayDesignProbeMapTaskCommand() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
 
ArrayDesignProbeMapTaskCommand(String, boolean, ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
 
ArrayDesignProbeRenamerCli - Class in ubic.gemma.core.apps
Deprecated.
renaming probes is not a good idea in general
ArrayDesignProbeRenamerCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli
Deprecated.
 
ArrayDesignProbeRenamingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Signifies that the probes were renamed from their original values.
ArrayDesignProbeRenamingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignProbeRenamingEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignPropertyEditor - Class in ubic.gemma.web.propertyeditor
Used to convert ArrayDesigns from and into strings for display in forms.
ArrayDesignPropertyEditor(ArrayDesignService) - Constructor for class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
 
ArrayDesignRepeatAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignRepeatAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignRepeatAnalysisEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignRepeatScanCli - Class in ubic.gemma.core.apps
Runs repeatmasker on array designs.
ArrayDesignRepeatScanCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
 
ArrayDesignRepeatScanController - Class in ubic.gemma.web.controller.analysis.sequence
A controller to run array design repeat scan either locally or in a space.
ArrayDesignRepeatScanController() - Constructor for class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController
 
ArrayDesignRepeatScanTask - Interface in ubic.gemma.core.tasks.analysis.sequence
 
ArrayDesignRepeatScanTaskCommand - Class in ubic.gemma.core.tasks.analysis.sequence
A command object to be used by spaces.
ArrayDesignRepeatScanTaskCommand(String, ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
NOTE: we can't pass in a we command as they are defined in the web module, which messes up the configuration.
ArrayDesignRepeatScanTaskCommand(ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
 
ArrayDesignRepeatScanTaskImpl - Class in ubic.gemma.core.tasks.analysis.sequence
An array design repeat scan spaces task
ArrayDesignRepeatScanTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl
 
ArrayDesignReportService - Interface in ubic.gemma.core.analysis.report
 
ArrayDesignReportServiceImpl - Class in ubic.gemma.core.analysis.report
 
ArrayDesignReportServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
 
arrayDesignSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettingsImpl
Convenience method to get pre-configured settings.
ArrayDesignSequenceAlignmentService - Interface in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignSequenceAlignmentServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
Aligns sequences from array designs to the genome, using blat, and persists the blat results.
ArrayDesignSequenceAlignmentServiceImpl(ArrayDesignReportService, ArrayDesignService, BioSequenceService, Persister) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
 
ArrayDesignSequenceAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
The sequence alignment analysis of an ArrayDesign
ArrayDesignSequenceAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignSequenceAnalysisEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignSequenceAssociationCli - Class in ubic.gemma.core.apps
Attach sequences to array design, fetching from BLAST database if requested.
ArrayDesignSequenceAssociationCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
 
ArrayDesignSequenceManipulatingCli - Class in ubic.gemma.core.apps
Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
ArrayDesignSequenceManipulatingCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
 
ArrayDesignSequenceProcessingService - Interface in ubic.gemma.core.loader.expression.arrayDesign
 
ArrayDesignSequenceProcessingServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
ArrayDesignSequenceProcessingServiceImpl(ArrayDesignReportService, ArrayDesignService, BioSequenceService, ExternalDatabaseService, Persister) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
 
ArrayDesignSequenceRemoveEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Used to indicate that all associations that this array design has with BioSequences have been removed.
ArrayDesignSequenceRemoveEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignSequenceRemoveEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignSequenceUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
The updating of the sequences associated with an ArrayDesign
ArrayDesignSequenceUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignSequenceUpdateEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
arrayDesignService - Variable in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
 
arrayDesignService - Variable in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
 
ArrayDesignService - Interface in ubic.gemma.persistence.service.expression.arrayDesign
 
ArrayDesignServiceImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign
 
ArrayDesignServiceImpl(ArrayDesignDao, AuditEventDao) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
ArrayDesignsForExperimentCache - Class in ubic.gemma.persistence.util
Used to hold information for matching to a new experiment, during persisting.
ArrayDesignsForExperimentCache() - Constructor for class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
 
ArrayDesignSubsumeCheckEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignSubsumeCheckEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
No-arg constructor added to satisfy javabean contract
ArrayDesignSubsumeCheckEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignSubsumptionTesterCli - Class in ubic.gemma.core.apps
Test two array designs to see if one subsumes the other, and if so update their information.
ArrayDesignSubsumptionTesterCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
 
ArrayDesignUsedEndpoint - Class in ubic.gemma.web.services
Used for determining which array designs were used in a given expression experiment (EE)
ArrayDesignUsedEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignUsedEndpoint
 
ArrayDesignValueObject - Class in ubic.gemma.model.expression.arrayDesign
Value object for quickly displaying varied information about Array Designs.
ArrayDesignValueObject() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
Required when using the class as a spring bean.
ArrayDesignValueObject(ArrayDesign) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
This will only work if the object is thawed (lightly).
ArrayDesignValueObject(ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
Copies constructor from other ArrayDesignValueObject
ArrayDesignValueObject(Date, Boolean, AuditEventValueObject, Boolean, AuditEventValueObject, String, AuditEventValueObject, String, String, String, Integer, Integer, Boolean, Boolean, Boolean, Long, Boolean, Boolean, Boolean, Boolean, Date, Date, Date, Date, String, String, String, String, String, String, String, Long, String, Boolean, Boolean) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
 
ArrayDesignValueObject(Long) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
 
ArrayDesignValueObject(Object[], Integer) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
 
ArrayDesignValueObjectExt - Class in ubic.gemma.web.controller.expression.arrayDesign
Extended value object to carry more data to client.
ArrayDesignValueObjectExt(ArrayDesignValueObject) - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
 
ArrayEntityArg<O extends Identifiable,VO extends IdentifiableValueObject<O>,S extends BaseVoEnabledService<O,VO>> - Class in ubic.gemma.web.services.rest.util.args
Array of identifiers of an Identifiable entity
ArrayExpressUtil - Class in ubic.gemma.core.loader.expression.arrayExpress.util
 
ArrayExpressUtil() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
 
ArrayGeneArg - Class in ubic.gemma.web.services.rest.util.args
 
ArrayPlatformArg - Class in ubic.gemma.web.services.rest.util.args
 
ArrayStringArg - Class in ubic.gemma.web.services.rest.util.args
Class representing an API argument that should be an array of Strings.
ArrayStringArg(List<String>) - Constructor for class ubic.gemma.web.services.rest.util.args.ArrayStringArg
 
ArrayStringArg(String, Exception) - Constructor for class ubic.gemma.web.services.rest.util.args.ArrayStringArg
 
ArrayTaxonArg - Class in ubic.gemma.web.services.rest.util.args
 
asDoubleArrayNegRanks() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
 
asDoubleArrayPosRanks() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
 
asFile() - Method in class ubic.gemma.model.common.description.LocalFile
Attempt to create a java.io.File from the local URI.
asIntArrayNeg() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
 
asIntArrayPos() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
 
asRegularGoId(Characteristic) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
asRegularGoId(OntologyTerm) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
asRegularGoId(String) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
AssayViewTag - Class in ubic.gemma.web.taglib.expression.experiment
Used to display table of biomaterials and bioassays.
AssayViewTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.analysis.expression.diff.DirectionEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.association.GOEvidenceCodeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditActionEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.description.DatabaseTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.measurement.MeasurementKindEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.measurement.MeasurementTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.quantitationtype.GeneralTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.quantitationtype.PrimitiveTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.quantitationtype.ScaleTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.common.quantitationtype.StandardQuantitationTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.expression.arrayDesign.TechnologyTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.expression.experiment.FactorTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.genome.biosequence.PolymerTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.genome.biosequence.SequenceTypeEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethodEnum
 
assemble(Serializable, Object) - Method in class ubic.gemma.persistence.model.usertypes.HibernateByteBlobType
 
assignSequencesToDesignElements(Collection<CompositeSequence>, Collection<BioSequence>) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
Associate sequences with an array design.
assignSequencesToDesignElements(Collection<CompositeSequence>, File) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
Associate sequences with an array design.
assignSequencesToDesignElements(Collection<CompositeSequence>, InputStream) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
 
assignSequencesToDesignElements(Collection<CompositeSequence>, Collection<BioSequence>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
 
assignSequencesToDesignElements(Collection<CompositeSequence>, File) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
 
assignSequencesToDesignElements(Collection<CompositeSequence>, InputStream) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
Associate sequences with an array design.
associateBatchFactor(Map<BioMaterial, T>, Map<T, FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
Associate dates with bioassays and any new factors with the biomaterials.
associateBatchFactor(Map<BioMaterial, T>, Map<T, FactorValue>) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
 
asUser() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
 
attach(Session, Object, Class<?>, Long) - Static method in class ubic.gemma.persistence.util.EntityUtils
Expert only.
attachCriteria(Criteria, BioSequence, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
Restricts the query to the provided BioSequence.
attachCriteria(Criteria, Characteristic, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
Restricts the query to the provided OntologyEntry.
attachCriteria(Criteria, DatabaseEntry, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
Restricts query to the given DatabaseEntry association
attachCriteria(Criteria, Gene, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
Restricts the query to the provided Gene.
attachCriteria(Criteria, PhysicalLocation, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
attachCriteria(Criteria, Taxon, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
Restricts query to the given Taxon.
attachCriteria(DetachedCriteria, DatabaseEntry, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
attributesToRetrieveFromBioMartForProteinQuery(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
Method that based on the taxon supplied constructs an array of attributes that can be queried on.
Auditable - Interface in ubic.gemma.model.common
Created by tesarst on 07/03/17.
AuditableObject - Class in ubic.gemma.core.analysis.report
 
AuditableObject() - Constructor for class ubic.gemma.core.analysis.report.AuditableObject
 
AuditableUtil - Interface in ubic.gemma.core.security.audit
 
AuditableUtilImpl - Class in ubic.gemma.core.security.audit
A few utility methods to filter collections
AuditableUtilImpl() - Constructor for class ubic.gemma.core.security.audit.AuditableUtilImpl
 
AuditAction - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditActionEnum - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditActionEnum() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditActionEnum
Default constructor.
AuditAdvice - Class in ubic.gemma.core.security.audit
Manage audit trails on objects.
AuditAdvice() - Constructor for class ubic.gemma.core.security.audit.AuditAdvice
 
AuditController - Class in ubic.gemma.web.remote
This is required solely for exposing auditables to remote services would try to marshall the abstract class Auditable.
AuditController() - Constructor for class ubic.gemma.web.remote.AuditController
 
AuditEvent - Class in ubic.gemma.model.common.auditAndSecurity
An event in the life of an object.
AuditEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEvent
 
AuditEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditEventDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditEventDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditEventDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
 
auditEvents2SampleRemovedFlags(Collection<AuditEvent>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
 
auditEventService - Variable in class ubic.gemma.core.util.AbstractSpringAwareCLI
 
AuditEventService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditEventServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditEventServiceImpl(AuditEventDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
 
AuditEventType - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
AuditEventType() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
No-arg constructor added to satisfy javabean contract
AuditEventValueObject - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditEventValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
Required when using the class as a spring bean.
AuditEventValueObject(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
 
AuditEventValueObject(AuditEvent) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
 
AuditHelper - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
This is to allow for a single way to deal with audit events and status update.
AuditHelperImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditHelperImpl() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelperImpl
 
AuditTrail - Class in ubic.gemma.model.common.auditAndSecurity
The trail of events (create or update) that occurred in an objects lifetime.
AuditTrail() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrail
 
AuditTrail.Factory - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditTrailDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditTrailDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditTrailDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl
 
AuditTrailImpl - Class in ubic.gemma.model.common.auditAndSecurity
 
AuditTrailImpl() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrailImpl
 
auditTrailService - Variable in class ubic.gemma.core.util.AbstractSpringAwareCLI
 
AuditTrailService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditTrailServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
AuditTrailServiceImpl(AuditTrailDao, AuditEventDao, CurationDetailsService) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
 
AUTH_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener
 
authenticate() - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
 
AUTO_OPTION_NAME - Static variable in class ubic.gemma.core.util.AbstractCLI
 
autoCode(Object, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Tries to guess the code of the response based on the given arguments, and creates a ResponseErrorObject if necessary.
AutomatedAnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Deprecated.
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.
AutomatedAnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent
Deprecated.
No-arg constructor added to satisfy javabean contract
AutomatedAnnotationEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Deprecated.
AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
 
autoSeek - Variable in class ubic.gemma.core.util.AbstractCLI
Automatically identify which entities to run the tool on.
autoSeekEventType - Variable in class ubic.gemma.core.util.AbstractCLI
The event type to look for the lack of, when using auto-seek.
avoidDownload - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
 

B

BAC - Static variable in class ubic.gemma.model.genome.biosequence.SequenceType
 
BackgroundJob<T extends TaskCommand,R extends TaskResult> - Class in ubic.gemma.core.job.executor.common
Deprecated.
BackgroundJob(T) - Constructor for class ubic.gemma.core.job.executor.common.BackgroundJob
Deprecated.
 
BASE_GO_URI - Static variable in interface ubic.gemma.core.ontology.providers.GeneOntologyService
 
BaseController - Class in ubic.gemma.web.controller
Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting messages in the session.
BaseController() - Constructor for class ubic.gemma.web.controller.BaseController
 
BaseDao<T> - Interface in ubic.gemma.persistence.service
Interface that supports basic CRUD operations.
BaseExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix
Base class for ExpressionDataMatrix implementations.
BaseExpressionDataMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
 
BaseFormController - Class in ubic.gemma.web.controller
Implementation of SimpleFormController that contains convenience methods for subclasses.
BaseFormController() - Constructor for class ubic.gemma.web.controller.BaseFormController
 
BaselineSelection - Class in ubic.gemma.core.analysis.expression.diff
Utilities for deciding if a factor value is a baseline condition.
BaselineSelection() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaselineSelection
 
BaseScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects
 
BaseScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
 
BaseService<O extends Identifiable> - Interface in ubic.gemma.persistence.service
Interface that supports basic CRUD operations.
BaseSpringContextTest - Class in ubic.gemma.core.util.test
subclass for tests that need the container and use the database
BaseSpringContextTest() - Constructor for class ubic.gemma.core.util.test.BaseSpringContextTest
 
BaseValueObject - Class in ubic.gemma.model
 
BaseValueObject() - Constructor for class ubic.gemma.model.BaseValueObject
 
BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service
Created by tesarst on 01/06/17.
BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service
Created by tesarst on 01/06/17.
BasicLineMapParser<K,T> - Class in ubic.gemma.core.loader.util.parser
A line parser that produces a Map instead of a Collection.
BasicLineMapParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineMapParser
 
BasicLineParser<T> - Class in ubic.gemma.core.loader.util.parser
A simple LineParser implementation that doesn't do anything.
BasicLineParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineParser
 
BATCH_CONF_HAS - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
BATCH_CONF_NO_HAS - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
BATCH_EFF_NONE - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
BATCH_EFF_STRONG - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
BATCH_EFF_WEAK - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
BATCH_FACTOR_CATEGORY_NAME - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
 
BATCH_FACTOR_CATEGORY_NAME - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
BATCH_FACTOR_CATEGORY_URI - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
 
BATCH_FACTOR_CATEGORY_URI - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
BATCH_FACTOR_NAME - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
 
BATCH_FACTOR_NAME - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
BATCH_FACTOR_NAME_PREFIX - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
 
BATCH_FACTOR_NAME_PREFIX - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
BatchConfound - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Test if an experimental design is confounded with batches.
BatchConfound() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
 
BatchConfoundValueObject - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Represents a summary of a batch effect confound.
BatchConfoundValueObject(ExpressionExperiment, ExperimentalFactor, double, int, double, int) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundValueObject
 
batchCorrect(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService
If possible, batch correct the processed data vectors.
batchCorrect(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl
 
BatchCorrectionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BatchCorrectionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent
No-arg constructor added to satisfy javabean contract
BatchCorrectionEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BatchEffectDetails - Class in ubic.gemma.core.analysis.preprocess.batcheffects
provide some basic information about the strength of a batch effect.
BatchEffectDetails(boolean, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
 
BatchEffectPopulationCli - Class in ubic.gemma.core.apps
For bulk processing of batch-info-fetching.
BatchEffectPopulationCli() - Constructor for class ubic.gemma.core.apps.BatchEffectPopulationCli
 
BatchInfoFetchController - Class in ubic.gemma.web.controller.analysis.preprocess
For populating "batch" information about experiments.
BatchInfoFetchController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
 
BatchInfoFetchTask - Interface in ubic.gemma.core.tasks.analysis.expression
 
BatchInfoFetchTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
 
BatchInfoFetchTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand
 
BatchInfoFetchTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
Task to try to get 'batch' information about an experiment.
BatchInfoFetchTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskImpl
 
BatchInfoParser - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Parse information on batch from raw data files.
BatchInfoParser() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
 
BatchInfoPopulationHelperService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects
 
BatchInfoPopulationHelperServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects
 
BatchInfoPopulationHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
 
BatchInfoPopulationService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects
Retrieve batch information from the data source, if possible, and populate it into experiments.
BatchInfoPopulationServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects
Retrieve batch information from the data source, if possible, and populate it into experiments.
BatchInfoPopulationServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
 
BatchInformationFetchingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Indicates that batch information was obtained
BatchInformationFetchingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent
No-arg constructor added to satisfy javabean contract
BatchInformationFetchingEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BatchProblemsUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BatchProblemsUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent
No-arg constructor added to satisfy javabean contract
BatchProblemsUpdateEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BeanNameGenerator - Class in ubic.gemma.persistence.util
Our \@Service etc.
BeanNameGenerator() - Constructor for class ubic.gemma.persistence.util.BeanNameGenerator
 
BibliographicPhenotypesValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
 
BibliographicPhenotypesValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
 
BibliographicPhenotypesValueObject(PhenotypeAssociation) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
 
BibliographicPhenotypesValueObject(String, Integer, Set<CharacteristicValueObject>) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
 
BibliographicReference - Class in ubic.gemma.model.common.description
 
BibliographicReference() - Constructor for class ubic.gemma.model.common.description.BibliographicReference
 
BibliographicReference.Factory - Class in ubic.gemma.model.common.description
 
BibliographicReferenceController - Interface in ubic.gemma.web.controller.common.description.bibref
Note: do not use parameterized collections as parameters for ajax methods.
BibliographicReferenceControllerImpl - Class in ubic.gemma.web.controller.common.description.bibref
This controller is responsible for showing a list of all bibliographic references, as well sending the user to the pubMed.Detail.view when they click on a specific link in that list.
BibliographicReferenceControllerImpl() - Constructor for class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
 
BibliographicReferenceDao - Interface in ubic.gemma.persistence.service.common.description
 
BibliographicReferenceDaoImpl - Class in ubic.gemma.persistence.service.common.description
 
BibliographicReferenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
bibliographicReferenceSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettingsImpl
Convenience method to get pre-configured settings.
BibliographicReferenceService - Interface in ubic.gemma.core.annotation.reference
 
BibliographicReferenceServiceImpl - Class in ubic.gemma.core.annotation.reference
Implementation of BibliographicReferenceService.
BibliographicReferenceServiceImpl(BibliographicReferenceDao) - Constructor for class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
 
BibliographicReferenceValueObject - Class in ubic.gemma.model.common.description
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
BibliographicReferenceValueObject() - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
Required when using the class as a spring bean.
BibliographicReferenceValueObject(Long) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
 
BibliographicReferenceValueObject(BibliographicReference) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
does not set related experiments field
BibliographicReferenceValueObject(Long, String, String, String, String, String, String, Date, String, String, String, Collection<ExpressionExperimentValueObject>) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
 
BibRefAnnotation - Class in ubic.gemma.model.common.description
 
BibRefAnnotation() - Constructor for class ubic.gemma.model.common.description.BibRefAnnotation
 
BibRefAnnotationImpl - Class in ubic.gemma.model.common.description
 
BibRefAnnotationImpl() - Constructor for class ubic.gemma.model.common.description.BibRefAnnotationImpl
 
BibRefUpdaterCli - Class in ubic.gemma.core.apps
Refreshes the information in all the bibliographic references in the system.
BibRefUpdaterCli() - Constructor for class ubic.gemma.core.apps.BibRefUpdaterCli
 
binFromRange(int, int) - Method in class ubic.gemma.model.genome.PhysicalLocation
 
binFromRange(int, int) - Static method in class ubic.gemma.persistence.util.SequenceBinUtils
return bin that this start-end segment is in
BIO_PROCESS_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
 
BioAssay - Class in ubic.gemma.model.expression.bioAssay
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
BioAssay() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssay
 
BioAssay.Factory - Class in ubic.gemma.model.expression.bioAssay
 
BioAssayController - Class in ubic.gemma.web.controller.expression.bioAssay
 
BioAssayController() - Constructor for class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
 
bioAssayCount - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
 
BioAssayDao - Interface in ubic.gemma.persistence.service.expression.bioAssay
 
BioAssayDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssay
 
BioAssayDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
 
BioAssayDimension - Class in ubic.gemma.model.expression.bioAssayData
Stores the order of BioAssays referred to in DataVectors.
BioAssayDimension() - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
 
BioAssayDimension.Factory - Class in ubic.gemma.model.expression.bioAssayData
 
BioAssayDimensionDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
 
BioAssayDimensionDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
BioAssayDimensionDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
 
BioAssayDimensionService - Interface in ubic.gemma.persistence.service.expression.bioAssayData
 
BioAssayDimensionServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
Spring Service base class for BioAssayDimensionService, provides access to all services and entities referenced by this service.
BioAssayDimensionServiceImpl(BioAssayDimensionDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
 
BioAssayDimensionValueObject - Class in ubic.gemma.model.expression.bioAssayData
 
BioAssayDimensionValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
Required when using the class as a spring bean.
BioAssayDimensionValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
Do not use this constructor unless this represents a subset of a persistent BioAssayDimension.
BioAssayDimensionValueObject(BioAssayDimension) - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
 
BioAssayOutlierProcessingTask - Interface in ubic.gemma.core.tasks.analysis.expression
 
BioAssayOutlierProcessingTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
 
BioAssayOutlierProcessingTaskCommand(Collection<Long>) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
 
BioAssayOutlierProcessingTaskCommand(Collection<Long>, boolean) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
 
BioAssayOutlierProcessingTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
Handle 'flagging' a sample as an outlier.
BioAssayOutlierProcessingTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskImpl
 
BioAssayService - Interface in ubic.gemma.persistence.service.expression.bioAssay
 
BioAssayServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssay
 
BioAssayServiceImpl(BioAssayDao, BioMaterialDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
 
BioAssaySet - Class in ubic.gemma.model.expression.experiment
Represents a set of BioAssays.
BioAssaySet() - Constructor for class ubic.gemma.model.expression.experiment.BioAssaySet
 
BioAssayValueObject - Class in ubic.gemma.model.expression.bioAssay
 
BioAssayValueObject() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
Required when using the class as a spring bean.
BioAssayValueObject(BioAssay, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
 
BioAssayValueObject(BioAssay, boolean, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
 
BioAssayValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
 
BiomartEnsembleNcbiParser - Class in ubic.gemma.core.loader.util.biomart
Parser for BioMart file.
BiomartEnsembleNcbiParser(Taxon, String[]) - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
Class needs to be initialised with taxon and which attributes have been used in query for biomart and thus what columns are in this file.
BiomartEnsemblNcbiFetcher - Class in ubic.gemma.core.loader.util.biomart
BioMart is a query-oriented data management system.
BiomartEnsemblNcbiFetcher() - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
 
biomartEnsemblNcbiFetcher - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
Fetcher is called to download files if bioMartFileName is null
BiomartEnsemblNcbiObjectGenerator - Class in ubic.gemma.core.loader.util.biomart
Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble protein id.
BiomartEnsemblNcbiObjectGenerator() - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
Constructor ensuring that fetcher is set.
bioMartEnsemblNcbiParser - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
A biomart parser which is constructed a new for each taxon due to slight file taxon differences
bioMartFileName - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
If this file name is set then implies that file is local and no remote call should be made to biomart service
BIOMARTPATH - Static variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
 
BioMaterial - Class in ubic.gemma.model.expression.biomaterial
In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
BioMaterial() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterial
 
BioMaterial.Factory - Class in ubic.gemma.model.expression.biomaterial
 
BioMaterialController - Class in ubic.gemma.web.controller.expression.biomaterial
 
BioMaterialController() - Constructor for class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
 
BioMaterialDao - Interface in ubic.gemma.persistence.service.expression.biomaterial
 
BioMaterialDaoImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
 
BioMaterialDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
 
BioMaterialMappingUpdate - Class in ubic.gemma.model.common.auditAndSecurity.eventType
To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.
BioMaterialMappingUpdate() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
No-arg constructor added to satisfy javabean contract
BioMaterialMappingUpdate.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
BioMaterialService - Interface in ubic.gemma.persistence.service.expression.biomaterial
 
BioMaterialServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
 
BioMaterialServiceImpl(BioMaterialDao, FactorValueDao, BioAssayDao, ExperimentalFactorDao) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
 
BioMaterialValueObject - Class in ubic.gemma.model.expression.biomaterial
 
BioMaterialValueObject() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
Required when using the class as a spring bean.
BioMaterialValueObject(Long) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
 
BioMaterialValueObject(BioMaterial) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
 
BioMaterialValueObject(BioMaterial, boolean) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
 
BioMaterialValueObject(BioMaterial, BioAssay) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
 
BioSequence - Class in ubic.gemma.model.genome.biosequence
The sequence of a biological polymer such as a protein or DNA.
BioSequence() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequence
No-arg constructor added to satisfy javabean contract
BioSequence.Factory - Class in ubic.gemma.model.genome.biosequence
 
BioSequence2GeneProduct - Class in ubic.gemma.model.association
An association between a BioSequence and a Gene Product.
BioSequence2GeneProduct() - Constructor for class ubic.gemma.model.association.BioSequence2GeneProduct
 
BioSequenceDao - Interface in ubic.gemma.persistence.service.genome.biosequence
 
BioSequenceDaoImpl - Class in ubic.gemma.persistence.service.genome.biosequence
 
BioSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
 
BioSequenceService - Interface in ubic.gemma.persistence.service.genome.biosequence
 
BioSequenceServiceImpl - Class in ubic.gemma.persistence.service.genome.biosequence
Spring Service base class for BioSequenceService, provides access to all services and entities referenced by this service.
BioSequenceServiceImpl(BioSequenceDao) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
 
BioSequenceValueObject - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BioSequenceValueObject() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
Required when using the class as a spring bean.
BlacklistCli - Class in ubic.gemma.core.apps
Add entries to the blacklist
BlacklistCli() - Constructor for class ubic.gemma.core.apps.BlacklistCli
 
BlacklistedEntity - Class in ubic.gemma.model.expression
 
BlacklistedEntity() - Constructor for class ubic.gemma.model.expression.BlacklistedEntity
 
BlacklistedEntityDao - Interface in ubic.gemma.persistence.service.expression.experiment
 
BlacklistedEntityDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
 
BlacklistedEntityDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
 
BlacklistedExperiment - Class in ubic.gemma.model.expression.experiment
TODO Document Me
BlacklistedExperiment() - Constructor for class ubic.gemma.model.expression.experiment.BlacklistedExperiment
 
BlacklistedPlatform - Class in ubic.gemma.model.expression.arrayDesign
 
BlacklistedPlatform() - Constructor for class ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform
 
BlacklistedValueObject - Class in ubic.gemma.model.expression
 
BlacklistedValueObject() - Constructor for class ubic.gemma.model.expression.BlacklistedValueObject
Required when using the class as a spring bean.
Blat - Interface in ubic.gemma.core.apps
 
BlatAssociation - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatAssociation() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
 
BlatAssociation.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatAssociationDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
BlatAssociationDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type BlatAssociation.
BlatAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
 
BlatAssociationScorer - Class in ubic.gemma.core.analysis.sequence
Given a set of BlatAssociations that might be redundant, clean them up and score them.
BlatAssociationScorer() - Constructor for class ubic.gemma.core.analysis.sequence.BlatAssociationScorer
 
BlatAssociationService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
BlatAssociationServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
Spring Service base class for BlatAssociationService, provides access to all services and entities referenced by this service.
BlatAssociationServiceImpl(BlatAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
 
blatFormatChromosomeName(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
Puts "chr" prefix on the chromosome name, if need be.
blatLocationsToIntArray(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
Convert a psl-formatted list (comma-delimited) to an int[].
blatQuery(BioSequence) - Method in interface ubic.gemma.core.apps.Blat
Run a BLAT search using the gfClient.
blatQuery(BioSequence, Taxon, boolean) - Method in interface ubic.gemma.core.apps.Blat
Run a BLAT search using the gfClient.
blatQuery(Collection<BioSequence>, boolean, Taxon) - Method in interface ubic.gemma.core.apps.Blat
 
blatQuery(Collection<BioSequence>, Taxon) - Method in interface ubic.gemma.core.apps.Blat
 
blatQuery(BioSequence) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
 
blatQuery(BioSequence, Taxon, boolean) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
 
blatQuery(Collection<BioSequence>, boolean, Taxon) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
 
blatQuery(Collection<BioSequence>, Taxon) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
 
BlatResult - Class in ubic.gemma.model.genome.sequenceAnalysis
Represents the result of a BLAT search.
BlatResult() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
 
BlatResult.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatResult2Psl - Class in ubic.gemma.core.analysis.sequence
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
BlatResult2Psl() - Constructor for class ubic.gemma.core.analysis.sequence.BlatResult2Psl
 
blatResult2PslTrack(BlatResult) - Static method in class ubic.gemma.core.analysis.sequence.BlatResult2Psl
Creates text that can be displayed directly as a track in UCSC, using their hgTracks program.
BlatResultDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
BlatResultDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.sequenceAnalysis.BlatResult.
BlatResultDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
 
BlatResultParser - Class in ubic.gemma.core.loader.genome
Loader to handle results generated by Jim Kent's Blat.
BlatResultParser() - Constructor for class ubic.gemma.core.loader.genome.BlatResultParser
 
BlatResultService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
BlatResultServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
Spring Service base class for BlatResultService, provides access to all services and entities referenced by this service.
BlatResultServiceImpl(BlatResultDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
 
BlatResultTrackController - Class in ubic.gemma.web.controller.genome
BlatResultTrackController() - Constructor for class ubic.gemma.web.controller.genome.BlatResultTrackController
 
BlatResultValueObject - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatResultValueObject() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
Required when using the class as a spring bean.
BlatResultValueObject(Long) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
 
BlatResultValueObject(BlatResult) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
 
BlatResultValueObject(Long, TaxonValueObject, Integer, String, Integer, Integer, Integer, Integer, Integer, Integer, BioSequenceValueObject, Integer, String, Integer, Double, Double, String, String, String, Long, Integer, Integer, Long, String) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
 
blockComplete(BioAssaySet, Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise.
blockingReceive() - Method in interface ubic.gemma.core.infrastructure.common.MessageReceiver
 
blockingReceive() - Method in class ubic.gemma.core.infrastructure.jms.JmsMessageReceiver
 
blockingReceiveMessage(Destination) - Method in interface ubic.gemma.core.infrastructure.jms.JMSHelper
 
blockingReceiveMessage(Destination) - Method in class ubic.gemma.core.infrastructure.jms.JMSHelperImpl
 
BoolArg - Class in ubic.gemma.web.services.rest.util.args
Class representing an API argument that should be a boolean.
BOOLEAN - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
BOOLEANARRAY - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
BooleanVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
This is used to represent missing value data.
BooleanVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
 
browse(Integer, Integer) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
 
browse(Integer, Integer, String, boolean) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
 
browse(Integer, Integer) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
 
browse(Integer, Integer, String, boolean) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
 
browse(Integer, Integer) - Method in interface ubic.gemma.persistence.service.BrowsingDao
 
browse(Integer, Integer, String, boolean) - Method in interface ubic.gemma.persistence.service.BrowsingDao
 
browse(Integer, Integer) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
browse(Integer, Integer, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
browse(Integer, Integer) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
Browse through the characteristics, excluding GO annotations.
browse(Integer, Integer, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
Browse through the characteristics, excluding GO annotations, with sorting.
browse(Integer, Integer) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
browse(Integer, Integer, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
browse(Integer, Integer) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
Browse through the characteristics, excluding GO annotations.
browse(Integer, Integer, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
Browse through the characteristics, excluding GO annotations.
browse(Integer, Integer) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
 
browse(Integer, Integer, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
 
browse(Integer, Integer) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
 
browse(Integer, Integer) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
browse(Integer, Integer) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
browse(Integer, Integer) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
 
browse(ListBatchCommand) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
 
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
 
browse(ListBatchCommand, Long[], boolean, boolean) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level? Is there security for ArrayDesigns? ids can be null
browse(ListBatchCommand, Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
 
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level.
browse(int, int, String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
AJAX
browseByTaxon(ListBatchCommand, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
 
browseSpecificIds(ListBatchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
AJAX call for remote paging store
BrowsingDao<T> - Interface in ubic.gemma.persistence.service
Support for paging through the data.
buildBadResponse(Document, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
 
buildDesignMatrix(List<ExperimentalFactor>, List<BioMaterial>, Map<ExperimentalFactor, FactorValue>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
Convert factors to a matrix usable in R.
buildFeedItems(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.rss.CustomRssViewer
 
buildFeedMetadata(Map<String, Object>, Channel, HttpServletRequest) - Method in class ubic.gemma.web.controller.common.rss.CustomRssViewer
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli
Deprecated.
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.BlacklistCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.CountObsoleteTermsCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeeqCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeoGrabberCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.IndexGemmaCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.LinkAnalysisCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.MeshTermFetcherCli
Deprecated.
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.MultifunctionalityCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.PubMedLoaderCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.ReplaceDataCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli
Deprecated.
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.SplitExperimentCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.SVDCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.TaxonLoaderCli
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.TwoChannelMissingValueCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.apps.VectorMergingCli
 
buildOptions(Options) - Method in class ubic.gemma.core.job.executor.worker.WorkerCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli
 
buildOptions(Options) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
 
buildOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI
Build option implementation.
buildStandardOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI
 
buildStandardOptions(Options) - Method in class ubic.gemma.core.util.AbstractSpringAwareCLI
 
buildWrapper(Document, Collection<String>, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
Function to handle the constructing of output in xml format for returning the response to the client.
BUNDLE_KEY - Static variable in class ubic.gemma.web.util.Constants
The name of the ResourceBundle used in this application
BusinessKey - Class in ubic.gemma.persistence.util
Methods to test business-key-related issues on objects.
BusinessKey() - Constructor for class ubic.gemma.persistence.util.BusinessKey
 
bytesRead(int) - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
 
bytesRead(int) - Method in class ubic.gemma.web.util.upload.UploadListener
 

C

cache(Map<Long, GeneCoexpressionTestedIn>) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
 
cache(Map<Long, GeneCoexpressionTestedIn>) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
 
CACHE_QUERY_STRINGENCY - Static variable in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
The stringency used to query when populating the cache.
cacheCoexpression(Long, Collection<CoexpressionValueObject>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
 
cacheCoexpression(Map<Long, List<CoexpressionValueObject>>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
 
cacheCoexpression(Long, Collection<CoexpressionValueObject>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
 
cacheCoexpression(Map<Long, List<CoexpressionValueObject>>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
 
CacheMonitor - Interface in ubic.gemma.web.util
 
CacheMonitorImpl - Class in ubic.gemma.web.util
Get statistics about and manage caches.
CacheMonitorImpl() - Constructor for class ubic.gemma.web.util.CacheMonitorImpl
 
cacheTestedIn(GeneCoexpressionTestedIn) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
 
cacheTestedIn(GeneCoexpressionTestedIn) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
 
CacheUtils - Class in ubic.gemma.persistence.util
Created by tesarst on 04/04/17.
CacheUtils() - Constructor for class ubic.gemma.persistence.util.CacheUtils
 
calculateExternalDatabasesStatistics() - Method in class ubic.gemma.web.controller.PhenotypeController
 
calculateGoTermOverlap(Gene, Collection<Long>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
Given a query Gene, and a collection of gene ids calculates the go term overlap for each pair of queryGene and gene in the given collection.
calculateGoTermOverlap(Gene, Gene) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
 
calculateGoTermOverlap(Long, Collection<Long>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
 
calculateGoTermOverlap(Gene, Collection<Long>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
calculateGoTermOverlap(Gene, Gene) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
calculateGoTermOverlap(Long, Collection<Long>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
calculateMetrics() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
 
calculateMetrics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
Calculate the linear correlation matrix of a matrix, allowing missing values.
calculateMetrics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
Compute correlations.
calculateScore(Long, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.GeeqService
Calculates the GEEQ score in the given mode for the experiment with the given id.
calculateScore(Long, String) - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
 
call() - Method in class ubic.gemma.core.job.executor.common.ExecutingTask
 
cancelJob(String) - Method in interface ubic.gemma.core.job.progress.ProgressStatusService
Attempt to cancel the job.
cancelJob(String) - Method in class ubic.gemma.core.job.progress.ProgressStatusServiceImpl
 
canCurrentUserEditExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
canCurrentUserEditGroup(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
canCurrentUserEditGroup(GeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
canDelete(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
 
canDelete(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
canDelete(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
 
canDelete(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
canRead() - Method in class ubic.gemma.model.common.description.LocalFile
 
canRetry(RetryContext) - Method in class ubic.gemma.persistence.retry.RetryPolicy
 
canServiceRemoteTasks() - Method in interface ubic.gemma.core.job.grid.util.JMSBrokerMonitor
 
canServiceRemoteTasks() - Method in class ubic.gemma.core.job.grid.util.JMSBrokerMonitorImpl
 
canSkipAclCheck(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
 
canSkipAssociationCheck(Object, String) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
 
canWrite() - Method in class ubic.gemma.model.common.description.LocalFile
 
CASE_INSENSITIVE_ORDER - Static variable in class ubic.gemma.web.util.LabelValue
Comparator that can be used for a case insensitive sort of LabelValue objects.
CATEGORICAL - Static variable in class ubic.gemma.model.common.quantitationtype.GeneralType
 
CATEGORICAL - Static variable in class ubic.gemma.model.expression.experiment.FactorType
 
category - Variable in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
 
categoryUri - Variable in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
 
Cell() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
 
CHANGE - Static variable in class ubic.gemma.model.common.measurement.MeasurementType
 
changePassword(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
changePasswordForUser(String, String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
ChannelUtils - Class in ubic.gemma.persistence.util
Determine if a quantitation type (by name) represents background or signal.
ChannelUtils() - Constructor for class ubic.gemma.persistence.util.ChannelUtils
 
CHAR - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
Characteristic - Class in ubic.gemma.model.common.description
Instances of this are used to describe other entities.
Characteristic() - Constructor for class ubic.gemma.model.common.description.Characteristic
No-arg constructor added to satisfy javabean contract
Characteristic.Factory - Class in ubic.gemma.model.common.description
 
characteristic2CharacteristicVO(Collection<? extends Characteristic>) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
CharacteristicBasicValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
 
CharacteristicBasicValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
Required when using the class as a spring bean.
CharacteristicBasicValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
 
CharacteristicBasicValueObject(Long, String, String, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
 
CharacteristicBasicValueObject(Characteristic) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
 
CharacteristicBrowserController - Class in ubic.gemma.web.controller.common
NOTE: Logging messages from this service are important for tracking changes to annotations.
CharacteristicBrowserController() - Constructor for class ubic.gemma.web.controller.common.CharacteristicBrowserController
 
CharacteristicConverter - Class in ubic.gemma.web.remote
 
CharacteristicConverter() - Constructor for class ubic.gemma.web.remote.CharacteristicConverter
 
CharacteristicDao - Interface in ubic.gemma.persistence.service.common.description
 
CharacteristicDaoImpl - Class in ubic.gemma.persistence.service.common.description
 
CharacteristicDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
CharacteristicService - Interface in ubic.gemma.persistence.service.common.description
 
CharacteristicServiceImpl - Class in ubic.gemma.persistence.service.common.description
 
CharacteristicServiceImpl(CharacteristicDao) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
 
CharacteristicUpdateCommand - Class in ubic.gemma.core.tasks.maintenance
 
CharacteristicUpdateCommand() - Constructor for class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
 
CharacteristicUpdateTask - Interface in ubic.gemma.core.tasks.maintenance
 
CharacteristicUpdateTaskImpl - Class in ubic.gemma.core.tasks.maintenance
This handles characteristic updates from the client: experiment tags, characteristic browser
CharacteristicUpdateTaskImpl(BioMaterialService, CharacteristicService, ExpressionExperimentService, FactorValueService, SecurityService) - Constructor for class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl
 
CharacteristicValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
ValueObject wrapper for a Characteristic
CharacteristicValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
Required when using the class as a spring bean.
CharacteristicValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
CharacteristicValueObject(Characteristic) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
CharacteristicValueObject(Long, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
CharacteristicValueObject(Long, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
CharacteristicValueObject(Long, String, String, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
characteristicValueObject2Characteristic(CharacteristicValueObject) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper
CharacteristicValueObject to Characteristic with no valueUri given
characteristicValueObject2Characteristic(CharacteristicValueObject) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl
 
CHARARRAY - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
check(O) - Method in class ubic.gemma.web.services.rest.util.args.MutableArg
Checks whether the given object is null, and throws an appropriate exception if necessary.
check(VO) - Method in class ubic.gemma.web.services.rest.util.args.MutableArg
Checks whether the response Value Object is null, and throws an appropriate exception if necessary.
checkCorrectability(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
Has it already been batch corrected? Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch?
checkCorrectability(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
 
checkForFile(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
 
checkHasBatchInfo(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
checkHasBatchInfo(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
checkKey(BibliographicReference) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(DesignElementDataVector) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(ExternalDatabase) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(FactorValue) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(User) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkKey(ExpressionExperimentSubSet) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkReqArg(Object, String) - Method in class ubic.gemma.web.services.rest.util.WebService
 
checkResult(String) - Method in interface ubic.gemma.core.job.progress.ProgressStatusService
 
checkResult(String) - Method in class ubic.gemma.core.job.progress.ProgressStatusServiceImpl
 
checkResult(String) - Method in class ubic.gemma.web.controller.TaskCompletionController
 
checkValidForLm(BioAssaySet, ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
Check that the factorValues are measurements, or that there are at least two assays for at least one factor value.
checkValidKey(ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(GeneProduct) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(LocalFile) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
checkValidKey(Unit) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
Chromosome - Class in ubic.gemma.model.genome
Immutable representation of a chromosome
Chromosome() - Constructor for class ubic.gemma.model.genome.Chromosome
No-arg constructor added to satisfy javabean contract
Chromosome(String, Taxon) - Constructor for class ubic.gemma.model.genome.Chromosome
 
Chromosome(String, ExternalDatabase, BioSequence, Taxon) - Constructor for class ubic.gemma.model.genome.Chromosome
 
ChromosomeDao - Interface in ubic.gemma.persistence.service.genome
 
ChromosomeDaoImpl - Class in ubic.gemma.persistence.service.genome
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.Chromosome.
ChromosomeDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeDaoImpl
 
ChromosomeFeature - Class in ubic.gemma.model.genome
Some part of a chromosome
ChromosomeFeature() - Constructor for class ubic.gemma.model.genome.ChromosomeFeature
No-arg constructor added to satisfy javabean contract
ChromosomeLocation - Class in ubic.gemma.model.genome
 
ChromosomeLocation() - Constructor for class ubic.gemma.model.genome.ChromosomeLocation
No-arg constructor added to satisfy javabean contract
ChromosomeService - Interface in ubic.gemma.persistence.service.genome
 
ChromosomeServiceImpl - Class in ubic.gemma.persistence.service.genome
Spring Service base class for ChromosomeService, provides access to all services and entities referenced by this service.
ChromosomeServiceImpl(ChromosomeDao) - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeServiceImpl
 
ChromosomeUtil - Class in ubic.gemma.persistence.util
A utility class for Chromosome
ChromosomeUtil() - Constructor for class ubic.gemma.persistence.util.ChromosomeUtil
 
CitationValueObject - Class in ubic.gemma.model.common.description
Represents a BibliographicReference as a citation string (which is really super light value object).
CitationValueObject() - Constructor for class ubic.gemma.model.common.description.CitationValueObject
 
ClassConverter - Class in ubic.gemma.web.remote
 
ClassConverter() - Constructor for class ubic.gemma.web.remote.ClassConverter
 
CLASSIC_HOME_PAGE - Static variable in class ubic.gemma.web.controller.WebConstants
 
clazz - Variable in class ubic.gemma.web.taglib.ConstantsTag
The class to expose the variables from.
cleanUp(File) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
 
cleanupMultipart(MultipartHttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
 
cleanUpQueryName(String) - Static method in class ubic.gemma.core.loader.genome.BlatResultParser
 
clear() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
Clear/null data so this object can be reused.
clear() - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
Remove old results.
clear() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
 
clear(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
Remove the data for a given platform (use to save memory)
clear(GeoPlatform, List<GeoSample>, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
If possible, null out the data for a quantitation type on a given platform.
clear() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
Used during recomputation only.
clearAllCaches() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
Flush (clear) all caches.
clearAllCaches() - Method in interface ubic.gemma.web.util.CacheMonitor
Remove all items from all caches.
clearAllCaches() - Method in class ubic.gemma.web.util.CacheMonitorImpl
 
clearBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
 
clearCache() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
clearCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
Remove all elements from the cache for the given result set, if the cache exists.
clearCache() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
clearCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
clearCache() - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
Remove all elements from the cache.
clearCache() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
 
clearCache() - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
 
clearCache() - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
 
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
 
clearCache(Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
 
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
 
clearCache(Long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
 
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
 
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
 
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
 
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
clearCache(String) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
Flush (clear) a cache.
clearCache(String) - Method in interface ubic.gemma.web.util.CacheMonitor
Remove all items from the cache given
clearCache(String) - Method in class ubic.gemma.web.util.CacheMonitorImpl
 
clearCaches(Long) - Method in interface ubic.gemma.core.visualization.ExperimentalDesignVisualizationService
removed the cached layouts and cached BioAssayDimensions for this experiment (could be a subset?)
clearCaches(Long) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
 
clearFromCaches(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
AJAX clear entries in caches relevant to experimental design for the experiment passed in.
clearTopHitCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
Remove all elements from the top hits cache for the given result set, if the cache exists.
clearTopHitCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
close() - Method in class ubic.gemma.core.job.executor.common.LogBasedProgressAppender
 
close(RetryContext, RetryCallback<T>, Throwable) - Method in class ubic.gemma.persistence.retry.RetryLogger
Called after the final attempt (successful or not).
close() - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
 
code(Response.Status, Object, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
 
code200(Object, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Creates a new 200 response object.
code204(HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Creates a new 204 response object.
code400(String, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Creates a new 400 response object.
code404(String, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Creates a new 404 response object.
code503(String, HttpServletResponse) - Static method in class ubic.gemma.web.services.rest.util.Responder
Creates a 503 response object.
CoexpCorrelationDistribution - Class in ubic.gemma.model.analysis.expression.coexpression
 
CoexpCorrelationDistribution() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
 
CoexpCorrelationDistribution.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
 
CoexpressionAnalysis - Class in ubic.gemma.model.analysis.expression.coexpression
A coexpression analysis of one experiment.
CoexpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
 
CoexpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
 
CoexpressionAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.coexpression
 
CoexpressionAnalysisDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.coexpression
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.
CoexpressionAnalysisDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl
 
CoexpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.coexpression
Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
CoexpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.coexpression
 
CoexpressionAnalysisServiceImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
 
CoexpressionCache - Interface in ubic.gemma.persistence.service.association.coexpression
Cache for coexpression results.
CoexpressionCacheImpl - Class in ubic.gemma.persistence.service.association.coexpression
Configures the cache for gene2gene coexpression.
CoexpressionCacheImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
 
CoexpressionCacheValueObject - Class in ubic.gemma.persistence.service.association.coexpression
Used to cache results; these objects are unmodifiable, and contains the coexpression data for one query gene and one result gene, in all experiments.
CoexpressionCacheValueObject(CoexpressionValueObject) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject
 
CoexpressionDao - Interface in ubic.gemma.persistence.service.association.coexpression
 
CoexpressionDaoImpl - Class in ubic.gemma.persistence.service.association.coexpression
Manages and queries coexpression 'links' between genes.
CoexpressionDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
 
CoexpressionMetaValueObject - Class in ubic.gemma.core.analysis.expression.coexpression
 
CoexpressionMetaValueObject() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
 
CoexpressionNodeDegreeDao - Interface in ubic.gemma.persistence.service.association.coexpression
 
CoexpressionNodeDegreeDaoImpl - Class in ubic.gemma.persistence.service.association.coexpression
 
CoexpressionNodeDegreeDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDaoImpl
 
coexpressionSearch(Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService
 
coexpressionSearch(Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
 
CoexpressionSearchCommand - Class in ubic.gemma.core.analysis.expression.coexpression
 
CoexpressionSearchCommand() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
 
CoexpressionSearchController - Class in ubic.gemma.web.controller.coexpressionSearch
 
CoexpressionSearchController() - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
 
coexpressionSearchQuick(Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService
Skips some of the postprocessing steps, use in situations where raw speed is more important than details.
coexpressionSearchQuick(Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
 
CoexpressionService - Interface in ubic.gemma.persistence.service.association.coexpression
A key service for working with coexpression at a fairly low level.
CoexpressionServiceImpl - Class in ubic.gemma.persistence.service.association.coexpression
 
CoexpressionServiceImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
 
CoexpressionSummaryValueObject - Class in ubic.gemma.core.analysis.expression.coexpression
 
CoexpressionSummaryValueObject(Long) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
 
CoexpressionValueObject - Class in ubic.gemma.persistence.service.association.coexpression
Lightweight/convenient object for manipulating coexpression for a pair of genes.
CoexpressionValueObject(Gene2GeneCoexpression) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
Construct a value object.
CoexpressionValueObject(Long, Long, Boolean, Integer, Long, Set<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
 
CoexpressionValueObject(Long, String, boolean, Long, String, Integer, Long, Collection<Long>, Collection<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
 
CoexpressionValueObject(Long, String, boolean, Long, String, Integer, Long, Set<Long>, Set<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
 
CoexpressionValueObjectExt - Class in ubic.gemma.core.analysis.expression.coexpression
A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
CoexpressionValueObjectExt() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
 
CoexSearchTaskCommand - Class in ubic.gemma.web.controller.coexpressionSearch
 
CoexSearchTaskCommand(CoexpressionSearchCommand) - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
 
collapse(Collection<Reporter>) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
Convert a CompositeSequence's immobilizedCharacteristics into a single sequence, using a simple merge-join strategy.
columns(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
 
columns() - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
 
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
 
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
 
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
 
columns() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
Total number of columns.
columns(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
Number of columns that use the given design element.
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
 
ComBat<R,C> - Class in ubic.gemma.core.analysis.preprocess.batcheffects
An implementation of the ComBat algorithm described by Johson et al as described in:
ComBat(DoubleMatrix<R, C>, ObjectMatrix<C, String, ?>) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat
 
comBat(ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
Run ComBat using default settings (parametric)
comBat(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
 
comBat(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
 
comBat(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
 
combineFilters(List<ObjectFilter[]>, S) - Method in class ubic.gemma.web.services.rest.util.args.ArrayEntityArg
Combines the given filters with the properties in this array to create a final filter to be used for VO retrieval.
commence(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ubic.gemma.web.services.rest.util.RestAuthEntryPoint
 
COMMENT_MARK - Static variable in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
Lines starting with this will be ignored.
CommentedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
An event indicating a comment was added to the auditable.
CommentedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent
No-arg constructor added to satisfy javabean contract
CommentedEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
CommonPersister - Class in ubic.gemma.persistence.persister
Persister for ubic.gemma.model.common package classes.
CommonPersister() - Constructor for class ubic.gemma.persistence.persister.CommonPersister
 
CommonQueries - Class in ubic.gemma.persistence.util
Contains methods to perform 'common' queries that are needed across DAOs.
CommonQueries() - Constructor for class ubic.gemma.persistence.util.CommonQueries
 
CommonsConfigurationPropertyPlaceholderConfigurer - Class in ubic.gemma.persistence.util
A PropertyPlaceholderConfigurer that also can take a Configuration.
CommonsConfigurationPropertyPlaceholderConfigurer() - Constructor for class ubic.gemma.persistence.util.CommonsConfigurationPropertyPlaceholderConfigurer
 
CommonsMultipartFile - Class in ubic.gemma.web.util.upload
Deprecated.
CommonsMultipartFile(FileItem) - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartFile
Deprecated.
Create an instance wrapping the given FileItem.
CommonsMultipartMonitoredResolver - Class in ubic.gemma.web.util.upload
An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
CommonsMultipartMonitoredResolver() - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
 
compare(Describable, Describable) - Method in class ubic.gemma.persistence.util.DescribableComparator
 
compare(DifferentialExpressionAnalysisResult, DifferentialExpressionAnalysisResult) - Method in class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator
 
compare(FactorValue, FactorValue) - Method in class ubic.gemma.persistence.util.FactorValueComparator
 
compare(Gene, Gene) - Method in class ubic.gemma.web.util.GeneSymbolComparator
 
compareTo(CoexpressionValueObjectExt) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
 
compareTo(CompositeSequenceMapValueObject) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
compareTo(ExpressionDataMatrixRowElement) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
 
compareTo(GeoData) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
compareTo(SearchResult) - Method in class ubic.gemma.core.search.SearchResult
 
compareTo(SearchResultDisplayObject) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
 
compareTo(Direction) - Method in class ubic.gemma.model.analysis.expression.diff.Direction
 
compareTo(Gene2GeneCoexpression) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
 
compareTo(GOEvidenceCode) - Method in class ubic.gemma.model.association.GOEvidenceCode
 
compareTo(PhenotypeMappingType) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
compareTo(AuditAction) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditAction
 
compareTo(AbstractCuratableValueObject<C>) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
 
compareTo(CitationValueObject) - Method in class ubic.gemma.model.common.description.CitationValueObject
 
compareTo(DatabaseType) - Method in class ubic.gemma.model.common.description.DatabaseType
 
compareTo(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
 
compareTo(MeasurementKind) - Method in class ubic.gemma.model.common.measurement.MeasurementKind
 
compareTo(MeasurementType) - Method in class ubic.gemma.model.common.measurement.MeasurementType
 
compareTo(GeneralType) - Method in class ubic.gemma.model.common.quantitationtype.GeneralType
 
compareTo(PrimitiveType) - Method in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
compareTo(ScaleType) - Method in class ubic.gemma.model.common.quantitationtype.ScaleType
 
compareTo(StandardQuantitationType) - Method in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
 
compareTo(TechnologyType) - Method in class ubic.gemma.model.expression.arrayDesign.TechnologyType
 
compareTo(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
 
compareTo(FactorType) - Method in class ubic.gemma.model.expression.experiment.FactorType
 
compareTo(PolymerType) - Method in class ubic.gemma.model.genome.biosequence.PolymerType
 
compareTo(SequenceType) - Method in class ubic.gemma.model.genome.biosequence.SequenceType
 
compareTo(Object) - Method in class ubic.gemma.model.genome.ChromosomeLocation
 
compareTo(BibliographicPhenotypesValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
 
compareTo(CharacteristicValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject
 
compareTo(EvidenceValueObject<E>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
 
compareTo(ExternalDatabaseStatisticsValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
 
compareTo(PhenotypeAssPubValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
 
compareTo(SimpleTreeValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
 
compareTo(Object) - Method in class ubic.gemma.model.genome.PhysicalLocation
 
compareTo(ThreePrimeDistanceMethod) - Method in class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
 
compareTo(CoexpressionValueObject) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
 
compareTo(NonPersistentNonOrderedCoexpLink) - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
 
compareTo(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
 
compareTo(LabelValue) - Method in class ubic.gemma.web.util.LabelValue
 
CompassUtils - Class in ubic.gemma.persistence.util
Utility methods to manipulate compass (and lucene).
CompassUtils() - Constructor for class ubic.gemma.persistence.util.CompassUtils
 
CompositeSequence - Class in ubic.gemma.model.expression.designElement
A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
CompositeSequence() - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequence
No-arg constructor added to satisfy javabean contract
CompositeSequence.Factory - Class in ubic.gemma.model.expression.designElement
 
CompositeSequenceArg<T> - Class in ubic.gemma.web.services.rest.util.args
Mutable argument type base class for Composite Sequence arguments.
CompositeSequenceArg() - Constructor for class ubic.gemma.web.services.rest.util.args.CompositeSequenceArg
 
CompositeSequenceController - Class in ubic.gemma.web.controller.expression.designElement
 
CompositeSequenceController() - Constructor for class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
 
CompositeSequenceDao - Interface in ubic.gemma.persistence.service.expression.designElement
 
CompositeSequenceDaoImpl - Class in ubic.gemma.persistence.service.expression.designElement
 
CompositeSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
 
CompositeSequenceGeneMapperService - Class in ubic.gemma.core.analysis.service
 
CompositeSequenceGeneMapperService() - Constructor for class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
 
CompositeSequenceIdArg - Class in ubic.gemma.web.services.rest.util.args
Composite Sequence argument for CS ID.
CompositeSequenceMapSummary - Class in ubic.gemma.core.analysis.sequence
This is a convenience object to hold the results of CompositeSequence mapping results.
CompositeSequenceMapSummary(CompositeSequence) - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
 
CompositeSequenceMapValueObject - Class in ubic.gemma.core.analysis.sequence
 
CompositeSequenceMapValueObject() - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
CompositeSequenceNameArg - Class in ubic.gemma.web.services.rest.util.args
Composite Sequence argument for CS name.
CompositeSequenceParser - Class in ubic.gemma.core.loader.expression.arrayDesign
Parse the "old" array description format.
CompositeSequenceParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
 
compositeSequenceSearch(String, ArrayDesign) - Static method in class ubic.gemma.model.common.search.SearchSettingsImpl
Convenience method to get pre-configured settings.
compositeSequenceService - Variable in class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
 
CompositeSequenceService - Interface in ubic.gemma.persistence.service.expression.designElement
 
CompositeSequenceServiceImpl - Class in ubic.gemma.persistence.service.expression.designElement
 
CompositeSequenceServiceImpl(CompositeSequenceDao, BioSequenceService, GeneProductService, BlatResultService) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
 
CompositeSequenceValueObject - Class in ubic.gemma.model.expression.designElement
 
CompositeSequenceValueObject() - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
Required when using the class as a spring bean.
CompositeSequenceValueObject(Long) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
 
CompositeSequenceValueObject(CompositeSequence) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
 
CompositeSequenceValueObject(Describable, ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
 
CompositeSequenceValueObject(Long, String, String, ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
 
compositeSequenceWithoutBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
compositeSequenceWithoutBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
compositeSequenceWithoutBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
 
compositeSequenceWithoutBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
compositeSequenceWithoutBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
compositeSequenceWithoutBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
compositeSequenceWithoutBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
 
compositeSequenceWithoutBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
compositeSequenceWithoutGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
compositeSequenceWithoutGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
compositeSequenceWithoutGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
 
compositeSequenceWithoutGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
Compound - Class in ubic.gemma.model.expression.biomaterial
 
Compound() - Constructor for class ubic.gemma.model.expression.biomaterial.Compound
No-arg constructor added to satisfy javabean contract
Compound.Factory - Class in ubic.gemma.model.expression.biomaterial
 
CompoundDao - Interface in ubic.gemma.persistence.service.expression.biomaterial
 
CompoundDaoImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.biomaterial.Compound.
CompoundDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.CompoundDaoImpl
 
CompoundService - Interface in ubic.gemma.persistence.service.expression.biomaterial
 
CompoundServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
Spring Service base class for CompoundService, provides access to all services and entities referenced by this service.
CompoundServiceImpl(CompoundDao) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl
 
compute(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
Computes sample correlation matrices for the given experiment.
compute(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
 
computeHitListSizes(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
Generate HitListSize entities that will be stored to count the number of diff.
computeHitListSizes(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
 
computeMatrixSimilarity(Gene, Gene, DoubleMatrix<Long, String>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetric
 
computeMaxSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetric
 
computeMergedOverlap(List<Gene>, List<Gene>, Map<Long, Collection<String>>) - Method in class ubic.gemma.core.ontology.GoMetric
Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs.
computeMissingValues(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
 
computeMissingValues(ExpressionExperiment, double, Collection<Double>) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
 
computeMissingValues(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
 
computeMissingValues(ExpressionExperiment, double, Collection<Double>) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
 
computeOverlap(PhysicalLocation, PhysicalLocation) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
Compute the overlap between two physical locations.
computeOverlap(Collection<OntologyTerm>, Collection<OntologyTerm>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
 
computeOverlap(Collection<OntologyTerm>, Collection<OntologyTerm>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
computeOverlap(long, long, long, long) - Static method in class ubic.gemma.model.genome.PhysicalLocation
 
computeOverlap(PhysicalLocation) - Method in class ubic.gemma.model.genome.PhysicalLocation
 
computeOverlapFraction(BlatAssociation) - Static method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorer
Compute how much the BLAT alignment with the target gene product is as a fraction of the query sequence length.
computeProcessedExpressionData(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
This method should not be called on its own, if possible.
computeProcessedExpressionData(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
computeSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetric
 
computeSimpleOverlap(Gene, Gene, Map<Long, Collection<String>>) - Method in class ubic.gemma.core.ontology.GoMetric
 
CONCENTRATION - Static variable in class ubic.gemma.model.common.measurement.MeasurementKind
 
Condition(ExpressionExperimentValueObject, DifferentialExpressionAnalysisValueObject, DiffExResultSetSummaryValueObject, FactorValueValueObject) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
 
Condition(Long, Long) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
 
CONFIDENCEINDICATOR - Static variable in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
 
CONFIG - Static variable in class ubic.gemma.web.util.Constants
The name of the configuration hashmap stored in application scope.
configExperimentalFactorValueObject(ExperimentalFactor) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
 
configExperimentalFactorValueObject(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
 
configExpressionExperimentValueObject(ExpressionExperimentValueObject) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
 
configExpressionExperimentValueObject(ExpressionExperimentValueObject) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
 
ConfigurationCookie - Class in ubic.gemma.web.util
Cookie class that also presents a commons configuration interface.
ConfigurationCookie(Cookie) - Constructor for class ubic.gemma.web.util.ConfigurationCookie
Used when loading cookies from the user.
ConfigurationCookie(String) - Constructor for class ubic.gemma.web.util.ConfigurationCookie
Create a cookie with the given name.
confirmRegistration(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
 
connect(int) - Method in class ubic.gemma.core.util.NetDatasourceUtil
 
Constants - Class in ubic.gemma.web.util
Constant values used throughout the application.
Constants() - Constructor for class ubic.gemma.web.util.Constants
 
ConstantsTag - Class in ubic.gemma.web.taglib
This class is designed to put all the public variables in a class to a specified scope - designed for exposing a Constants class to Tag Libraries.
ConstantsTag() - Constructor for class ubic.gemma.web.taglib.ConstantsTag
 
ConstantsTei - Class in ubic.gemma.web.taglib
Implementation of TagExtraInfo for the constants tag, identifying the scripting object(s) to be made visible.
ConstantsTei() - Constructor for class ubic.gemma.web.taglib.ConstantsTei
 
constructBioAssayName(BioMaterial, Collection<BioAssay>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
 
constructBioAssayName(ExpressionDataMatrix<?>, int) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
Constructs a bioassay name.
constructCitation(BibliographicReference) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
 
constructCitations(Collection<BibliographicReference>) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
 
constructConditionId(long, long) - Static method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
constructFactorValueName(FactorValue) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
Replaces spaces and hyphens with underscores.
Contact - Class in ubic.gemma.model.common.auditAndSecurity
Representing a person or organization that can be contacted about, or is the source of, data in the system.
Contact() - Constructor for class ubic.gemma.model.common.auditAndSecurity.Contact
No-arg constructor added to satisfy javabean contract
Contact.Factory - Class in ubic.gemma.model.common.auditAndSecurity
 
ContactDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
ContactDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
ContactDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl
 
ContactService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
 
ContactServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
 
ContactServiceImpl(ContactDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.ContactServiceImpl
 
contains(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
 
contains(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
 
containsGene(Gene, GeneSet) - Static method in class ubic.gemma.model.genome.gene.GeneSet
 
containsKey(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
 
containsKey(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
 
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
 
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
 
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
 
containsKey(String) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
 
containsKey(Integer) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
 
containsKey(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
containsKey(K) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
 
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
 
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.web.listener.StartupListener
 
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
 
CONTINUOUS - Static variable in class ubic.gemma.model.expression.experiment.FactorType
 
ContrastResult - Class in ubic.gemma.model.analysis.expression.diff
Represents a contrast between "conditions".
ContrastResult() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastResult
 
ContrastResult.Factory - Class in ubic.gemma.model.analysis.expression.diff
 
ContrastsValueObject - Class in ubic.gemma.model.analysis.expression.diff
Stores selected details of the contrasts for a single DifferentialExpressionResult
ContrastsValueObject(Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
 
ContrastVO - Class in ubic.gemma.model.analysis.expression.diff
Helper object, not for general use.
ContrastVO(Long, Long, Double, Double, Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastVO
 
ControllerUtils - Class in ubic.gemma.web.controller
Created by tesarst on 09/03/17.
ControllerUtils() - Constructor for class ubic.gemma.web.controller.ControllerUtils
 
convert(Collection<? extends GeoData>) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
 
convert(GeoData) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
 
convert(Collection<? extends GeoData>) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
 
convert(GeoData) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
 
convert(SimpleExpressionExperimentMetaData, DoubleMatrix<String, String>) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
 
convert(SimpleExpressionExperimentMetaData, DoubleMatrix<String, String>) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
 
convert(Collection<?>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(Object) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(NCBIGene2Accession, Gene) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(NcbiGeneData) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(BlockingQueue<NcbiGeneData>, BlockingQueue<Gene>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(Collection<? extends S>) - Method in interface ubic.gemma.core.loader.util.converter.Converter
 
convert(S) - Method in interface ubic.gemma.core.loader.util.converter.Converter
 
convert2CitationValueObject(BibliographicReference) - Static method in class ubic.gemma.model.common.description.CitationValueObject
 
convert2CitationValueObjects(Collection<BibliographicReference>) - Static method in class ubic.gemma.model.common.description.CitationValueObject
 
convert2ValueObject(Gene) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject
Converts a Gene to a GeneValueObject
convert2ValueObjects(Collection<SubmittedTask<? extends TaskResult>>) - Static method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
 
convert2ValueObjects(Collection<BibliographicReference>) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
does not set related experiments field
convert2ValueObjects(Collection<BioAssay>) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
 
convertData(List<Object>, QuantitationType) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
 
convertData(List<Object>, QuantitationType) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
Convert a vector of strings into a byte[] for saving in the database.
converter - Variable in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
 
Converter<S,T> - Interface in ubic.gemma.core.loader.util.converter
Defines a class that can convert objects from one type to another.
convertFromBytes(List<Object>, PrimitiveType, DesignElementDataVector) - Method in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
 
convertFromGeneSetValueObject(GeneSetValueObject, String) - Static method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
 
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.CharacteristicConverter
 
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.DirectionConverter
 
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.GOEvidenceCodeConverter
 
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.ScaleTypeConverter
 
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.StandardQuantitationTypeConverter
 
convertMembers2GeneValueObjects(Collection<GeneSetMember>) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject
A static method for easily converting GeneSetMembers into GeneValueObjects
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.ClassConverter
 
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.DoublePointConverter
 
convertSearchResults2SearchResultDisplayObjects(List<SearchResult>) - Static method in class ubic.gemma.core.search.SearchResultDisplayObject
Creates a collection of SearchResultDisplayObjects from a collection of objects.
convertStringToExperimentType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
gene expression array-based, gene expression SAGE-based, gene expression MPSS-based, gene expression RT-PCR-based, protein expression array-based, protein expression MS-based, array CGH, ChIP-chip, SNP Complete list of possibilities according to Nathaniel (6/2018) Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Non-coding RNA profiling by array Genome variation profiling by genome tiling array Genome variation profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing Genome variation profiling by SNP array SNP genotyping by SNP array Expression profiling by genome tiling array Genome variation profiling by array Expression profiling by RT-PCR Methylation profiling by high throughput sequencing Genome binding/occupancy profiling by genome tiling array Methylation profiling by genome tiling array Methylation profiling by array Genome binding/occupancy profiling by array Expression profiling by SAGE Protein profiling by protein array Genome binding/occupancy profiling by SNP array Non-coding RNA profiling by genome tiling array Third-party reanalysis Expression profiling by MPSS Expression profiling by SNP array Methylation profiling by SNP array Protein profiling by Mass Spec
convertStringToMolecule(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
convertStringToPlatformType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
 
convertStringToRepeatType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
Convert a string e.g.
convertStringToSampleType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
 
convertStringToSeriesType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
See also GeoDataset.convertStringToExperimentType
convertStringToType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
Convert a string found in the GEO sample descriptions e.g., "age" to the corresponding category, represented here by VariableType.
convertStringToValueType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
count, log ratio, log2 ratio, log10 ratio, logE ratio, log e ratio, transformed count
convertSubsetToExperimentalFactor(ExpressionExperiment, GeoSubset) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
Converts Geo subsets to experimental factors.
convertSubsetToExperimentalFactor(ExpressionExperiment, GeoSubset) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
 
convertToEntity(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelper
Tries to load an existing experiment set with the param's id, if no experiment can be loaded, create a new one with id = null.
convertToEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
 
convertToGOValueObject(GeneSet, String, String) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
Method to create a GO group object from an ad hoc entity
convertToGOValueObject(GeneSet, String, String) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
convertToLightValueObject(GeneSet) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
Constructor to build value object from GeneSet.
convertToLightValueObject(GeneSet) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
results will be sorted by size
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
convertToValueObject(GeneDifferentialExpressionMetaAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService
Convert the given meta-analysis into detail value object.
convertToValueObject(GeneDifferentialExpressionMetaAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl
 
convertToValueObject(GeneSet) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
Constructor to build value object from GeneSet.
convertToValueObject(GeneSet) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
convertToValueObjects(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
 
convertToValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
 
convertToValueObjects(Collection<GeneSet>) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
convertToValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
 
COORDINATE - Static variable in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
Used to represent a value for a spatial coordinate
copy() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
 
copy(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
 
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
 
copy(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
Copies a bioMaterial.
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
 
copyUploadedFile(HttpServletRequest, String) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
 
copyUploadedFile(MultipartFile, HttpServletRequest) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
 
copyUploadedInputStream(InputStream) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
 
correctedPvalue(int, int, double, int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
 
CORRELATION - Static variable in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
 
correlFast(double[], double[], int, int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
 
CORSFilter - Class in ubic.gemma.web.services.rest.util
 
CORSFilter() - Constructor for class ubic.gemma.web.services.rest.util.CORSFilter
 
COUNT - Static variable in class ubic.gemma.model.common.measurement.MeasurementKind
 
COUNT - Static variable in class ubic.gemma.model.common.quantitationtype.ScaleType
Indicates value was (originally) an integer count of something, such as RNAseq reads.
COUNT - Static variable in class ubic.gemma.model.common.quantitationtype.StandardQuantitationType
Indicates value is a count, such as the number of sequencing reads.
count() - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
 
COUNT_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener
 
countAll() - Method in class ubic.gemma.persistence.service.AbstractDao
 
countAll() - Method in class ubic.gemma.persistence.service.AbstractService
 
countAll() - Method in interface ubic.gemma.persistence.service.BaseDao
Counts all instances of specific class in the persitent storage.
countAll() - Method in interface ubic.gemma.persistence.service.BaseService
 
countAll() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
 
countDownregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
 
countDownregulated(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
 
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
counts the evidence that from neurocarta that came from a specific MetaAnalysis
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
 
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
 
countLinks(Gene, BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
 
countLinks(Gene, BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
 
countLinks(BioAssaySet, Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
 
countLinks(BioAssaySet, Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
 
countNotTroubled() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
 
countNotTroubled() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
countNotTroubled() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
countNotTroubled() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
countObsoleteOccurrences(int, int, int) - Method in interface ubic.gemma.core.ontology.OntologyService
 
countObsoleteOccurrences(int, int, int) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
 
CountObsoleteTermsCli - Class in ubic.gemma.core.apps
 
CountObsoleteTermsCli() - Constructor for class ubic.gemma.core.apps.CountObsoleteTermsCli
 
countOccurrences(Collection<CharacteristicValueObject>, Map<String, CharacteristicValueObject>) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
 
countOldLinks(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
 
countOldLinks(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
 
countOldLinks(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
 
countOldLinks(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
 
countPrivateGeneForEachNode(Map<String, Set<Integer>>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
counts each private occurrence of genes for a phenotype
countProbesMeetingThreshold(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
 
countProbesMeetingThreshold(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
countPublicGeneForEachNode(Map<String, Set<Integer>>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
counts each public occurrence of genes for a phenotype
countRowsInTable(String) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
Count the rows in the given table.
countUpregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
 
countUpregulated(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
create(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
 
create(ExpressionAnalysisResultSet) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl
 
create(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceService
Retrieve (and if necessary compute) the mean-variance relationship for the experiment
create(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceImpl
 
create(ArrayDesign, Boolean) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
Create (or update) all the annotation files for the given platform.
create(ArrayDesign, Boolean) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
 
create(BibliographicReference) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
 
create(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
 
create(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
 
create(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
 
create(Collection<GeneSet>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
 
create(GeneSet) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
 
create(SimpleExpressionExperimentMetaData, InputStream) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
Parses, converts (into Gemma objects), and loads data into the database.
create(SimpleExpressionExperimentMetaData, InputStream) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
 
create(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
create(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
CREATE - Static variable in class ubic.gemma.model.common.auditAndSecurity.AuditAction
 
create(Collection<ArrayDesign>) - Static method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
 
create(Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractDao
 
create(T) - Method in class ubic.gemma.persistence.service.AbstractDao
 
create(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractService
 
create(O) - Method in class ubic.gemma.persistence.service.AbstractService
 
create(CoexpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
 
create(CoexpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
 
create(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
 
create(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
create(GeneDifferentialExpressionMetaAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
 
create(GeneDifferentialExpressionMetaAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
 
create(ExpressionExperiment, DoubleMatrix<CompositeSequence, Integer>, double[], DoubleMatrix<Integer, BioMaterial>, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
 
create(ExpressionExperiment, DoubleMatrix<CompositeSequence, Integer>, double[], DoubleMatrix<Integer, BioMaterial>, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
 
create(double, Long, Long) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
 
create(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
 
create(PhenotypeAssociation) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
 
create(GenericExperiment) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
 
create(PhenotypeAssociation) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
 
create(GenericExperiment) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
 
create(Collection<T>) - Method in interface ubic.gemma.persistence.service.BaseDao
Crates all the given entities in the persistent storage.
create(T) - Method in interface ubic.gemma.persistence.service.BaseDao
Create an object.
create(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseService
Creates all the given entities in a persistent storage
create(O) - Method in interface ubic.gemma.persistence.service.BaseService
Creates the given entity in the persistent storage.
create(AuditTrail) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
 
create(Collection<C>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
 
create(C) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
 
create() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsDao
 
create() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsDaoImpl
Creates new CurationDetails object and persists it.
create(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
 
create(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
 
create(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
 
create(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
 
create(Collection<BioAssay>) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
 
create(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
 
create(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
 
create(Collection<T>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
Creates a new instance of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector and adds from the passed in entities collection
create(T) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
 
create(Collection<T>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDaoImpl
 
create(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
 
create(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
 
create(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
create(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
 
create(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
 
create(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
 
create(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
 
create(Collection<GeneSet>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
create(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
create(Collection<GeneSetMember>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetMemberDaoImpl
 
create(Collection<AnnotationAssociation>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
 
create(AnnotationAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
 
create(BlatAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
 
create(Collection<BlatResult>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
 
create(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
 
create(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
AJAX create an entities in the database based on the value objects passed in
createBatchFactor(ExpressionExperiment, Map<BioMaterial, Date>) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
 
createBatchFactor(ExpressionExperiment, Map<BioMaterial, Date>) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
 
createBioMartEnsembleNcbi(String[]) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
Given an array of strings representing the line to parse then create a BioMartEnsembleNcbi value object with some validation.
createBiomaterialTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
 
createDatabaseEntity(GeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
create an entity in the database based on the value object parameter
createDatabaseEntity(GeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
 
createDesignFromFile(Long, String) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
 
createDesignFromFile(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
createEELink(BioAssaySet, Long, Long, Long) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
 
createExperimentalFactor(EntityDelegator, ExperimentalFactorValueObject) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Creates a new ExperimentalFactor and adds it to the ExperimentalDesign specified by the EntityDelegator.
createExperimentalFactor(EntityDelegator, ExperimentalFactorValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
createExperimentTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
Ajax
createFactorValue(EntityDelegator) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Creates a new FactorValue and adds it to the ExperimentalFactor specified by the EntityDelegator.
createFactorValue(EntityDelegator) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
createFactorValueCharacteristic(EntityDelegator, Characteristic) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Creates a new Characteristic and adds it to the FactorValue specified by the EntityDelegator.
createFactorValueCharacteristic(EntityDelegator, Characteristic) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
createFile(File) - Static method in class ubic.gemma.persistence.util.EntityUtils
 
createFromValueObject(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
 
createFromValueObject(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
createGroup(String, List<GrantedAuthority>) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
createGroup(String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
 
createGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
 
createItem(String, String, boolean, String) - Method in class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
 
createMeanVariance(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
 
createMeanVariance(ExpressionExperiment, MeanVarianceRelation) - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelperImpl
 
createOrLoadCache(CacheManager, String, boolean, int, boolean, boolean, int, int, boolean) - Static method in class ubic.gemma.persistence.util.CacheUtils
Either creates new Cache instance of given name, or retrieves it from the CacheManager, if it already exists.
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
 
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
 
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
Maintenance method.
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
 
createOrUpdateAclSpecialCases(MutableAcl, Acl, Sid, Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
 
createPrimaryPublication(String) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperService
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperServiceImpl
 
createProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
Populate the processed data for the given experiment.
createProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
 
createProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
Populate the processed data for the given experiment.
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
createProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
createProcessedExpressionData(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperService
 
createProcessedExpressionData(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperServiceImpl
 
createQueryObject(Criteria, FactorValue) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Criteria, Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Criteria, GeneProduct) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Session, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Session, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Session, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Session, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Session, Unit) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryObject(Criteria, ExpressionExperimentSubSet) - Static method in class ubic.gemma.persistence.util.BusinessKey
 
createQueryStringFromMap(Map<String, String[]>, String) - Static method in class ubic.gemma.web.util.RequestUtil
Builds a query string from a given map of parameters
createRelevantPublication(String) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
 
createRnaSeqBatchFactor(ExpressionExperiment, Map<BioMaterial, String>) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
For RNA-seq, we based the batching on the available device/run/flowcell/lane information
createRnaSeqBatchFactor(ExpressionExperiment, Map<BioMaterial, String>) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
 
createSpringContext(CommandLine) - Method in class ubic.gemma.core.job.executor.worker.WorkerCLI
 
createSpringContext(CommandLine) - Method in class ubic.gemma.core.util.AbstractSpringAwareCLI
check if using test or production contexts
createSupportDetails(Gene, Gene, Boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
 
createSupportDetails(Long, Long, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
 
createUser(UserDetails) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
createValueObject() - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
Special use case.
createValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
 
createValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
 
createVectorMatrix(Map<Long, Collection<String>>, boolean) - Method in class ubic.gemma.core.ontology.GoMetric
 
createWriteFolder() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI
 
creator() - Method in class ubic.gemma.core.util.SystemArchitectureAspect
Methods that create new objects in the persistent store
crud() - Method in class ubic.gemma.core.util.SystemArchitectureAspect
 
CtdDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype
 
CtdDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
 
ctx - Variable in class ubic.gemma.core.util.AbstractSpringAwareCLI
 
Curatable - Interface in ubic.gemma.model.common.auditAndSecurity.curation
Created by tesarst on 06/03/17.
CuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation
Created by tesarst on 13/03/17.
CURATED - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
CurationDetails - Class in ubic.gemma.model.common.auditAndSecurity.curation
Class encapsulating all the curation information for Curatable objects.
CurationDetails() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
 
CurationDetails(Date, AuditEvent, Boolean, AuditEvent, Boolean, AuditEvent, String) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
 
CurationDetailsDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
Created by tesarst on 13/03/17.
CurationDetailsDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
Data access object for Curation Details
CurationDetailsDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsDaoImpl
 
CurationDetailsEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Event types that can change CurationDetails of Curatable objects.
CurationDetailsEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent
No-arg constructor added to satisfy javabean contract
CurationDetailsEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Throws an exception, as CurationDetailsEvent can not be instantiated.
CurationDetailsService - Class in ubic.gemma.persistence.service.common.auditAndSecurity
Service handling manipulation with Curation Details.
CurationDetailsService() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsService
 
curationNote - Variable in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
 
CurationNoteUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Indicates that previous validation is being invalidated
CurationNoteUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent
No-arg constructor added to satisfy javabean contract
CurationNoteUpdateEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
CustomRssViewer - Class in ubic.gemma.web.controller.common.rss
 
CustomRssViewer() - Constructor for class ubic.gemma.web.controller.common.rss.CustomRssViewer
 
cvs2tsv(String) - Static method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
 

D

daily(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
 
DAO_AD_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_BIOASSAY_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_CHARACTERISTIC_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_EE_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_GEEQ_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_GENE_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_PROBE_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
DAO_TAXON_ALIAS - Static variable in class ubic.gemma.persistence.util.ObjectFilter
 
daoMethod() - Method in class ubic.gemma.core.util.SystemArchitectureAspect
This pointcut is used to apply audit and acl advice at DAO boundary.
DATA_ARCHIVE_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
DATA_DIR - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
DATA_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
DATA_FILE_SUFFIX_COMPRESSED - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
DataAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Indicates that a data type (for a specific QuantitationType, possibly new) was added.
DataAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent
No-arg constructor added to satisfy javabean contract
DataAddedEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
DataAnalysisEvidence - Class in ubic.gemma.model.association.phenotype
Evidence due to a data analysis
DataAnalysisEvidence() - Constructor for class ubic.gemma.model.association.phenotype.DataAnalysisEvidence
 
DatabaseBackedGeneSetValueObject - Class in ubic.gemma.model.genome.gene
 
DatabaseBackedGeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject
default constructor to satisfy java bean contract
DatabaseEntry - Class in ubic.gemma.model.common.description
A reference to a record in a database.
DatabaseEntry() - Constructor for class ubic.gemma.model.common.description.DatabaseEntry
No-arg constructor added to satisfy javabean contract
DatabaseEntry.Factory - Class in ubic.gemma.model.common.description
 
DatabaseEntryArg<T> - Class in ubic.gemma.web.services.rest.util.args
Mutable argument type base class for DatabaseEntry API.
DatabaseEntryArg() - Constructor for class ubic.gemma.web.services.rest.util.args.DatabaseEntryArg
 
DatabaseEntryDao - Interface in ubic.gemma.persistence.service.common.description
 
DatabaseEntryDaoImpl - Class in ubic.gemma.persistence.service.common.description
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type DatabaseEntry.
DatabaseEntryDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
 
DatabaseEntryIdArg - Class in ubic.gemma.web.services.rest.util.args
Long argument type for DatabaseEntry API, referencing the Taxon ID.
DatabaseEntryService - Interface in ubic.gemma.persistence.service.common.description
 
DatabaseEntryServiceImpl - Class in ubic.gemma.persistence.service.common.description
Spring Service base class for DatabaseEntryService, provides access to all services and entities referenced by this service.
DatabaseEntryServiceImpl(DatabaseEntryDao) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl
 
DatabaseEntryStringArg - Class in ubic.gemma.web.services.rest.util.args
String argument type for DatabaseEntry API, Can also be null.
DatabaseEntryTag - Class in ubic.gemma.web.taglib
 
DatabaseEntryTag() - Constructor for class ubic.gemma.web.taglib.DatabaseEntryTag
 
DatabaseEntryValueObject - Class in ubic.gemma.model.common.description
ValueObject for database entry
DatabaseEntryValueObject(DatabaseEntry) - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
 
DatabaseEntryValueObject(long) - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
 
DatabaseEntryValueObject() - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
Required when using the class as a spring bean.
DatabaseType - Class in ubic.gemma.model.common.description
 
DatabaseTypeEnum - Class in ubic.gemma.model.common.description
 
DatabaseTypeEnum() - Constructor for class ubic.gemma.model.common.description.DatabaseTypeEnum
Default constructor.
DatabaseViewGenerator - Interface in ubic.gemma.core.analysis.report
 
DatabaseViewGeneratorCLI - Class in ubic.gemma.core.apps
Simple driver of DatabaseViewGenerator.
DatabaseViewGeneratorCLI() - Constructor for class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
 
DatabaseViewGeneratorImpl - Class in ubic.gemma.core.analysis.report
Generates textual views of the database so other people can use the data.
DatabaseViewGeneratorImpl() - Constructor for class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl
 
DataFileFetcher - Class in ubic.gemma.core.loader.expression.arrayExpress
ArrayExpress stores files in an FTP site as tarred-gzipped archives.
DataFileFetcher() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
 
DataReplacedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the system.
DataReplacedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent
No-arg constructor added to satisfy javabean contract
DataReplacedEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
DATASET_FOLDER_NAME - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
 
datasetAnnotations(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the annotations for the given dataset.
DatasetArg<T> - Class in ubic.gemma.web.services.rest.util.args
Mutable argument type base class for dataset (ExpressionExperiment) API.
DatasetArg() - Constructor for class ubic.gemma.web.services.rest.util.args.DatasetArg
 
DatasetCombiner - Class in ubic.gemma.core.loader.expression.geo
Class to handle cases where there are multiple GEO dataset for a single actual experiment.
DatasetCombiner() - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombiner
 
DatasetCombiner(boolean) - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombiner
 
datasetData(DatasetArg<Object>, BoolArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the data for the given dataset.
datasetDesign(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the design for the given dataset.
datasetDiffAnalysis(DatasetArg<Object>, IntArg, IntArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the differential analysis results for the given dataset.
datasetExpressions(ArrayDatasetArg, ArrayGeneArg, BoolArg, ExpLevelConsolidationArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the expression levels of given genes on given datasets.
datasetExpressionsDiffEx(ArrayDatasetArg, LongArg, DoubleArg, IntArg, BoolArg, ExpLevelConsolidationArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the expression levels of genes highly expressed in the given component on given datasets.
datasetExpressionsPca(ArrayDatasetArg, IntArg, IntArg, BoolArg, ExpLevelConsolidationArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the expression levels of genes highly expressed in the given component on given datasets.
DatasetFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher
Retrieve GEO GDS files from the NCBI FTP server.
DatasetFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
 
datasetFetcher - Variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
 
DatasetFilterArg - Class in ubic.gemma.web.services.rest.util.args
Filter argument for ExpressionExperiment filtering.
datasetHasBatch(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Returns true if the experiment has had batch information successfully filled in.
DatasetIdArg - Class in ubic.gemma.web.services.rest.util.args
Long argument type for dataset API, referencing the Dataset ID.
datasetPlatforms(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves platforms for the given dataset.
datasets(ArrayStringArg, DatasetFilterArg, IntArg, IntArg, SortArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.AnnotationsWebService
Does a search for datasets containing characteristics matching the given string.
datasets(ArrayDatasetArg, DatasetFilterArg, IntArg, IntArg, SortArg, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves all datasets matching the given identifiers.
datasetSamples(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the samples for the given dataset.
DatasetStringArg - Class in ubic.gemma.web.services.rest.util.args
String argument type for dataset API, referencing the Dataset short name.
datasetSVD(DatasetArg<Object>, HttpServletResponse) - Method in class ubic.gemma.web.services.rest.DatasetsWebService
Retrieves the design for the given dataset.
DatasetsWebService - Class in ubic.gemma.web.services.rest
RESTful interface for datasets.
DatasetsWebService() - Constructor for class ubic.gemma.web.services.rest.DatasetsWebService
Required by spring
DatasetsWebService(ExpressionExperimentService, ExpressionDataFileService, ArrayDesignService, BioAssayService, ProcessedExpressionDataVectorService, GeneService, SVDService, DifferentialExpressionAnalysisService, AuditEventService) - Constructor for class ubic.gemma.web.services.rest.DatasetsWebService
Constructor for service autowiring
DataUpdater - Class in ubic.gemma.core.loader.expression
Update or fill in the data associated with an experiment.
DataUpdater() - Constructor for class ubic.gemma.core.loader.expression.DataUpdater
 
DataVector - Class in ubic.gemma.model.expression.bioAssayData
An abstract class representing a one-dimensional vector of data about some aspect of an experiment.
DataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVector
 
DataVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
 
DataVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
Required when using the class as a spring bean.
DataVectorValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
 
DataVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
 
DataVectorValueObject(DesignElementDataVector, Collection<Long>, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
 
date - Variable in class ubic.gemma.core.analysis.report.AuditableObject
 
deBlatFormatChromosomeName(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
Removes "chr" prefix from the chromosome name, if it is there.
debugMap(Map<?, ?>) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
Print content of map if debug is set to true.
decrementSessions() - Static method in class ubic.gemma.web.listener.UserTracker
 
DEDVController - Class in ubic.gemma.web.controller.expression.experiment
Exposes methods for accessing underlying Design Element Data Vectors.
DEDVController() - Constructor for class ubic.gemma.web.controller.expression.experiment.DEDVController
 
DEDVfromEEIDGeneIDEndpoint - Class in ubic.gemma.web.services
Given a list Experiment IDs and a list gene IDs will return design element data vectors (DEDV), all the genes that could have been responsible for that DEDV (only needs to contain 1 of the given genes) and the Expression Experiment that the data came from.
DEDVfromEEIDGeneIDEndpoint() - Constructor for class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
 
DEDVRankEndpoint - Class in ubic.gemma.web.services
Given a collection of gene IDs, a collection of experiment IDs, and the method, the service will return a list of genes mapped to a list of space delimited ranks.
DEDVRankEndpoint() - Constructor for class ubic.gemma.web.services.DEDVRankEndpoint
 
deepCopy(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DirectionEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.association.GOEvidenceCodeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
deepCopy(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditActionEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.description.DatabaseTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.measurement.MeasurementKindEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.measurement.MeasurementTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.quantitationtype.GeneralTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.quantitationtype.PrimitiveTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.quantitationtype.ScaleTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.common.quantitationtype.StandardQuantitationTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.expression.arrayDesign.TechnologyTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.expression.experiment.FactorTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.genome.biosequence.PolymerTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.genome.biosequence.SequenceTypeEnum
 
deepCopy(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethodEnum
 
deepCopy(Object) - Method in class ubic.gemma.persistence.model.usertypes.HibernateByteBlobType
 
DEFAULT_ALLOW_PARS - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
 
DEFAULT_ALLOW_PREDICTED - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
 
DEFAULT_BLAT_SCORE_THRESHOLD - Static variable in interface ubic.gemma.core.apps.Blat
This value is basically a threshold fraction of aligned bases in the query.
DEFAULT_DISTINCTVALUE_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_EBAYES - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
Default value for whether empirical Bayes moderation of test statistics should be used.
DEFAULT_HIGHEXPRESSION_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_IDENTITY_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
Sequence identity below which we throw hits away (expressed as a fraction)
DEFAULT_LOWEXPRESSIONCUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_LOWVARIANCECUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
Fraction of bases which must overlap with an annotated exon.
DEFAULT_MINPRESENT_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_PA_LIMIT - Static variable in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
 
DEFAULT_PROBE_DEGREE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
probes with more links than this are ignored.
DEFAULT_QC_IMAGE_SIZE_PX - Static variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
 
DEFAULT_SCORE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
BLAT score threshold below which we do not consider hits.
DEFAULT_SIGNAL_TO_NOISE_THRESHOLD - Static variable in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
 
DEFAULT_THRESHOLD - Static variable in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
 
DEFAULT_TOOSMALLTOKEEP - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
 
DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
 
defineTask(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
 
defineTask(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
 
delete(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
delete(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
 
DELETE - Static variable in class ubic.gemma.model.common.auditAndSecurity.AuditAction
 
delete(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
 
delete(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
 
delete(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
Delete the factor, its associated factor values and all differential expression analyses in which it is used.
delete(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
 
delete(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
 
delete(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
 
delete(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
Delete an arrayDesign.
delete(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
 
deleteAlignmentData(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
deleteAlignmentData(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
deleteAlignmentData(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
remove sequence alignment results associated with the bioSequences for this array design.
deleteAlignmentData(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
deleteAllFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
Delete any existing coexpression, data, or differential expression data files.
deleteAllFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
 
deleteAnalyses(BioAssaySet) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister
Remove any links and coexpression analyses for the given experiment.
deleteAnalyses(BioAssaySet) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl
 
deleteAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
Delete any differential expression analyses associated with the experiment.
deleteAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
 
deleteAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
Deletes the given analysis.
deleteAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
 
deleteById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
Exposed for AJAX calls.
deleteCookie(HttpServletResponse, Cookie, String) - Static method in class ubic.gemma.web.util.RequestUtil
Convenience method for deleting a cookie by name
deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
Security is handled within method
deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
 
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
Security is handled within method, when the set is loaded
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
 
deleteDatabaseEntity(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
Security is handled within method, when the set is loaded
deleteDatabaseEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
 
DeleteDiffExCli - Class in ubic.gemma.core.apps
Delete differential expression analsyes on a per-experiment basis.
DeleteDiffExCli() - Constructor for class ubic.gemma.core.apps.DeleteDiffExCli
 
DeleteEvidenceCLI - Class in ubic.gemma.core.loader.association.phenotype
When we need to remove all evidence from an external database, usually to reimport them after
DeleteEvidenceCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
 
deleteExistingFiles(ArrayDesign) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
 
deleteExistingFiles(ArrayDesign) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
 
deleteExperimentalFactors(EntityDelegator, Long[]) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Deletes the specified ExperimentalFactors and removes them from the ExperimentalDesign specified by the EntityDelegator.
deleteExperimentalFactors(EntityDelegator, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
DeleteExperimentsCli - Class in ubic.gemma.core.apps
Delete one or more experiments from the system.
DeleteExperimentsCli() - Constructor for class ubic.gemma.core.apps.DeleteExperimentsCli
 
deleteFactorValueCharacteristics(FactorValueValueObject[]) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Deletes the specified Characteristics from their parent FactorValues.
deleteFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
deleteFactorValues(Collection<Long>) - Method in interface ubic.gemma.core.expression.experiment.FactorValueDeletion
 
deleteFactorValues(Collection<Long>) - Method in class ubic.gemma.core.expression.experiment.FactorValueDeletionImpl
 
deleteFactorValues(EntityDelegator, Long[]) - Method in interface ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
Deletes the specified FactorValues and removes them from the ExperimentalFactor specified by the EntityDelegator.
deleteFactorValues(EntityDelegator, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl
 
deleteFile(File) - Static method in class ubic.gemma.persistence.util.EntityUtils
 
deleteFromTables(String...) - Method in class ubic.gemma.core.util.test.BaseSpringContextTest
Convenience method for deleting all rows from the specified tables.
deleteGeneProductAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
deleteGeneProductAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
deleteGeneProductAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
deletes the gene product associations on the specified array design F
deleteGeneProductAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
deleteGroup(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
deleteGroup(String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
AJAX
deleteGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
 
deleteLinks(Taxon, BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
 
deleteLinks(Taxon, BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
 
deleteLinks(BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
Maintenance method.
deleteLinks(BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
 
deleteOldAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.AnalysisUtilService
Remove all analyses for the experiment (Differential, Coexpression and PCA).
deleteOldAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl
 
deleteOldFiles(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
Delete outdated annotation and associated experiment files.
deleteOldFiles(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
 
deleter() - Method in class ubic.gemma.core.util.SystemArchitectureAspect
Methods that remove items in the persistent store
deleteStatistics(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
Remove old files which will otherwise be cruft.
deleteUser(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
DELIMITER - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint
 
DELIMITER_BETWEEN_BIOMATERIAL_AND_BIOASSAYS - Static variable in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
 
Describable - Class in ubic.gemma.model.common
 
Describable() - Constructor for class ubic.gemma.model.common.Describable
No-arg constructor added to satisfy javabean contract
DescribableComparator - Class in ubic.gemma.persistence.util
 
DescribableComparator() - Constructor for class ubic.gemma.persistence.util.DescribableComparator
 
description - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
 
DesignElementDataVector - Class in ubic.gemma.model.expression.bioAssayData
 
DesignElementDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
 
DesignElementDataVectorDao<T extends DesignElementDataVector> - Interface in ubic.gemma.persistence.service.expression.bioAssayData
 
DesignElementDataVectorDaoImpl<T extends DesignElementDataVector> - Class in ubic.gemma.persistence.service.expression.bioAssayData
 
DesignElementDataVectorServiceImpl<T extends DesignElementDataVector> - Class in ubic.gemma.persistence.service.expression.bioAssayData
 
DesignMatrixRowValueObject - Class in ubic.gemma.web.controller.expression.experiment
For the display of a summary table about experimental design.
DesignMatrixRowValueObject(FactorValueVector, int) - Constructor for class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
 
DesignMatrixRowValueObject.Factory - Class in ubic.gemma.web.controller.expression.experiment
 
destroy() - Method in class ubic.gemma.web.services.rest.util.CORSFilter
 
detailedFactorAnalysis(Long, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
 
determineAnalysis(BioAssaySet, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
 
determineAnalysis(BioAssaySet, Collection<ExperimentalFactor>, ExperimentalFactor, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
Determines the analysis to execute based on the experimental factors, factor values, and block design.
determineAnalysis(BioAssaySet, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
determineAnalysis(BioAssaySet, Collection<ExperimentalFactor>, ExperimentalFactor, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
determineAnalysisType(Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
Ajax method.
determineEncoding(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
Determine the encoding for the given request.
determineInterceptFactor(Collection<ExperimentalFactor>, QuantitationType) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
 
determineInterceptFactor(Collection<ExperimentalFactor>, QuantitationType) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
Determine if any factor should be treated as the intercept term.
DgaDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype
this importer cannot automatically download files it expects the files to already be there
DgaDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
 
diagnostics(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController
Only update the daignostics
diagnosticsOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
 
DifferentialExpressionAnalysis - Class in ubic.gemma.model.analysis.expression.diff
An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
 
DifferentialExpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.diff
 
DifferentialExpressionAnalysisCli - Class in ubic.gemma.core.apps
A command line interface to the DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisCli() - Constructor for class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
 
DifferentialExpressionAnalysisConfig - Class in ubic.gemma.core.analysis.expression.diff
Holds the settings used for differential expression analysis, and defines some defaults.
DifferentialExpressionAnalysisConfig() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
 
DifferentialExpressionAnalysisController - Class in ubic.gemma.web.controller.diff
A controller to run differential expression analysis either locally or in a space.
DifferentialExpressionAnalysisController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
 
DifferentialExpressionAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Indicates the experiment was the subject of a differential expression analysis.
DifferentialExpressionAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent
No-arg constructor added to satisfy javabean contract
DifferentialExpressionAnalysisEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
DifferentialExpressionAnalysisHelperService - Interface in ubic.gemma.core.analysis.expression.diff
Service methods to do database-related work for differential expression analysis
DifferentialExpressionAnalysisHelperServiceImpl - Class in ubic.gemma.core.analysis.expression.diff
Transactional methods for dealing with differential expression analyses.
DifferentialExpressionAnalysisHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl
 
DifferentialExpressionAnalysisRemoveTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex
Specialized command object for removing analysis results.
DifferentialExpressionAnalysisRemoveTaskCommand(ExpressionExperiment, DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
 
DifferentialExpressionAnalysisResult - Class in ubic.gemma.model.analysis.expression.diff
Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
DifferentialExpressionAnalysisResult() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
No-arg constructor added to satisfy javabean contract
DifferentialExpressionAnalysisResult.Factory - Class in ubic.gemma.model.analysis.expression.diff
 
DifferentialExpressionAnalysisResultComparator - Class in ubic.gemma.persistence.util
 
DifferentialExpressionAnalysisResultComparator() - Constructor for class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator
 
DifferentialExpressionAnalysisResultComparator.Factory - Class in ubic.gemma.persistence.util
 
DifferentialExpressionAnalysisResultSetVisualizationValueObject - Class in ubic.gemma.core.tasks.visualization
This class contains data for a column in metaheatmap visualization.
DifferentialExpressionAnalysisResultSetVisualizationValueObject(int[]) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
 
DifferentialExpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.diff
 
DifferentialExpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
 
DifferentialExpressionAnalysisServiceImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
 
DifferentialExpressionAnalysisTask - Interface in ubic.gemma.core.tasks.analysis.diffex
 
DifferentialExpressionAnalysisTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex
A command object to be used by spaces.
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
 
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment, DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
 
DifferentialExpressionAnalysisTaskCommand(String, boolean, ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
 
DifferentialExpressionAnalysisTaskImpl - Class in ubic.gemma.core.tasks.analysis.diffex
A differential expression analysis spaces task
DifferentialExpressionAnalysisTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImpl
 
DifferentialExpressionAnalysisUtil - Class in ubic.gemma.core.analysis.expression.diff
A helper class for the differential expression analyzers.
DifferentialExpressionAnalysisUtil() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
 
DifferentialExpressionAnalysisValueObject - Class in ubic.gemma.model.analysis.expression.diff
Summary of a differential expression analysis
DifferentialExpressionAnalysisValueObject(DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
Does not populate the resultSets.
DifferentialExpressionAnalyzerInfo - Class in ubic.gemma.web.controller.diff
Used to carry information about the experimental design analysis settings to clients.
DifferentialExpressionAnalyzerInfo() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
 
DifferentialExpressionAnalyzerService - Interface in ubic.gemma.core.analysis.expression.diff
 
DifferentialExpressionAnalyzerServiceImpl - Class in ubic.gemma.core.analysis.expression.diff
Differential expression service to run the differential expression analysis (and persist the results using the appropriate data access objects).
DifferentialExpressionAnalyzerServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
 
DifferentialExpressionAnalyzerServiceImpl.AnalysisType - Enum in ubic.gemma.core.analysis.expression.diff
Defines the different types of analyses our linear modeling framework supports: GENERICLM - generic linear regression (interactions are omitted, but this could change) OSTTEST - one sample t-test OWA - one-way ANOVA TTEST - two sample t-test TWO_WAY_ANOVA_WITH_INTERACTION TWO_WAY_ANOVA_NO_INTERACTION
DifferentialExpressionEvidence - Class in ubic.gemma.model.association.phenotype
Evidence documented by a differential expression result stored in the system
DifferentialExpressionEvidence() - Constructor for class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence
 
DifferentialExpressionEvidence.Factory - Class in ubic.gemma.model.association.phenotype
 
DifferentialExpressionEvidenceDao - Interface in ubic.gemma.persistence.service.association.phenotype
 
DifferentialExpressionEvidenceDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
 
DifferentialExpressionEvidenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDaoImpl
 
DifferentialExpressionEvidenceImpl - Class in ubic.gemma.model.association.phenotype
 
DifferentialExpressionEvidenceImpl() - Constructor for class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidenceImpl
 
DifferentialExpressionFileUtils - Class in ubic.gemma.core.analysis.expression.diff
 
DifferentialExpressionFileUtils() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
 
DifferentialExpressionGenesConditionsValueObject - Class in ubic.gemma.core.tasks.visualization
Represents a complete set of data for a differential expression query over a set of genes x conditions (resultSets x contrasts).
DifferentialExpressionGenesConditionsValueObject() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
DifferentialExpressionGenesConditionsValueObject.Cell - Class in ubic.gemma.core.tasks.visualization
 
DifferentialExpressionGenesConditionsValueObject.Condition - Class in ubic.gemma.core.tasks.visualization
Represents one column in the differential expression view; one contrast in a resultset in an experiment.
DifferentialExpressionGenesConditionsValueObject.DiffExGene - Class in ubic.gemma.core.tasks.visualization
 
DifferentialExpressionMetaAnalysisValueObject - Class in ubic.gemma.core.analysis.expression.diff
A value object with meta analysis results.
DifferentialExpressionMetaAnalysisValueObject() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
 
DifferentialExpressionProbeResultEndpoint - Class in ubic.gemma.web.services
Allows access to the differential expression analysis.
DifferentialExpressionProbeResultEndpoint() - Constructor for class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
 
DifferentialExpressionResultCache - Interface in ubic.gemma.persistence.service.analysis.expression.diff
Cache for differential expression results.
DifferentialExpressionResultCacheImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
Cache for data from differential expression result queries.
DifferentialExpressionResultCacheImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
DifferentialExpressionResultDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
 
DifferentialExpressionResultDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).
DifferentialExpressionResultDaoImpl(SessionFactory, DifferentialExpressionResultCache) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
 
DifferentialExpressionResultService - Interface in ubic.gemma.persistence.service.analysis.expression.diff
Main entry point to retrieve differential expression data.
DifferentialExpressionResultServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
 
DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao, ExpressionAnalysisResultSetDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
 
DifferentialExpressionSearchController - Class in ubic.gemma.web.controller.diff
A controller used to get differential expression analysis and meta analysis results.
DifferentialExpressionSearchController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController
 
DifferentialExpressionSearchTask - Interface in ubic.gemma.core.tasks.visualization
Created with IntelliJ IDEA.
DifferentialExpressionSearchTaskCommand - Class in ubic.gemma.core.tasks.visualization
Created with IntelliJ IDEA.
DifferentialExpressionSearchTaskCommand(Collection<GeneValueObject>, Collection<ExpressionExperimentDetailsValueObject>, String, String) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
 
DifferentialExpressionSearchTaskImpl - Class in ubic.gemma.core.tasks.visualization
Encapsulates the search for differential expression results, for a set of genes and experiments (which can be grouped)
DifferentialExpressionSearchTaskImpl() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl
 
DifferentialExpressionValueObject - Class in ubic.gemma.model.analysis.expression.diff
Represents the results for one probe.
DifferentialExpressionValueObject(DifferentialExpressionAnalysisResult) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
 
DifferentialExpressionValueObject(Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
 
DiffExAnalyzer - Interface in ubic.gemma.core.analysis.expression.diff
 
DiffExGene(long, String, String) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
 
DiffExMetaAnalyzerController - Class in ubic.gemma.web.controller.diff
A controller to analyze result sets either locally or in a space.
DiffExMetaAnalyzerController() - Constructor for class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
 
DiffExMetaAnalyzerService - Interface in ubic.gemma.core.analysis.expression.diff
Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially store the results.
DiffExMetaAnalyzerServiceImpl - Class in ubic.gemma.core.analysis.expression.diff
 
DiffExMetaAnalyzerServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
 
DiffExMetaAnalyzerTask - Interface in ubic.gemma.core.tasks.analysis.diffex
 
DiffExMetaAnalyzerTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex
A command object to be used by spaces.
DiffExMetaAnalyzerTaskCommand(Collection<Long>) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
 
DiffExMetaAnalyzerTaskCommand(Collection<Long>, String, String, boolean) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
 
DiffExMetaAnalyzerTaskImpl - Class in ubic.gemma.core.tasks.analysis.diffex
A differential expression meta-analysis space task
DiffExMetaAnalyzerTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskImpl
 
DiffExpressionEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
 
DiffExpressionEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
Required when using the class as a spring bean.
DiffExpressionEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
 
DiffExpressionEvidenceValueObject(DifferentialExpressionEvidence, GeneDifferentialExpressionMetaAnalysisSummaryValueObject) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
 
DiffExpressionEvidenceValueObject(Long, GeneDifferentialExpressionMetaAnalysis, GeneDifferentialExpressionMetaAnalysisResult, SortedSet<CharacteristicValueObject>, String, Double) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
 
DiffExpressionSearchCommand - Class in ubic.gemma.web.controller.diff
 
DiffExpressionSearchCommand() - Constructor for class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
 
DiffExpressionSelectedFactorCommand - Class in ubic.gemma.core.analysis.expression.diff
A command object with a selected factor and associated experiment.
DiffExpressionSelectedFactorCommand() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
 
DiffExpressionSelectedFactorCommand(Long, Long) - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
 
DiffExprGeneSearchResult - Class in ubic.gemma.model.analysis.expression.diff
Value object for differential expression result for one result - corresponds to the DifferentialExpressionAnalysisResults for one gene in one ResultSet (combined for multiple probes), but represents only the "selected" analysisResult.
DiffExprGeneSearchResult(Long, Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
 
DiffExResultSetSummaryValueObject - Class in ubic.gemma.model.analysis.expression.diff
Summary of a result set.
DiffExResultSetSummaryValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
 
DIRECT - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
Direction - Class in ubic.gemma.model.analysis.expression.diff
Represents the direction of a change e.g.
DirectionConverter - Class in ubic.gemma.web.remote
DWR converter for Direction type.
DirectionConverter() - Constructor for class ubic.gemma.web.remote.DirectionConverter
 
DirectionEnum - Class in ubic.gemma.model.analysis.expression.diff
Represents the direction of a change e.g.
DirectionEnum() - Constructor for class ubic.gemma.model.analysis.expression.diff.DirectionEnum
Default constructor.
disableEmail() - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil
 
disableEmail() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
For use in tests.
disableIndexMirroring(CompassGpsInterfaceDevice) - Static method in class ubic.gemma.persistence.util.CompassUtils
disables the index mirroring operation.
disableQuartzScheduler(StdScheduler) - Static method in class ubic.gemma.core.util.QuartzUtils
Turn off a scheduler.
disableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
Exposed to AJAX
disableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor
 
disableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl
 
disassemble(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DirectionEnum
 
disassemble(Object) - Method in class ubic.gemma.model.association.GOEvidenceCodeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
 
disassemble(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditActionEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.description.DatabaseTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.measurement.MeasurementKindEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.measurement.MeasurementTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.quantitationtype.GeneralTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.quantitationtype.PrimitiveTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.quantitationtype.ScaleTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.common.quantitationtype.StandardQuantitationTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.expression.arrayDesign.TechnologyTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.expression.experiment.FactorTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.genome.biosequence.PolymerTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.genome.biosequence.SequenceTypeEnum
 
disassemble(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethodEnum
 
disassemble(Object) - Method in class ubic.gemma.persistence.model.usertypes.HibernateByteBlobType
 
DISCLAIMER - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
 
disconnect(FTPClient) - Method in class ubic.gemma.core.util.NetDatasourceUtil
 
discontinuedIdForSymbol(String, Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
 
DISEASE_ONTOLOGY_ROOT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
 
dissociateFromSeries(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
This is used when we break a series up into two, along organism lines.
DISTANCE - Static variable in class ubic.gemma.model.common.measurement.MeasurementKind
 
DNA - Static variable in class ubic.gemma.model.genome.biosequence.PolymerType
 
DNA - Static variable in class ubic.gemma.model.genome.biosequence.SequenceType
Generic DNA sequence of any other type not representable by another value
doAll() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
 
doAuditAdvice(JoinPoint, Object) - Method in class ubic.gemma.core.security.audit.AuditAdvice
Entry point.
doBackgroundCoexSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
Used by CoexpressionSearchData.js - the main home page coexpression search.
doDelete - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
 
doEndTag() - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
 
doEndTag() - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
 
doEndTag() - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
 
doEndTag() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
 
doEndTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
 
doEndTag() - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
 
doesCurrentUserOwnExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
DoesNotNeedAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
An event that occurs when a curator has validated the entity and indicated that it is "approved".
DoesNotNeedAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent
No-arg constructor added to satisfy javabean contract
DoesNotNeedAttentionEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class ubic.gemma.web.services.rest.util.CORSFilter
 
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.web.services.rest.util.ExceptionHandlerFilter
 
done() - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
 
done() - Method in class ubic.gemma.web.util.upload.UploadListener
 
doNothingFilter(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
 
doSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
Important entry point - called by the CoexpressionSearchTask
doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in interface ubic.gemma.web.controller.GeneralSearchController
 
doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
 
doSearchQuickComplete(CoexpressionSearchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
Do a search that fills in the edges among the genes already found.
doStartTag() - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.ConstantsTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
 
doStartTag() - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
 
doSubmittedTasksMaintenance() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTasksMaintenance
Check if a task has been running or queued for too long, and cancel it if necessary.
doTask(FutureTask<Boolean>, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
 
doTask(FutureTask<Boolean>, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
 
doTask(FutureTask<Boolean>, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
 
DOUBLE - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
DoubleArg - Class in ubic.gemma.web.services.rest.util.args
Class representing an API argument that should be a double.
DOUBLEARRAY - Static variable in class ubic.gemma.model.common.quantitationtype.PrimitiveType
 
DoublePointConverter - Class in ubic.gemma.web.remote
The 8 decimal precision of a double is just a waste of bandwidth in most cases.
DoublePointConverter() - Constructor for class ubic.gemma.web.remote.DoublePointConverter
 
DoubleVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
Simple wrapper for a double[] that is derived from a DesignElementDataVector.
DoubleVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
Required when using the class as a spring bean.
DoubleVectorValueObject(ExpressionExperimentSubSet, DoubleVectorValueObject, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
Create a vector that is a slice of another one.
DoubleVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
 
DoubleVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject, Collection<Long>, BioAssayDimension) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.
DoubleVectorValueObject(DesignElementDataVector, Collection<Long>, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
 
DOWN - Static variable in class ubic.gemma.model.analysis.expression.diff.Direction
 
downloadAnnotationFile(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
 
downloadAnnotationFile(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
 
downloadFile(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
Regular spring MVC request to fetch a file that already has been generated.
downloadMetaFile(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
 
doWork() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
 
doWork() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli
Deprecated.
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
 
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
 
doWork() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
 
doWork() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
 
doWork() - Method in class ubic.gemma.core.apps.BlacklistCli
 
doWork() - Method in class ubic.gemma.core.apps.CountObsoleteTermsCli
 
doWork() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
 
doWork() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
 
doWork() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
 
doWork() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
 
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
 
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
 
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
 
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
 
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
 
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
 
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
 
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
 
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
 
doWork() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
 
doWork() - Method in class ubic.gemma.core.apps.GeeqCli
 
doWork() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
 
doWork() - Method in class ubic.gemma.core.apps.GeoGrabberCli
 
doWork() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
 
doWork() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
 
doWork() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
 
doWork() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
 
doWork() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
 
doWork() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli
Deprecated.
 
doWork() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
 
doWork() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
 
doWork() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
 
doWork() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
 
doWork() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
 
doWork() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
 
doWork() - Method in class ubic.gemma.core.apps.ReplaceDataCli
 
doWork() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli
Deprecated.
 
doWork() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
 
doWork() - Method in class ubic.gemma.core.apps.SplitExperimentCli
 
doWork() - Method in class ubic.gemma.core.apps.SVDCli
 
doWork() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
 
doWork() - Method in class ubic.gemma.core.apps.TwoChannelMissingValueCLI
 
doWork() - Method in class ubic.gemma.core.apps.VectorMergingCli
 
doWork() - Method in class ubic.gemma.core.job.executor.worker.WorkerCLI
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli
 
doWork() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
 
doWork() - Method in class ubic.gemma.core.util.AbstractCLI
Command line implementation.
DUALMODE - Static variable in class ubic.gemma.model.expression.arrayDesign.TechnologyType
Indicates this platform can be used in either a one- or two- channel mode.
DummyMailSender - Class in ubic.gemma.core.util.test
Mock mail sender for testing.
DummyMailSender() - Constructor for class ubic.gemma.core.util.test.DummyMailSender
 
dumps(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.PhenotypeWebService
Finds all dumps.
DumpsValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
 
DumpsValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
 
DumpsValueObject(String, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
 
DUPLICATE_PROBE_NAME_MUNGE_SEPARATOR - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
When we encounter two probes with the same name, we add this string along with a unique identifier to the end of the name.

E

editUser(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
Entry point for updates.
Eigenvalue - Class in ubic.gemma.model.analysis.expression.pca
 
Eigenvalue() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvalue
No-arg constructor added to satisfy javabean contract
Eigenvalue.Factory - Class in ubic.gemma.model.analysis.expression.pca
 
Eigenvector - Class in ubic.gemma.model.analysis.expression.pca
A right singular vector (a.k.a.
Eigenvector() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvector
No-arg constructor added to satisfy javabean contract
Eigenvector.Factory - Class in ubic.gemma.model.analysis.expression.pca
 
EITHER - Static variable in class ubic.gemma.model.analysis.expression.diff.Direction
 
EmailNotificationContext - Class in ubic.gemma.core.job
author: anton date: 10/02/13
EmailNotificationContext(String, String, String) - Constructor for class ubic.gemma.core.job.EmailNotificationContext
 
EMPTY_FILTER() - Static method in class ubic.gemma.web.services.rest.util.args.FilterArg
 
EmptyController - Class in ubic.gemma.web.controller
This exists just to have an easy way to trick web pages into importing DWR-defined classes that are not in dwrServices.js.
EmptyController() - Constructor for class ubic.gemma.web.controller.EmptyController
 
EmptyExpressionMatrix - Class in ubic.gemma.core.datastructure.matrix
Used to make a 'dummy matrix' that has the column information populated.
EmptyExpressionMatrix(BioAssayDimension) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
 
EmptyExpressionMatrix(Collection<BioAssayDimension>) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
 
emptySearch(HttpServletResponse) - Method in class ubic.gemma.web.services.rest.AnnotationsWebService
Placeholder for search call without a query parameter
enableIndexMirroring(CompassGpsInterfaceDevice) - Static method in class ubic.gemma.persistence.util.CompassUtils
enables the index mirroring operation.
enableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
Exposed to AJAX
enableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor
 
enableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl
 
encode(Object[]) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
 
Ensembl2NcbiValueObject - Class in ubic.gemma.core.loader.util.biomart
Value object that represents a file record line from BioMart as configured with query parameters.
Ensembl2NcbiValueObject() - Constructor for class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
 
ensureLog2Scale(QuantitationType, ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil
Ensures that the given matrix is on a Log2 scale.
ensureLog2Scale(Collection<RawExpressionDataVector>, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
Make sure the data are on a log2 scale
EntityDelegator - Class in ubic.gemma.web.remote
Bean to expose for remote access via AJAX, when all that is needed is the ID and a way to know what the class is.
EntityDelegator() - Constructor for class ubic.gemma.web.remote.EntityDelegator
 
EntityDelegator(Object) - Constructor for class ubic.gemma.web.remote.EntityDelegator