Index (Gemma Web 1.32.4 Test API)

A B C D E F G H I J L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractHeatmapTag<T> - Class in ubic.gemma.web.taglib.expression.experiment
AbstractHeatmapTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
AbstractHtmlElementTag - Class in ubic.gemma.web.taglib: An alternative to Spring's AbstractHtmlElementTag that does not carry the complexity of form data bindings.
AbstractHtmlElementTag() - Constructor for class ubic.gemma.web.taglib.AbstractHtmlElementTag
AbstractSetListContainer - Class in ubic.gemma.web.controller.persistence
AbstractSetListContainer() - Constructor for class ubic.gemma.web.controller.persistence.AbstractSetListContainer
AbstractStaticAssetTag - Class in ubic.gemma.web.taglib: Base class for tags that refers to static assets.
AbstractStaticAssetTag(String) - Constructor for class ubic.gemma.web.taglib.AbstractStaticAssetTag
add(String, Boolean) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
addAlternateName(Long, String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
addAuditEvent(EntityDelegator<? extends Auditable>, String, String, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.AuditController
addCountsForTaxonPieChart(ModelAndView) - Method in class ubic.gemma.web.controller.common.HomePageController: For the show-off graph that shows number of data sets per taxon.
addEmailAlert(String) - Method in class ubic.gemma.web.controller.job.ProgressStatusController: Set up an email alert for this job; an email will be sent when it has finished (or failed).
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
addFactorValueTo(Collection<Long>, EntityDelegator<FactorValue>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController: AJAX
addGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
addGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
addQCInfo(ExpressionExperiment) - Method in class ubic.gemma.web.service.ExpressionExperimentControllerHelperService
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.controller.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
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.web.controller.common.auditAndSecurity.SecurityController
afterPropertiesSet() - Method in class ubic.gemma.web.assets.StaticAssetResolver
afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
afterPropertiesSet() - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
ajaxLoginCheck(HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
ajaxSearch(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.search.GeneralSearchController
alt - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Alternative text to use for the image.
analyzeResultSets(Collection<Long>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
annot(Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
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
APP_NAME - Static variable in class ubic.gemma.web.util.Constants
ArrayDesignAddCommand - Class in ubic.gemma.web.controller.expression.arrayDesign
ArrayDesignAddCommand() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
ArrayDesignController - 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.
ArrayDesignController() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
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
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
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
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
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
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
AuditController - Class in ubic.gemma.web.controller.common.auditAndSecurity: 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.controller.common.auditAndSecurity.AuditController
AUTH_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener

B

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
BibliographicReferenceController - 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.
BibliographicReferenceController() - Constructor for class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
BioAssayController - Class in ubic.gemma.web.controller.expression.bioAssay
BioAssayController() - Constructor for class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
BioMaterialController - Class in ubic.gemma.web.controller.expression.biomaterial
BioMaterialController() - Constructor for class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
BlatResultTrackController - Class in ubic.gemma.web.controller.genome: See goldenPath help on custom track.
BlatResultTrackController() - Constructor for class ubic.gemma.web.controller.genome.BlatResultTrackController
browse(int, int, String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController: AJAX
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
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(ListBatchCommand, Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
browseByTaxon(ListBatchCommand, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
browseSpecificIds(ListBatchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX call for remote paging store
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
BUNDLE_KEY - Static variable in class ubic.gemma.web.util.Constants: The name of the ResourceBundle used in this application
bytesRead(int) - Method in interface ubic.gemma.web.controller.util.upload.OutputStreamListener
bytesRead(int) - Method in class ubic.gemma.web.controller.util.upload.UploadListener

C

CacheMonitor - Interface in ubic.gemma.web.controller.monitoring
CacheMonitorImpl - Class in ubic.gemma.web.controller.monitoring: Get statistics about and manage caches.
CacheMonitorImpl() - Constructor for class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
cancelJob(String) - Method in class ubic.gemma.web.controller.job.ProgressStatusController: Attempt to cancel the job.
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
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
canEqual(Object) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
CellLevelCharacteristicsEditForm() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
CellLevelCharacteristicsEditForm(CellLevelCharacteristics) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
CellTypeAssignmentEditForm() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
CellTypeAssignmentEditForm(CellTypeAssignment) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
CharacteristicBrowserController - Class in ubic.gemma.web.controller.common.description: NOTE: Logging messages from this service are important for tracking changes to annotations.
CharacteristicBrowserController() - Constructor for class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
CharacteristicConverter - Class in ubic.gemma.web.controller.dwr
CharacteristicConverter() - Constructor for class ubic.gemma.web.controller.dwr.CharacteristicConverter
CharacteristicTag - Class in ubic.gemma.web.taglib
CharacteristicTag() - Constructor for class ubic.gemma.web.taglib.CharacteristicTag
checkResult(String) - Method in class ubic.gemma.web.controller.job.ProgressStatusController
checkResult(String) - Method in class ubic.gemma.web.controller.job.TaskCompletionController
ClassConverter - Class in ubic.gemma.web.controller.dwr
ClassConverter() - Constructor for class ubic.gemma.web.controller.dwr.ClassConverter
clazz - Variable in class ubic.gemma.web.taglib.ConstantsTag: The class to expose the variables from.
cleanupMultipart(MultipartHttpServletRequest) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver
clearAllCaches() - Method in interface ubic.gemma.web.controller.monitoring.CacheMonitor: Remove all items from all caches.
clearAllCaches() - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
clearAllCaches() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Flush (clear) all caches.
clearCache(String) - Method in interface ubic.gemma.web.controller.monitoring.CacheMonitor: Remove all items from the cache with the given name.
clearCache(String) - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
clearCache(String) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Flush (clear) a cache.
clearFactorValuesNeedsAttention(Long[], String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
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.
ClientAbortExceptionResolver - Class in ubic.gemma.web.controller.util: Resolves a ClientAbortException to an empty view.
ClientAbortExceptionResolver() - Constructor for class ubic.gemma.web.controller.util.ClientAbortExceptionResolver
close() - Method in class ubic.gemma.web.controller.util.upload.MonitoredOutputStream
CoexpressionSearchController - Class in ubic.gemma.web.controller.analysis.expression.coexpression
CoexpressionSearchController() - Constructor for class ubic.gemma.web.controller.analysis.expression.coexpression.CoexpressionSearchController
CoexSearchTaskCommand - Class in ubic.gemma.web.controller.analysis.expression.coexpression
CoexSearchTaskCommand(CoexpressionSearchCommand) - Constructor for class ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand
CommonsMultipartFile - Class in ubic.gemma.web.controller.util.upload: Deprecated.
CommonsMultipartFile(FileItem) - Constructor for class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.

Create an instance wrapping the given FileItem.
CommonsMultipartMonitoredResolver - Class in ubic.gemma.web.controller.util.upload: An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
CommonsMultipartMonitoredResolver() - Constructor for class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver
compareTo(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
CompositeSequenceController - Class in ubic.gemma.web.controller.expression.designElement
CompositeSequenceController() - Constructor for class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
CONFIG - Static variable in class ubic.gemma.web.util.Constants: The name of the configuration hashmap stored in application scope.
configure(MeterRegistry) - Method in class ubic.gemma.web.metrics.MeterRegistryWebConfigurer
confirmRegistration(String, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
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
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
ControllerUtils - Class in ubic.gemma.web.controller.util: Created by tesarst on 09/03/17.
ControllerUtils() - Constructor for class ubic.gemma.web.controller.util.ControllerUtils
convert2ValueObjects(Collection<SubmittedTask>) - Static method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.controller.dwr.CharacteristicConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.controller.dwr.DirectionConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.controller.dwr.GOEvidenceCodeConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.controller.dwr.ScaleTypeConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.controller.dwr.StandardQuantitationTypeConverter
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.controller.dwr.ClassConverter
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.controller.dwr.DoublePointConverter
copyUploadedFile(HttpServletRequest, String, Path) - Static method in class ubic.gemma.web.controller.util.upload.FileUploadUtil
copyUploadedFile(MultipartFile, HttpServletRequest, Path) - Static method in class ubic.gemma.web.controller.util.upload.FileUploadUtil
copyUploadedInputStream(InputStream, Path) - Static method in class ubic.gemma.web.controller.util.upload.FileUploadUtil
count() - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
COUNT_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener
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
createBiomaterialTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
createDesignFromFile(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
createExperimentalFactor(EntityDelegator<ExperimentalDesign>, ExperimentalFactorValueWebUIObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: Create an experimental factor.
createExperimentTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: Ajax
createFactorValue(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
createFactorValueCharacteristic(EntityDelegator<FactorValue>, CharacteristicValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
createGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
createItem(String, String, boolean, String) - Method in class ubic.gemma.web.controller.util.upload.MonitoredDiskFileItemFactory
CustomRssViewer - Class in ubic.gemma.web.controller.common.rss
CustomRssViewer() - Constructor for class ubic.gemma.web.controller.common.rss.CustomRssViewer

D

daily() - Method in class ubic.gemma.web.controller.analysis.report.WhatsNewController
DatabaseEntryTag - Class in ubic.gemma.web.taglib
DatabaseEntryTag() - Constructor for class ubic.gemma.web.taglib.DatabaseEntryTag
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
DEFAULT_QC_IMAGE_SIZE_PX - Static variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController: Default size for an image, in pixel.
DefaultHandlerExceptionResolver - Class in ubic.gemma.web.controller.util: Custom exception resolver for Gemma.
DefaultHandlerExceptionResolver() - Constructor for class ubic.gemma.web.controller.util.DefaultHandlerExceptionResolver
delete(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
delete(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
deleteById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Exposed for AJAX calls.
deleteExperimentalFactors(EntityDelegator<ExperimentalDesign>, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
deleteFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
deleteFactorValues(EntityDelegator<ExperimentalFactor>, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
deleteGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
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
detailedFactorAnalysis(Long, double, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
detectFont(HttpServletRequest) - Method in class ubic.gemma.web.service.ExpressionExperimentControllerHelperService: Detect the theme to use for rendering plots.
determineAnalysisType(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController: Ajax method.
determineEncoding(HttpServletRequest) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver: Determine the encoding for the given request.
diagnostics(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController: Only update the daignostics
DifferentialExpressionAnalysisController - Class in ubic.gemma.web.controller.analysis.expression.diff: A controller to run differential expression analysis either locally or in a space.
DifferentialExpressionAnalysisController() - Constructor for class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController
DifferentialExpressionAnalyzerInfo - Class in ubic.gemma.web.controller.analysis.expression.diff: Used to carry information about the experimental design analysis settings to clients.
DifferentialExpressionAnalyzerInfo() - Constructor for class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
DifferentialExpressionSearchController - Class in ubic.gemma.web.controller.analysis.expression.diff: A controller used to get differential expression analysis and meta analysis results.
DifferentialExpressionSearchController() - Constructor for class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController
DiffExMetaAnalyzerController - Class in ubic.gemma.web.controller.analysis.expression.diff: A controller to analyze result sets either locally or in a space.
DiffExMetaAnalyzerController() - Constructor for class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
DiffExpressionSearchCommand - Class in ubic.gemma.web.controller.analysis.expression.diff
DiffExpressionSearchCommand() - Constructor for class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
DirectionConverter - Class in ubic.gemma.web.controller.dwr: DWR converter for Direction type.
DirectionConverter() - Constructor for class ubic.gemma.web.controller.dwr.DirectionConverter
disableStatistics() - Method in interface ubic.gemma.web.controller.monitoring.CacheMonitor: Disable collection of statistics on the caches.
disableStatistics() - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
disableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Exposed to AJAX
doBackgroundCoexSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.CoexpressionSearchController: Used by CoexpressionSearchData.js - the main home page coexpression search.
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.EntityLinkTag
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
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
done() - Method in interface ubic.gemma.web.controller.util.upload.OutputStreamListener
done() - Method in class ubic.gemma.web.controller.util.upload.UploadListener
doResolveException(HttpServletRequest, HttpServletResponse, Object, Exception) - Method in class ubic.gemma.web.controller.util.ClientAbortExceptionResolver
doSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.CoexpressionSearchController: Important entry point - called by the CoexpressionSearchTask
doSearchQuickComplete(CoexpressionSearchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.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.ConstantsTag
doStartTag() - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
doStartTag() - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.CharacteristicTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.EntityLinkTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.FactorValueTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.ImageTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.OntologyHierarchyTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.OntologyResourceTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.ScriptTag
doStartTagInternal() - Method in class ubic.gemma.web.taglib.StyleTag
DoublePointConverter - Class in ubic.gemma.web.controller.dwr: The 8 decimal precision of a double is just a waste of bandwidth in most cases.
DoublePointConverter() - Constructor for class ubic.gemma.web.controller.dwr.DoublePointConverter
download(Path, String, String, boolean, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.util.DownloadUtil: Provide a file download to the response.
downloadAnnotationFile(Long, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
downloadDEDV(Long, Long, String, double) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController
downloadDEDV(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: Handle case of text export of the results.
downloadExpressionExperimentList(String, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
downloadFile(String, 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.
downloadGeneList(String, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
downloadMetaFile(Long, Integer, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
downloadPCA(Long, String, Integer, int) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController
DownloadUtil - Class in ubic.gemma.web.controller.util: Utility class for providing Path as downloads.
DownloadUtil() - Constructor for class ubic.gemma.web.controller.util.DownloadUtil
duplicateFactorValue(EntityDelegator<ExperimentalFactor>, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: Make an exact copy of a factorvalue and add it to the experiment.

E

editUser(String, String, String, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: Entry point for updates.
enableStatistics() - Method in interface ubic.gemma.web.controller.monitoring.CacheMonitor: Enable collection of statistics on the caches.
enableStatistics() - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
enableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Exposed to AJAX
EntityDelegator<T> - Class in ubic.gemma.web.controller.util: 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.controller.util.EntityDelegator
EntityDelegator(T) - Constructor for class ubic.gemma.web.controller.util.EntityDelegator
EntityLinkTag - Class in ubic.gemma.web.taglib: Tag that generates an HTML link for a given Identifiable entity.
EntityLinkTag() - Constructor for class ubic.gemma.web.taglib.EntityLinkTag
EntityNotFoundException - Exception Class in ubic.gemma.web.controller.util: Signals that an entity was not found in the system.
EntityNotFoundException(String) - Constructor for exception class ubic.gemma.web.controller.util.EntityNotFoundException
EntityNotFoundException(String, Throwable) - Constructor for exception class ubic.gemma.web.controller.util.EntityNotFoundException
equals(Object) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
equals(Object) - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
equals(Object) - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
error(String) - Method in interface ubic.gemma.web.controller.util.upload.OutputStreamListener
error(String) - Method in class ubic.gemma.web.controller.util.upload.UploadListener
ExceptionTag - Class in ubic.gemma.web.taglib.common.auditAndSecurity
ExceptionTag() - Constructor for class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
ExperimentalDesignController - Class in ubic.gemma.web.controller.expression.experiment: Main entry point to editing and viewing experimental designs.
ExperimentalDesignController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
ExperimentalFactorValueWebUIObject - Class in ubic.gemma.web.controller.expression.experiment
ExperimentalFactorValueWebUIObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
ExperimentalFactorValueWebUIObject(Long) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
ExperimentQCTag - Class in ubic.gemma.web.taglib.expression.experiment
ExperimentQCTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
ExperimentQCTag(boolean) - Constructor for class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
ExperimentSetListContainer - Class in ubic.gemma.web.controller.persistence
ExperimentSetListContainer() - Constructor for class ubic.gemma.web.controller.persistence.ExperimentSetListContainer
ExpressionDataFileUploadController - Class in ubic.gemma.web.controller.expression.experiment: Replaces SimpleExpressionExperimentLoadController
ExpressionDataFileUploadController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
ExpressionDataHeatmapTag - Class in ubic.gemma.web.taglib.expression.experiment
ExpressionDataHeatmapTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
ExpressionExperimentController - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
ExpressionExperimentControllerHelperService - Class in ubic.gemma.web.service
ExpressionExperimentControllerHelperService() - Constructor for class ubic.gemma.web.service.ExpressionExperimentControllerHelperService
ExpressionExperimentDataFetchCommand - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentDataFetchCommand() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
ExpressionExperimentDataFetchController - Class in ubic.gemma.web.controller.expression.experiment: For the download of data files from the browser.
ExpressionExperimentDataFetchController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
ExpressionExperimentEditController - Class in ubic.gemma.web.controller.expression.experiment: Handle advanced editing of expression experiments.
ExpressionExperimentEditController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
ExpressionExperimentEditController.CellLevelCharacteristicsEditForm - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditController.CellTypeAssignmentEditForm - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditController.ExpressionExperimentEditForm - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditController.QuantitationTypeEditForm - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditController.SingleCellDimensionEditForm - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditForm() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
ExpressionExperimentEditValueObject - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditValueObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject: Required when using the class as a spring bean.
ExpressionExperimentEditValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
ExpressionExperimentExperimentalFactorValueObject - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentExperimentalFactorValueObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
ExpressionExperimentLoadController - Class in ubic.gemma.web.controller.expression.experiment: Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
ExpressionExperimentLoadController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
ExpressionExperimentQCController - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentQCController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
ExpressionExperimentReportGenerationController - Class in ubic.gemma.web.controller.analysis.report
ExpressionExperimentReportGenerationController() - Constructor for class ubic.gemma.web.controller.analysis.report.ExpressionExperimentReportGenerationController
ExpressionExperimentSetController - Class in ubic.gemma.web.controller.expression.experiment: For fetching and manipulating ExpressionExperimentSets.
ExpressionExperimentSetController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
ExpressionExperimentUploadResponse - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentUploadResponse() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
ExpressionExperimentVisualizationCommand - Class in ubic.gemma.web.controller.visualization: Expression experiment command object that wraps expression experiment visualization preferences.
ExpressionExperimentVisualizationCommand() - Constructor for class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
ExpressionProfileDataObject - Class in ubic.gemma.web.controller.visualization: A lightweight object to hold expression data for a single probe.
ExpressionProfileDataObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
ExternalStaticAssetServer - Class in ubic.gemma.web.assets: An external static asset server that provide assets from a specified base URL.
ExternalStaticAssetServer(String) - Constructor for class ubic.gemma.web.assets.ExternalStaticAssetServer
extractIds(String) - Static method in class ubic.gemma.web.controller.util.ControllerUtils: Returns a collection of Long ids from strings.

F

FactorProfile - Class in ubic.gemma.web.controller.visualization: Represents data for displaying a factor (+ factor values) in a chart.
FactorProfile() - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
FactorProfile(List<Double>, boolean) - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
FactorProfile(ExperimentalFactor, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>) - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
FactorValueTag - Class in ubic.gemma.web.taglib
FactorValueTag() - Constructor for class ubic.gemma.web.taglib.FactorValueTag
FailedMultipartHttpServletRequest - Class in ubic.gemma.web.controller.util.upload: Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
FailedMultipartHttpServletRequest(HttpServletRequest) - Constructor for class ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
FailedMultipartHttpServletRequest(HttpServletRequest, String) - Constructor for class ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
FileUpload - Class in ubic.gemma.web.controller.common.auditAndSecurity: Command class to handle uploading of a file
FileUpload() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
FileUploadController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller class to upload Files.
FileUploadController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
FileUploadUtil - Class in ubic.gemma.web.controller.util.upload: Utility methods for uploading files.
FileUploadUtil() - Constructor for class ubic.gemma.web.controller.util.upload.FileUploadUtil
filter(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
filter(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
filter(String, String) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
find(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX TODO --- include a search of subsets.
findCharacteristics(String) - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
findCharacteristicsCustom(String, boolean, boolean, boolean, boolean, boolean, boolean, String) - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
findDetailMetaAnalysisById(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
findGeneSetsByGene(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Given a Gemma Gene Id will find all gene groups that the current user is allowed to use
findGeneSetsByName(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController
findGOTerms(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
findTerm(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: AJAX.
flush() - Method in class ubic.gemma.web.controller.util.upload.MonitoredOutputStream
formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController: Case = GET: Step 1 - return instance of command class (from database).
fromContextPath() - Method in class ubic.gemma.web.util.WebEntityUrlBuilder: Obtain an EntityUrlBuilder.EntityUrlChooser relative to the servlet context path.
fromRoot() - Method in class ubic.gemma.web.util.WebEntityUrlBuilder: Obtain an EntityUrlBuilder.EntityUrlChooser relative to a root URL (i.e.

G

GeneController - Class in ubic.gemma.web.controller.genome.gene
GeneController() - Constructor for class ubic.gemma.web.controller.genome.gene.GeneController
GeneExpressionProfile - Class in ubic.gemma.web.controller.visualization: Expression data for one probe; designed for conveying small amounts of data to clients.
GeneExpressionProfile(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>, String, Integer, Double) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>, String, Integer, Double, boolean) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GenePickerController - Class in ubic.gemma.web.controller.genome.gene: For 'live searches' from the web interface.
GenePickerController() - Constructor for class ubic.gemma.web.controller.genome.gene.GenePickerController
GeneralSearchController - Class in ubic.gemma.web.controller.search: 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.
GeneralSearchController() - Constructor for class ubic.gemma.web.controller.search.GeneralSearchController
GeneralSearchController.SearchResultValueObject<T> - Class in ubic.gemma.web.controller.search
generateCache() - Method in class ubic.gemma.web.controller.analysis.report.WhatsNewController
generateSummary(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
GeneSetController - Class in ubic.gemma.web.controller.genome.gene: Exposes GeneSetServices methods over ajax.
GeneSetController() - Constructor for class ubic.gemma.web.controller.genome.gene.GeneSetController
GeneSetListContainer - Class in ubic.gemma.web.controller.persistence
GeneSetListContainer() - Constructor for class ubic.gemma.web.controller.persistence.GeneSetListContainer
GeoRecordBrowserController - Class in ubic.gemma.web.controller.expression.experiment
GeoRecordBrowserController() - Constructor for class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
getAccession() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
getActiveSessions() - Static method in class ubic.gemma.web.listener.UserTracker
getActiveUsers() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListController
getAdditionalTaxa() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAllExperimentSets() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getAllExperimentSets() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getAllGeneSets() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getAllGeneSets() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getAllGeneSets(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getAllGeneSets(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getAllowedDirs() - Method in class ubic.gemma.web.assets.StaticAssetResolver: Resource directories that are allowed to be served.
getAllParentsAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAllSessionBoundGroups() - Method in class ubic.gemma.web.controller.persistence.AbstractSetListContainer
getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getAlternateNames() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAlternative() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAnalysisId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getAnnotation(EntityDelegator<BioMaterial>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getAnnotation(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getArrayDesign() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getArrayDesignIds() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getArrayDesignMismatchProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getArrayDesigns(Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getAssayIds() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getAssayToMaterialMap() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getAuthenticatedUserCount() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAuthenticatedUserNames() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAuthority() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
getAvailableGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAvailableGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getAvailablePrincipalSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAvailableSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getBaseUrl() - Method in class ubic.gemma.web.assets.ExternalStaticAssetServer
getBaseUrl() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
getBaseUrl() - Method in class ubic.gemma.web.assets.ServletStaticAssetServer
getBaseUrl() - Method in interface ubic.gemma.web.assets.StaticAssetServer: Obtain the base URL for resolving static assets from the server.
getBioAssays() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getBioAssays() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
getBioAssays(Long) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
getBioMaterialCharacteristicCategories(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: Extract just the categories from the biomaterial's characteristics.
getBioMaterialCharacteristicCategoryToUse() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
getBioMaterials(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getBioMaterials(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
getBioMaterialsForEE(Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getBioProcessAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getBuildInfo() - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
getBytes() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getBytesRead() - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
getCacheStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
getCancelView(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
getCategory() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
getCategoryTerms() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
getCellLevelCharacteristics() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
getCellLevelCharacteristics() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getCellLevelCharacteristics1() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getCellTypeAssignment() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getCellTypeAssignments() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
getCellTypeAssignments() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getClassDelegatingFor() - Method in class ubic.gemma.web.controller.util.EntityDelegator
getClassName() - Method in class ubic.gemma.web.taglib.ConstantsTag
getCoExpressionDataFile(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited co-expression data file
getColor() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getColorString() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getContentType() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getContentType() - Method in class ubic.gemma.web.controller.util.view.JSONView
getCount() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getCsSummaries(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls (Probe browser) FIXME can probably remove soon since we should use getGeneCsSummaries? Might be another use for this
getCsSummaries(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getCurrentGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getCurrentGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject: Deprecated.
use UserValueObject.getGroups() instead
getCurrentUserCanwrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getCurrentUserOwns() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getData() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getDataFile(ExpressionExperimentDataFetchCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited experiment design data file
getDataFileFormatProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getDEDV(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes.
getDEDVForCoexpressionVisualization(Collection<Long>, Long, Long) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForDiffExVisualization(Collection<Long>, Collection<Long>, Double, Collection<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow, DifferentialExpressionAnalysesSummaryTree
getDEDVForDiffExVisualizationByExperiment(Long, Long, Double, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method Batch factor value analyses are filtered out; for ProbeLevelDiffExGrid:VisualizationDifferentialWindow.
getDEDVForDiffExVisualizationByThreshold(Long, Double, Long) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForPcaVisualization(Long, int, int) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX
getDEDVForVisualization(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForVisualizationByProbe(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDedvId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getDescription() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
getDescription() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getDescription() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getDescription() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getDescription() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getDescription(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX call
getDesignElement() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getDesignMatrixRows(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getDesignSummaries(ArrayDesign) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getDetails(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getDetails(String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
getDifferentialExpression(Long, double) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
getDifferentialExpression(Long, double, Integer) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
getDifferentialExpressionWithoutBatch(Long, double, Integer) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
getDiffExpressionDataFile(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited differential expression data file
getDir() - Method in class ubic.gemma.web.controller.util.ListBatchCommand
getDisplayName() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile
getDone() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getEeId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getEeIds() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getEeQuery() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getEeSetId() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getEeSetName() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getEevo() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getEmail() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getEmailAlert() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getEntityClazz() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityDescription() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityId() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityShortName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEnvironment() - Method in class ubic.gemma.web.assets.StaticAssetResolver
getErrorMessage() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
getErrorMessage() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
getErrorMessage() - Method in class ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
getEvents(EntityDelegator<? extends Auditable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.AuditController
getExperimentalDesignId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getExperimentalFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getExperimentalFactors(EntityDelegator<?>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
getExperimentalFactors(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getExperimentIdsInSet(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
getExperimentIdsInSet(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getExperimentIdsInSet(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getExperimentSetById(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager: Get the session-bound group using the group's id
getExperimentSetById(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getExperimentsInSet(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getExperimentsInSet(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getExperimentsInSet(Long, Integer) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
getExpressionExperiment() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getExpressionExperiment() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getExpressionExperimentEditPage(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
getExpressionExperimentId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getExpressionExperimentId() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getFactor() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getFactorNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactorProfiles() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactors() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
getFactors() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactors(Collection<Long>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController: AJAX entry.
getFactorTypes() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactorValue(Long, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.ontology.OntologyController
getFactorValueAnnotation(Long, Long, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.ontology.OntologyController
getFactorValueMap() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactorValueOntologyAsRdf(HttpServletRequest, HttpServletResponse, boolean) - Method in class ubic.gemma.web.controller.ontology.OntologyController
getFactorValueOntologyHome(int, int, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.ontology.OntologyController
getFactorValues() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactorValues(EntityDelegator<BioMaterial>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getFactorValues(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
getFactorValues(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getFactorValuesToNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
getFile() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
getFile() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getFileIndex() - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
getFileItem() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.

Return the underlying org.apache.commons.fileupload.FileItem instance.
getFinishTime() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getFocusedCharacteristic() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getFont() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getForm() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
getFormat() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getGemmaOntologyAsRdf() - Method in class ubic.gemma.web.controller.ontology.OntologyController
getGemmaOntologyHome() - Method in class ubic.gemma.web.controller.ontology.OntologyController
getGemmaOntologyTerm(String) - Method in class ubic.gemma.web.controller.ontology.OntologyController
getGene() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getGeneCsSummaries(Long) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls (Elements tab on gene details page)
getGeneIds() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getGeneIds() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getGeneIdsInGroup(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX
getGeneMappingSummary(EntityDelegator<CompositeSequence>) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls.
getGeneralType() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getGenes() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getGenes(Collection<Long>) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getGenesByGOId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: for AJAX get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
getGeneSetByGOId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: for AJAX get a gene set with all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
getGeneSetById(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager: Get the session-bound group using the group's id
getGeneSetById(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getGenesInGroup(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager: AJAX If the current user has access to given gene group will return the gene ids in the gene group
getGenesInGroup(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getGenesInGroup(Long, Integer) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX If the current user has access to given gene group, will return the gene value objects in the gene group
getGroupMembers(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getGroupName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
getGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getGroupsThatCanRead() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getGroupsThatCanWrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getHibernateStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
getHighlightedText() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
getId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
getId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
getId() - Method in class ubic.gemma.web.controller.util.EntityDelegator
getInputStream() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getIsBackground() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsBackgroundSubtracted() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsBatchCorrected() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsContinuous() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
getIsMaskedPreferred() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm: Deprecated.
getIsNormalized() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsPreferred() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getIsPreferred() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsRatio() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsRatio() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getIsRecomputedFromRawData() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getIsSingleCellPreferred() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getKeywords() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getKeywords(ExpressionExperiment) - Method in class ubic.gemma.web.service.ExpressionExperimentControllerHelperService
getLastLogMessage() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getLatestExperiments() - Method in class ubic.gemma.web.controller.common.rss.RssFeedController: Show all experiments
getLaunchInstruction() - Method in class ubic.gemma.web.assets.ExternalStaticAssetServer
getLaunchInstruction() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
getLaunchInstruction() - Method in class ubic.gemma.web.assets.ServletStaticAssetServer
getLaunchInstruction() - Method in interface ubic.gemma.web.assets.StaticAssetServer: Obtain launch instructions if the server is not running.
getLimit() - Method in class ubic.gemma.web.controller.util.ListBatchCommand
getLocalPath() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
getLogMessages() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getMergees() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getMerger() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getMessage() - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
getMetadataFiles(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: Scans the metadata directory for any files associated with the given experiment.
getModifiedExperimentSets() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getModifiedExperimentSets() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getModifiedExperimentSets(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getModifiedExperimentSets(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getModifiedGeneSets() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getModifiedGeneSets() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getModifiedGeneSets(Long) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
getModifiedGeneSets(Long) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
getMultipartContentType(String) - Method in class ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
getMultipartHeaders(String) - Method in class ubic.gemma.web.controller.util.upload.FailedMultipartHttpServletRequest
getName() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
getName() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getName() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getName() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getName() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getName() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getNonMatchingProbeNameExamples() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNoParentsAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getNumberMatchingProbes() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumberOfNonMatchingProbes() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumColumns() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getNumRows() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getOriginalFilename() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getOriginalFileName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getOtherProblemsMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getOutputStream() - Method in class ubic.gemma.web.controller.util.upload.MonitoredDiskFileItem
getOwner() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getOwnersGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getPhase() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
getPlots() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
getProbe() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getProbeId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getProbeName() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getProducts(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
getProfile() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getProfiles() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getProgressStatus(String) - Method in class ubic.gemma.web.controller.job.ProgressStatusController: Get the latest information about how a job is doing.
getProtocolId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getPubMedId() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getPValue() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getQuantitationType() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
getQuantitationType() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getQuantitationTypeDescription() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getQuantitationTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getQuantitationTypeName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getQuantitationTypeProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getQuantitationTypes() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getQuantitationTypes() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
getQuantitationTypesByVectorType() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm: ExpressionExperimentEditController.ExpressionExperimentEditForm.quantitationTypes, organized by the type of data vector they apply to and in the same order.
getRank() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getRecords() - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
getRelationTerms() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
getReportHtml(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getRepresentation() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm: This is disabled by default in the UI because we don't want users to mess with the representation accidentally.
getResultClass() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
getResultObject() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
getRole() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject: Deprecated.
use UserValueObject.getGroups() instead
getRunningRemotely() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getSampleNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getScale() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getScale() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getScope() - Method in class ubic.gemma.web.taglib.ConstantsTag
getScope(String) - Method in class ubic.gemma.web.taglib.ConstantsTag: Converts the scope name into its corresponding PageContext constant value.
getScore() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
getSearchCriteria() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getSearchOptions() - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand
getSearchString() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getSecurityInfo(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getSelectedFactors() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getServerFilePath() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getSessionBoundModifiedGroups() - Method in class ubic.gemma.web.controller.persistence.AbstractSetListContainer
getShortName() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getShortName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getSingleCellDimensions() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
getSize() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
getSort() - Method in class ubic.gemma.web.controller.util.ListBatchCommand
getStart() - Method in class ubic.gemma.web.controller.util.ListBatchCommand
getStartTime() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getStaticAssetServer() - Method in class ubic.gemma.web.assets.StaticAssetResolver
getStats() - Method in interface ubic.gemma.web.controller.monitoring.HibernateMonitor
getStats() - Method in class ubic.gemma.web.controller.monitoring.HibernateMonitorImpl
getStats(boolean, boolean, boolean) - Method in interface ubic.gemma.web.controller.monitoring.HibernateMonitor: Log some statistics.
getStats(boolean, boolean, boolean) - Method in class ubic.gemma.web.controller.monitoring.HibernateMonitorImpl
getStats(Locale) - Method in interface ubic.gemma.web.controller.monitoring.CacheMonitor: Obtain the cache statistics in HTML format.
getStats(Locale) - Method in class ubic.gemma.web.controller.monitoring.CacheMonitorImpl
getStatus() - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
getStorageDescription() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.

Return a description for the storage location of the multipart content.
getSubmissionTime() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getSubmittedTask(String) - Method in class ubic.gemma.web.controller.job.ProgressStatusController
getSubmittedTasks() - Method in class ubic.gemma.web.controller.job.ProgressStatusController
getSubmitter() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getSubsumees() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getSubsumer() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getSummaryForArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getSummaryHtml(ArrayDesignValueObject) - Static method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil: Generate a pretty HTML table with the array design stats summary, used for AJAX version.
getTaskClass() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getTaskId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
getTaskId() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getTaskStatus() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getTaskType() - Method in class ubic.gemma.web.controller.job.SubmittedTaskValueObject
getTaxa() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithArrays() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithDatasets() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithGenes() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxon() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getTaxonId() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getTaxonId() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getThreshold() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
getTotalRecords() - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
getTotalSize() - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
getType() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
getType() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
getTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile
getUploadedFile(String, Path) - Static method in class ubic.gemma.web.controller.util.upload.FileUploadUtil: Obtain the path for a previously uploaded file.
getUploadStatus() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
getUserAndSessionGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns the current users gene sets as well as their session gene sets
getUserName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getUsers() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListController
getUsersData(String, boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getUserSessionGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns just the current users gene sets
getUsersGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns just the current users gene sets
getValues() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
getValues() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
getVar() - Method in class ubic.gemma.web.taglib.ConstantsTag
getVariableInfo(TagData) - Method in class ubic.gemma.web.taglib.ConstantsTei: Return information about the scripting variables to be created.
getView() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
getView() - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
getViewNameForRequest(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController
GOEvidenceCodeConverter - Class in ubic.gemma.web.controller.dwr
GOEvidenceCodeConverter() - Constructor for class ubic.gemma.web.controller.dwr.GOEvidenceCodeConverter

H

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.genome.BlatResultTrackController
hashCode() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
hashCode() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
hashCode() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
heatmap - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Heatmap to render.
HibernateMonitor - Interface in ubic.gemma.web.controller.monitoring
HibernateMonitorImpl - Class in ubic.gemma.web.controller.monitoring: Monitoring of Hibernate status.
HibernateMonitorImpl() - Constructor for class ubic.gemma.web.controller.monitoring.HibernateMonitorImpl
holds(Class<?>) - Method in class ubic.gemma.web.controller.util.EntityDelegator: Check if the entity delegator holds the given type.
HomePageController - Class in ubic.gemma.web.controller.common: Responsible for display of the Gemma 2.0 home page.
HomePageController() - Constructor for class ubic.gemma.web.controller.common.HomePageController
htmlEscape(String) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag

I

identifyOutliersRemoved(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
identifyPossibleOutliers(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
ImageTag - Class in ubic.gemma.web.taglib: Write an <img/> tag.
ImageTag() - Constructor for class ubic.gemma.web.taglib.ImageTag
incrementAndGetLargestExperimentSetSessionId() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
incrementAndGetLargestExperimentSetSessionId() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
incrementAndGetLargestGeneSetSessionId() - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
incrementAndGetLargestGeneSetSessionId() - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
incrementAndGetLargestSessionId() - Method in class ubic.gemma.web.controller.persistence.AbstractSetListContainer
incrementSessions() - Static method in class ubic.gemma.web.listener.UserTracker
index(IndexerTaskCommand) - Method in class ubic.gemma.web.controller.common.IndexController
IndexController - Class in ubic.gemma.web.controller.common
IndexController() - Constructor for class ubic.gemma.web.controller.common.IndexController
initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController: Set up a custom property editor for converting form inputs to real objects.
initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
initialize(ConfigurableWebApplicationContext) - Method in class ubic.gemma.web.context.InitializeContext
InitializeContext - Class in ubic.gemma.web.context: Performs the standard context preparation from SpringContextUtils.prepareContext(ApplicationContext) as well as some more specific Web-related setups.
InitializeContext() - Constructor for class ubic.gemma.web.context.InitializeContext
InternalStaticAssetServer - Class in ubic.gemma.web.assets: An internal static asset server that uses npm to serve static assets.
InternalStaticAssetServer(Path, Path, String, boolean, Path) - Constructor for class ubic.gemma.web.assets.InternalStaticAssetServer
isAlive() - Method in class ubic.gemma.web.assets.ExternalStaticAssetServer
isAlive() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
isAlive() - Method in class ubic.gemma.web.assets.ServletStaticAssetServer
isAlive() - Method in interface ubic.gemma.web.assets.StaticAssetServer: Indicate if the static asset server is running.
isAllMissing() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
isAllowModification() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
isArrayDesignMatchesDataFile() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isAutoStartup() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
isAvailable() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.

Determine whether the multipart content is still available.
isCanEdit() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
isCurrentGroupCanRead() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isCurrentGroupCanWrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isDataFileIsValidFormat() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isDirty() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
isEmpty() - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
isEnabled() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
isError() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
isFilter() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
isForceRewrite() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
isHtmlEscape() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
isHtmlEscape() - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
isInGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
isInProgress() - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
isMaskMissing() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
isMember() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
isMultipart(HttpServletRequest) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver
isNormalized() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
isPrincipal() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
isPrivateKeySet() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
isPubliclyReadable() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isQuantitationTypeIsValid() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isReturnToExperiment() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm: Return to the experiment page after a successful update.
isRunning() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
isShared() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isShortNameIsUnique() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isStandardized() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
isSuccess() - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
isValid() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
isValid() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isValidateOnly() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
isViewSampling() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

J

JavascriptLogger - Class in ubic.gemma.web.controller.common: Class to handle saving client-side javascript error messages and warnings to a server-side log.
JavascriptLogger() - Constructor for class ubic.gemma.web.controller.common.JavascriptLogger
JsonReaderResponse<T> - Class in ubic.gemma.web.controller.util.view: Creates a response that can be consumed by an Ext.data.JsonReader.
JsonReaderResponse(String) - Constructor for class ubic.gemma.web.controller.util.view.JsonReaderResponse: Creates an unJsonReaderResponse.successful JsonReaderResponse with null JsonReaderResponse.records.
JsonReaderResponse(Collection<T>, long) - Constructor for class ubic.gemma.web.controller.util.view.JsonReaderResponse: Use for remote paging applications.
JsonReaderResponse(List<T>) - Constructor for class ubic.gemma.web.controller.util.view.JsonReaderResponse: Creates a successful JsonReaderResponse with the provided objectsToConvertToRecords.
JsonUtil - Class in ubic.gemma.web.controller.util: Utilities for writing JSON payloads to HttpServletResponse.
JsonUtil() - Constructor for class ubic.gemma.web.controller.util.JsonUtil
JSONView - Class in ubic.gemma.web.controller.util.view
JSONView() - Constructor for class ubic.gemma.web.controller.util.view.JSONView
JSONView(String) - Constructor for class ubic.gemma.web.controller.util.view.JSONView

L

LinkAnalysisController - Class in ubic.gemma.web.controller.analysis.expression.coexpression.links: A controller to pre-process expression data vectors.
LinkAnalysisController() - Constructor for class ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
ListBatchCommand - Class in ubic.gemma.web.controller.util: Encapsulates information needed for generic list browsing.
ListBatchCommand() - Constructor for class ubic.gemma.web.controller.util.ListBatchCommand
load(Long) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
load(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
load(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX - load with the IDs filled in
load(Long) - Method in class ubic.gemma.web.service.ExpressionExperimentControllerHelperService
load(ExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
load(SimpleExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
loadAll() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments
loadAllMetaAnalyses() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
loadAllSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadAllUserAndSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadAllUserOwnedAndSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadArrayDesignsForShowAll(Long[]) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
loadArrayDesignsSummary() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
loadByName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
loadCountsForDataSummaryTable() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX method to get data for database summary table, returned as a JSON object the slow part here is loading each new or updated object in whatsNewService.retrieveReport() -> fetch()
loadDetailedExpressionExperiments(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables.
loadExperimentsForPlatform(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX get experiments that used a given platform.
loadExpressionExperimentDetails(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX; Populate all the details.
loadExpressionExperiments(List<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables.
loadExpressionExperimentsWithQcIssues() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX; get a collection of experiments that have had samples removed due to outliers TODO: and experiment that have possible batch effects detected
loadFromPubmedID(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
loadGeneDetails(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
loadQuantitationTypes(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables
loadSingleCellExpressionData(Long, Long, Long, Long[], Long, Long, Long, HttpServletRequest) - Method in class ubic.gemma.web.service.ExpressionExperimentControllerHelperService
loadStatusSummaries(Long, List<Long>, Integer, Integer, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX.
loadUser(HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: AJAX entry point.
log - Static variable in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController
log - Static variable in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
log - Variable in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
log - Variable in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
log - Variable in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
log - Variable in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
log - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
log - Variable in class ubic.gemma.web.controller.genome.gene.GeneController
log - Static variable in class ubic.gemma.web.controller.util.ControllerUtils
logger - Static variable in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
loginCheck() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController: AJAX DWR

M

MaintenanceModeController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave normally.
MaintenanceModeController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
makeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makePrivate(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makePublic(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
markFactorValuesAsNeedsAttention(Long[], String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
markOutlier(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
MAX_QC_IMAGE_SIZE_PX - Static variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController: Maximum size for an image, in pixels.
maxHeight - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Maximum height of the heatmap in pixels.
maxWidth - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Maximum width of the heatmap in pixels.
message - Variable in class ubic.gemma.web.controller.util.view.JsonReaderResponse
MESSAGES_ATTRIBUTE - Static variable in class ubic.gemma.web.controller.util.MessageUtil
messageSource - Variable in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
messageSource - Variable in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
messageSource - Variable in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
messageSource - Variable in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
messageSource - Variable in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
messageSource - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
messageSource - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
messageSource - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
messageSource - Variable in class ubic.gemma.web.controller.genome.gene.GeneController
messageUtil - Variable in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
messageUtil - Variable in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
messageUtil - Variable in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
messageUtil - Variable in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
messageUtil - Variable in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
messageUtil - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
messageUtil - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
messageUtil - Variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
messageUtil - Variable in class ubic.gemma.web.controller.genome.gene.GeneController
MessageUtil - Class in ubic.gemma.web.controller.util
MessageUtil() - Constructor for class ubic.gemma.web.controller.util.MessageUtil
MetaFile - Class in ubic.gemma.web.controller.expression.experiment: Wrapper for metadata file information for the frontend
MetaFile(int, String) - Constructor for class ubic.gemma.web.controller.expression.experiment.MetaFile
MeterRegistryWebConfigurer - Class in ubic.gemma.web.metrics: Configured the environment='web' tag to the provided registry.
MeterRegistryWebConfigurer(MeterRegistry) - Constructor for class ubic.gemma.web.metrics.MeterRegistryWebConfigurer
MIN_PASSWORD_LENGTH - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
MonitoredDiskFileItem - Class in ubic.gemma.web.controller.util.upload: Commons FileItem that uses a MonitoredOutputStream
MonitoredDiskFileItem(String, String, boolean, String, int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.controller.util.upload.MonitoredDiskFileItem
MonitoredDiskFileItemFactory - Class in ubic.gemma.web.controller.util.upload
MonitoredDiskFileItemFactory(int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.controller.util.upload.MonitoredDiskFileItemFactory
MonitoredDiskFileItemFactory(OutputStreamListener) - Constructor for class ubic.gemma.web.controller.util.upload.MonitoredDiskFileItemFactory
MonitoredOutputStream - Class in ubic.gemma.web.controller.util.upload: OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
MonitoredOutputStream(OutputStream, OutputStreamListener) - Constructor for class ubic.gemma.web.controller.util.upload.MonitoredOutputStream

N

newFileUpload(HttpServletRequest) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver: Create a factory for disk-based file items with a listener we can check for progress.

O

onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
onSubmit(HttpServletRequest, PubMedSearchCommand, BindingResult, SessionStatus) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
OntologyController - Class in ubic.gemma.web.controller.ontology: Provide minimal support for exposing Gemma ontology.
OntologyController() - Constructor for class ubic.gemma.web.controller.ontology.OntologyController
OntologyHierarchyTag - Class in ubic.gemma.web.taglib
OntologyHierarchyTag() - Constructor for class ubic.gemma.web.taglib.OntologyHierarchyTag
OntologyResourceTag - Class in ubic.gemma.web.taglib
OntologyResourceTag() - Constructor for class ubic.gemma.web.taglib.OntologyResourceTag
OutputStreamListener - Interface in ubic.gemma.web.controller.util.upload

P

pcaFactors(Long, double, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
pcaScree(Long, double, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
POPUP_WINDOW_PADDING_PX - Static variable in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Amount of padding (vertical and horizontal) to apply to popup windows that display QC images.
PreprocessController - Class in ubic.gemma.web.controller.analysis.preprocess: A controller to pre-process expression data (including updating diagnostics)
PreprocessController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.PreprocessController
processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
ProgressStatusController - Class in ubic.gemma.web.controller.job: This class exposes methods for AJAX calls.
ProgressStatusController() - Constructor for class ubic.gemma.web.controller.job.ProgressStatusController
PubMedQueryController - Class in ubic.gemma.web.controller.common.description.bibref: Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
PubMedQueryController() - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
PubMedSearchCommand - Class in ubic.gemma.web.controller.common.description.bibref: Supports seaching of pubmed references
PubMedSearchCommand(String) - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand

Q

QuantitationTypeEditForm() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
QuantitationTypeEditForm(QuantitationType) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm

R

recalculateBatchConfound(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
recalculateBatchEffect(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
ReCaptcha - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptcha(String) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
ReCaptchaException - Exception Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptchaException(String) - Constructor for exception class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
ReCaptchaException(String, Throwable) - Constructor for exception class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
ReCaptchaResponse - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptchaResponse(boolean, String) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
records - Variable in class ubic.gemma.web.controller.util.view.JsonReaderResponse
redirectToHomePage(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.HomePageController
redo(Long, Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController: AJAX entry point to redo an analysis.
referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
refreshStats(Long, Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController
reinitializeOntologyIndices() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: AJAX Note that this completely scraps the indices, and runs asynchronously.
release() - Method in class ubic.gemma.web.taglib.ConstantsTag: Release all allocated resources.
remove(Long, Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController: AJAX entry point to remove an analysis given by the ID
remove(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
remove(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
remove(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
removeBiomaterialTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
removeCharacteristics(Collection<AnnotationValueObject>) - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController
removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
removeExperimentTag(Collection<Long>, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
removeGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
removeGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
removeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
removeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
removeMetaAnalysis(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
removePrimaryPublication(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Remove the primary publication for the given expression experiment (by id).
removeSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Given a valid experiment group will remove it from the session.
removeSessionGroups(Collection<SessionBoundGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Deprecated.
removeSet(GemmaSessionBackedValueObject) - Method in class ubic.gemma.web.controller.persistence.AbstractSetListContainer
removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Given valid experiment groups will remove them from the session or the database appropriately.
removeUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Given valid gene groups will remove them from the session or the database appropriately.
removeUsersFromGroup(String[], String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
render(Map<String, ?>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.util.view.JSONView
renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.util.view.TextView
resetHibernateStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
resetPassword(String, String, Locale, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: Resets the password to a random alphanumeric (of length MIN_PASSWORD_LENGTH).
resetStats() - Method in interface ubic.gemma.web.controller.monitoring.HibernateMonitor: Clear all statistics.
resetStats() - Method in class ubic.gemma.web.controller.monitoring.HibernateMonitorImpl
resolveException(HttpServletRequest, HttpServletResponse, Object, Exception) - Method in class ubic.gemma.web.controller.util.UnhandledExceptionResolver
resolveMultipart(HttpServletRequest) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver
resolveUrl(String) - Method in class ubic.gemma.web.assets.StaticAssetResolver: Resolve a URL to a static asset.
resolveUrl(String) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag
RFC_5322_EMAIL_PATTERN - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: RFC 5322 email pattern.
RssFeedController - Class in ubic.gemma.web.controller.common.rss
RssFeedController() - Constructor for class ubic.gemma.web.controller.common.rss.RssFeedController
run(Long) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
run(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController: AJAX entry point when running completely automatically.
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController: Update the processed data vectors as well as diagnostics
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.SvdController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.analysis.report.ExpressionExperimentReportGenerationController
run(Long) - Method in class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController: AJAX entry point.
runAll() - Method in class ubic.gemma.web.controller.analysis.report.ExpressionExperimentReportGenerationController
runCustom(Long, Collection<Long>, boolean, Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalysisController: Perform a customized DEA based on user input on web interface.
runGeeq(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX

S

saveMessage(String) - Method in class ubic.gemma.web.controller.util.MessageUtil
saveMessage(String, Object[], String) - Method in class ubic.gemma.web.controller.util.MessageUtil
saveMessage(String, Object, String) - Method in class ubic.gemma.web.controller.util.MessageUtil
saveMessage(String, String) - Method in class ubic.gemma.web.controller.util.MessageUtil
saveResultSets(Collection<Long>, String, String) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
saveUser(UserValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListController
ScaleTypeConverter - Class in ubic.gemma.web.controller.dwr
ScaleTypeConverter() - Constructor for class ubic.gemma.web.controller.dwr.ScaleTypeConverter
scheduleDiffExpSearchTask(Long, ExpressionExperimentSetValueObject, GeneSetValueObject) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionSearchController: AJAX - method used for main display metaheatmap.
scope - Variable in class ubic.gemma.web.taglib.ConstantsTag: The scope to be put the variable in.
ScriptTag - Class in ubic.gemma.web.taglib: Write a <style/> tag.
ScriptTag() - Constructor for class ubic.gemma.web.taglib.ScriptTag
search(String, String) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
search(String, String, String, String) - Method in class ubic.gemma.web.controller.search.GeneralSearchController
search(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
searchBibRefs() - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
searchExperimentsAndExperimentGroups(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX (used by experimentAndExperimentGroupCombo.js)
searchExpressionExperiments(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX (used by ExperimentCombo.js)
searchGenes(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by GeneCombo.js)
searchGenesAndGeneGroups(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by GeneAndGeneGroupCombo.js)
searchGenesWithNCBIId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by Phenocarta)
searchMultipleGenes(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX Search for multiple genes at once.
searchMultipleGenesGetMap(Collection<String>, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX Search for multiple genes at once.
SearchResultValueObject(SearchResult<T>) - Constructor for class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
SecurityController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Manages data-level security (ie.
SecurityController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
SecurityInfoValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity: Carries extensive security information about an entity.
SecurityInfoValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
SecurityInfoValueObject(Securable) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
ServiceUnavailableException - Exception Class in ubic.gemma.web.controller.util: Exception raised when a service is unavailable.
ServiceUnavailableException(String) - Constructor for exception class ubic.gemma.web.controller.util.ServiceUnavailableException
ServletMetricsFilter - Class in ubic.gemma.web.metrics.binder.servlet: Metrics for servlet requests.
ServletMetricsFilter() - Constructor for class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
ServletStaticAssetServer - Class in ubic.gemma.web.assets: Serve static assets from the servlet context.
ServletStaticAssetServer(ServletContext) - Constructor for class ubic.gemma.web.assets.ServletStaticAssetServer
sessionCreated(HttpSessionEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
sessionDestroyed(HttpSessionEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
SessionListManager - Interface in ubic.gemma.web.controller.persistence
SessionListManagerImpl - Class in ubic.gemma.web.controller.persistence
SessionListManagerImpl() - Constructor for class ubic.gemma.web.controller.persistence.SessionListManagerImpl
setAccession(String) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
setAdditionalTaxa(Collection<Taxon>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt: Method to format taxon list for display.
setAdditionalTaxa(Set<String>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setAllowModification(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setAllParentsAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setAlt(String) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Alternative text to use for the image.
setAlt(String) - Method in class ubic.gemma.web.taglib.ImageTag
setAlt(String, SingleCellSparsityHeatmap.SingleCellHeatmapType) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag: Set the alternative text for a specific heatmap type.
setAlternateNames(Collection<String>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setAlternative(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setAnalysisId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
setArrayDesignIds(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setArrayDesignMatchesDataFile(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setArrayDesignMismatchProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
setAssayToMaterialMap(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setAsync(boolean) - Method in class ubic.gemma.web.taglib.ScriptTag
setAuthority(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
setAvailableGroups(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
setBioMaterialCharacteristicCategoryToUse(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
setBioProcessAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setBuildInfo(BuildInfo) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
setBuildInfo(BuildInfo) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setBytesRead(long) - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
setCanEdit(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setCategory(boolean) - Method in class ubic.gemma.web.taglib.CharacteristicTag: Only render the category part of the characteristic.
setCategory(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
setCellLevelCharacteristics(List<ExpressionExperimentEditController.CellLevelCharacteristicsEditForm>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
setCellTypeAssignments(List<ExpressionExperimentEditController.CellTypeAssignmentEditForm>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
setCharacteristic(Characteristic) - Method in class ubic.gemma.web.taglib.CharacteristicTag: Characteristic to generate the tag for.
setCitation(BibliographicReference) - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
setClassDelegatingFor(String) - Method in class ubic.gemma.web.controller.util.EntityDelegator
setClassName(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
setColor(String) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setColorString(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setContentDisposition(String) - Method in class ubic.gemma.web.controller.util.view.TextView
setCount(int) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setCssClass(String) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag
setCssStyle(String) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag
setCurrentGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setCurrentGroupCanRead(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentGroupCanWrite(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentUserCanwrite(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentUserOwns(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setData(double[]) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setDatabaseEntry(DatabaseEntry) - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
setDatabaseEntryValueObject(DatabaseEntryValueObject) - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
setDataFileFormatProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setDataFileIsValidFormat(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setDedvId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setDefer(boolean) - Method in class ubic.gemma.web.taglib.ScriptTag
setDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
setDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setDimension(BioAssayDimension) - Method in class ubic.gemma.web.taglib.EntityLinkTag
setDir(String) - Method in class ubic.gemma.web.controller.util.ListBatchCommand
setDirty(boolean) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag
setEdit(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
setEeId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setEeIds(Collection<Long>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setEeManagerId(String) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: DOM ID of the manager for the experiment.
setEeQuery(String) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setEeSetId(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setEeSetName(String) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setEevo(BioAssaySetValueObject) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setEEwithPvalue(BioAssaySetValueObject, Double) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setEmail(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setEnabled(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setEntity(Identifiable) - Method in class ubic.gemma.web.taglib.EntityLinkTag
setEntityClazz(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityDescription(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityId(Long) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityShortName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityUrlBuilder(WebEntityUrlBuilder) - Method in class ubic.gemma.web.taglib.EntityLinkTag
setEntityUrlBuilder(WebEntityUrlBuilder) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setEntityUrlBuilder(WebEntityUrlBuilder) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
setEntityUrlBuilder(WebEntityUrlBuilder) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
setError(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setErrorCategory(String) - Method in class ubic.gemma.web.controller.util.UnhandledExceptionResolver: Set the name of the logger to use for reporting unhandled exceptions.
setErrorMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setErrorView(String) - Method in class ubic.gemma.web.controller.util.UnhandledExceptionResolver: Set the view to use for reporting unhandled exception.
setException(Exception) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag: Exception to display.
setExperimentalDesignId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Expression experiment to display the QC info for.
setExpressionExperiment(ExpressionExperimentValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
setExpressionExperimentId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setExpressionExperimentId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setExpressionExperimentId(Long) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag: An identifier to the expression experiment that owns the biossays.
setExternal(boolean) - Method in class ubic.gemma.web.taglib.CharacteristicTag: Generate an external link.
setExternal(boolean) - Method in class ubic.gemma.web.taglib.EntityLinkTag
setFactor(Integer) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setFactorNames(LinkedHashMap<String, LinkedHashMap<String, String>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactorProfiles(Collection<FactorProfile>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactors(Collection<ExperimentalFactorValueObject>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
setFactors(List<String>) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setFactorValue(FactorValue) - Method in class ubic.gemma.web.taglib.FactorValueTag
setFactorValueMap(Map<String, String>) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setFactorValues(List<List<String>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactorValuesToNames(List<LinkedHashMap<String, String[]>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFile(byte[]) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
setFile(FileUpload) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
setFileIndex(int) - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
setFilter(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setFont(String) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Font to use for the rendering diagnostic plots.
setForceRewrite(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setFormat(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setGeneIds(Collection<Long>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setGeneIds(Collection<Long>) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setGeneralType(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setGenes(Collection<GeneValueObject>) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setGroupName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setGroups(Set<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setGroupsThatCanRead(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setGroupsThatCanWrite(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setHasCorrMat(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Indicate if there is a correlation matrix.
setHasMeanVariance(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Indicate if there is a mean-variance relation.
setHasPCA(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Indicate if there is a PCA.
setHasSingleCellData(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Indicate if the experiment has single-cell data.
setHeatmap(T) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Heatmap to render.
setHeatmap(ExpressionDataHeatmap) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
setHeatmap(SingleCellSparsityHeatmap) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
setHeight(String) - Method in class ubic.gemma.web.taglib.ImageTag
setId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
setId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
setId(Long) - Method in class ubic.gemma.web.controller.util.EntityDelegator
setInGroup(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setIsBackground(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsBackgroundSubtracted(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsBatchCorrected(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsContinuous(Boolean) - Method in class ubic.gemma.web.controller.visualization.FactorProfile
setIsMaskedPreferred(Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm: Deprecated.
setIsNormalized(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsPreferred(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setIsPreferred(Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsRatio(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsRatio(Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setIsRecomputedFromRawData(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setIsSingleCellPreferred(Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setLimit(Integer) - Method in class ubic.gemma.web.controller.util.ListBatchCommand
setLocalPath(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
setMaskMissing(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setMaxHeight(int) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Maximum height of the heatmap in pixels.
setMaxUploadSize(long) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver: Set the maximum allowed size (in bytes) before uploads are refused.
setMaxWidth(int) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Maximum width of the heatmap in pixels.
setMember(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setMergees(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setMerger(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setMessage(String) - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
setMessageUtil(MessageUtil) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
setMetricName(String) - Method in class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter: Set the name under which servlet metrics are reported.
setMode(String, String, HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
setName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
setName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setName(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setNonMatchingProbeNameExamples(Collection<String>) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNoParentsAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setNormalized(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setNumberMatchingProbes(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNumberOfNonMatchingProbes(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNumColumns(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNumFactors(int) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
setNumFactors(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: How many factors (including batch etc) are available for PCA display?
setNumOutliersRemoved(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Number of outliers removed.
setNumPcsToDisplay(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Number of principal components to display.
setNumPossibleOutliers(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Number of possible outliers.
setNumRows(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setOntologyExternalLinks(OntologyExternalLinks) - Method in class ubic.gemma.web.taglib.OntologyResourceTag
setOriginalFileName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setOtherProblemsMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setOwner(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setOwnersGroups(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setPlots(List<List<DoublePoint>>) - Method in class ubic.gemma.web.controller.visualization.FactorProfile
setPrincipal(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
setProbe(CompositeSequenceValueObject) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setProbeId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setProbeName(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setProfile(double[]) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setProfiles(Collection<GeneExpressionProfile>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setProtocolId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setPubliclyReadable(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setPubMedId(Integer) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setPValue(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setQuantitationType(QuantitationType) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setQuantitationTypeDescription(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setQuantitationTypeId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setQuantitationTypeIsValid(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setQuantitationTypeName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setQuantitationTypeProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setQuantitationTypes(Collection<QuantitationTypeValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
setQuantitationTypes(List<ExpressionExperimentEditController.QuantitationTypeEditForm>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setQuantitationTypesByVectorType(Map<Class<? extends DataVector>, List<ExpressionExperimentEditController.QuantitationTypeEditForm>>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm: ExpressionExperimentEditController.ExpressionExperimentEditForm.quantitationTypes, organized by the type of data vector they apply to and in the same order.
setRank(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setReCaptcha(ReCaptcha) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
setRecords(List<T>) - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
setRepresentation(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm: This is disabled by default in the UI because we don't want users to mess with the representation accidentally.
setResource(OntologyResource) - Method in class ubic.gemma.web.taglib.OntologyResourceTag
setReturnToExperiment(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm: Return to the experiment page after a successful update.
setSampleNames(List<String>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setScale(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setScale(ScaleType) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setScope(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
setSearchCriteria(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setSearchOptions(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand
setSearchString(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setSelectedFactors(Collection<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setServerFilePath(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setServletContext(ServletContext) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartMonitoredResolver
setShared(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setShortNameIsUnique(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setShowStackTrace(boolean) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag: Display the stacktrace.
setShowXLabels(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Display row labels.
setShowYLabels(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Display column labels.
setSingleCellDimensions(List<ExpressionExperimentEditController.SingleCellDimensionEditForm>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
setSingleCellSparsityHeatmap(SingleCellSparsityHeatmap) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: Heatmap for single-cell data.
setSort(String) - Method in class ubic.gemma.web.controller.util.ListBatchCommand
setSrc(String) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag
setStandardized(boolean) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setStart(Integer) - Method in class ubic.gemma.web.controller.util.ListBatchCommand
setStaticAssetResolver(StaticAssetResolver) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setStatus(String) - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
setStatusCode(int) - Method in class ubic.gemma.web.controller.util.UnhandledExceptionResolver: Set the status code to use for reporting unhandled exception.
setSubsumees(Collection<ArrayDesign>) - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
setSubsumees(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setSubsumer(ArrayDesign) - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
setSubsumer(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setSuccess(boolean) - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
setTagWriter(TagWriter) - Method in class ubic.gemma.web.taglib.EntityLinkTag
setTaskId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setTaxon(Taxon) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
setTaxonId(Long) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setTaxonId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setTerm(OntologyTerm) - Method in class ubic.gemma.web.taglib.OntologyHierarchyTag
setThreshold(Double) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
setTitle(String) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag
setTotalRecords(long) - Method in class ubic.gemma.web.controller.util.view.JsonReaderResponse
setTotalSize(long) - Method in class ubic.gemma.web.controller.util.upload.UploadInfo
setType(String) - Method in class ubic.gemma.web.controller.analysis.expression.diff.DifferentialExpressionAnalyzerInfo
setType(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
setUpFactorProfiles(LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject: Initialize the factor profiles.
setUseResizeTrick(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Use the resize trick to render the heatmap by generating one pixel per cell and scaling it with CSS.
setUserName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setValid(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setValidateOnly(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setValues(List<String>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
setValues(List<String>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
setVar(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
setViewSampling(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setWidth(String) - Method in class ubic.gemma.web.taglib.ImageTag
ShortBibliographicReferenceTag - Class in ubic.gemma.web.taglib
ShortBibliographicReferenceTag() - Constructor for class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
show() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
show() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
show() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
show(Long) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
show(Long, Integer, String, String, String) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
show(Long, Long) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
show(Long, Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
showAllArrayDesigns() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showAllExpressionExperiments() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Show all experiments (optionally conditioned on either a taxon, a list of ids, or a platform)
showAllForExperiments(int, int) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
showAllLinkSummaries() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showAllSubSets(Long, Long, HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showAllSubSets(String, Long, HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showAllTxa() - Method in class ubic.gemma.web.controller.expression.experiment.TaxonController
showArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showArrayDesignByName(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showBioAssays(Long, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showBioMaterials(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showByAccession(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
showByExperimentId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showByExperimentShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showById(Long) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
showById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showByShortName(String, Long) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
showCompositeSequences(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showExpressionExperimentById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showExpressionExperimentByShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showExpressionExperiments(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showExpressionExperimentSet(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
showGeneSet(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: If the current user has access to given gene group will return the gene ids in the gene group;
showHomePage() - Method in class ubic.gemma.web.controller.common.HomePageController
showMetaAnalysisManager() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExMetaAnalyzerController
showSingleCellExpressionData(Long, Long, Long, Long[], Long, Long, Long, HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showSubSet(Long, Long, HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Shows a list of BioAssays for an expression experiment subset.
showTaxonByCommonName(String) - Method in class ubic.gemma.web.controller.expression.experiment.TaxonController
showTaxonById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.TaxonController
showTaxonByNcbiId(Integer) - Method in class ubic.gemma.web.controller.expression.experiment.TaxonController
showTaxonByScientificName(String) - Method in class ubic.gemma.web.controller.expression.experiment.TaxonController
showXLabels - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Display row labels.
showYLabels - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Display column labels.
SidValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
SidValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
SidValueObject(Sid) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
signup(String, String, String, String, String, boolean, HttpServletRequest, HttpServletResponse, Locale) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
SignupController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller to signup new users.
SignupController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
signupForm() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
SimpleExpressionExperimentCommandValidation - Class in ubic.gemma.web.controller.expression.experiment: Stores information about the validation status of an attempted expression experiment load.
SimpleExpressionExperimentCommandValidation() - Constructor for class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
SimpleExpressionExperimentLoadTaskCommand - Class in ubic.gemma.web.controller.expression.experiment: Extends a SimpleExpressionExperimentMetaData with information about the file and provide simplified taxon/platform information.
SimpleExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
SingleCellDimensionEditForm() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
SingleCellDimensionEditForm(SingleCellDimension) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
SingleCellExpressionDataModel - Class in ubic.gemma.web.controller.expression.experiment
SingleCellExpressionDataModel(ExpressionExperiment, Collection<CellTypeAssignment>, Collection<CellLevelCharacteristics>, QuantitationType, CompositeSequence, Gene, Long[], CellTypeAssignment, CellLevelCharacteristics, Characteristic, String, String) - Constructor for class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
SingleCellSparsityHeatmapTag - Class in ubic.gemma.web.taglib.expression.experiment: Tag for displaying a single-cell sparsity heatmap.
SingleCellSparsityHeatmapTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
SingleCellSparsityHeatmapTag(String, boolean) - Constructor for class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
StandardQuantitationTypeConverter - Class in ubic.gemma.web.controller.dwr
StandardQuantitationTypeConverter() - Constructor for class ubic.gemma.web.controller.dwr.StandardQuantitationTypeConverter
start() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
start() - Method in interface ubic.gemma.web.controller.util.upload.OutputStreamListener
start() - Method in class ubic.gemma.web.controller.util.upload.UploadListener
StartupListener - Class in ubic.gemma.web.listener: Slight variant of ContextLoaderListener that logs the time taken to initialize the context.
StartupListener() - Constructor for class ubic.gemma.web.listener.StartupListener
StaticAssetResolver - Class in ubic.gemma.web.assets: Resolve static assets either froma InternalStaticAssetServer or from the webapp resources.
StaticAssetResolver() - Constructor for class ubic.gemma.web.assets.StaticAssetResolver
staticAssetServer() - Method in class ubic.gemma.web.assets.StaticAssetServerConfig
StaticAssetServer - Interface in ubic.gemma.web.assets
StaticAssetServerConfig - Class in ubic.gemma.web.assets
StaticAssetServerConfig() - Constructor for class ubic.gemma.web.assets.StaticAssetServerConfig
stop() - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
stop(Runnable) - Method in class ubic.gemma.web.assets.InternalStaticAssetServer
StyleTag - Class in ubic.gemma.web.taglib: write a <style/> tag.
StyleTag() - Constructor for class ubic.gemma.web.taglib.StyleTag
SubmittedTaskValueObject - Class in ubic.gemma.web.controller.job
SubmittedTaskValueObject() - Constructor for class ubic.gemma.web.controller.job.SubmittedTaskValueObject
SubmittedTaskValueObject(SubmittedTask) - Constructor for class ubic.gemma.web.controller.job.SubmittedTaskValueObject
success - Variable in class ubic.gemma.web.controller.util.view.JsonReaderResponse
SvdController - Class in ubic.gemma.web.controller.analysis.preprocess: Run SVD on a data set.
SvdController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.SvdController
SystemMonitorController - Class in ubic.gemma.web.controller.monitoring: Provide statistics about the system: hibernate, caches etc.
SystemMonitorController() - Constructor for class ubic.gemma.web.controller.monitoring.SystemMonitorController
SystemStatsController - Class in ubic.gemma.web.controller.common.auditAndSecurity: System statistics
SystemStatsController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController

T

TagWriterUtils - Class in ubic.gemma.web.taglib
TagWriterUtils() - Constructor for class ubic.gemma.web.taglib.TagWriterUtils
TaskCompletionController - Class in ubic.gemma.web.controller.job: Exposes progress status service check result to the front end.
TaskCompletionController() - Constructor for class ubic.gemma.web.controller.job.TaskCompletionController
TaxonController - Class in ubic.gemma.web.controller.expression.experiment
TaxonController() - Constructor for class ubic.gemma.web.controller.expression.experiment.TaxonController
TEXT_PARAM - Static variable in class ubic.gemma.web.controller.util.view.TextView: Name of parameter used to retrieve the text from the model.
TextView - Class in ubic.gemma.web.controller.util.view: Simply prints text to the client.
TextView() - Constructor for class ubic.gemma.web.controller.util.view.TextView: Create a text view for text/plain content.
TextView(String) - Constructor for class ubic.gemma.web.controller.util.view.TextView
TGEMO_URI_PREFIX - Static variable in class ubic.gemma.web.controller.ontology.OntologyController
TGFVO_URI_PREFIX - Static variable in class ubic.gemma.web.controller.ontology.OntologyController
toggleUsability(String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
toString() - Method in class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellLevelCharacteristicsEditForm
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.CellTypeAssignmentEditForm
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.ExpressionExperimentEditForm
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm
toString() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.SingleCellDimensionEditForm
toString() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
toString() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
toString() - Method in class ubic.gemma.web.controller.expression.experiment.SingleCellExpressionDataModel
toString() - Method in class ubic.gemma.web.controller.search.GeneralSearchController.SearchResultValueObject
toString() - Method in class ubic.gemma.web.controller.util.EntityDelegator
toString() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
toString() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
toString() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
totalRecords - Variable in class ubic.gemma.web.controller.util.view.JsonReaderResponse
transferTo(File) - Method in class ubic.gemma.web.controller.util.upload.CommonsMultipartFile: Deprecated.
TwoChannelMissingValueController - Class in ubic.gemma.web.controller.analysis.preprocess: Run misssing value computation via web request.
TwoChannelMissingValueController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController

U

ubic.gemma.web.assets - package ubic.gemma.web.assets: This package contains classes related to static assets management, such as CSS and JavaScript files.
ubic.gemma.web.context - package ubic.gemma.web.context
ubic.gemma.web.controller.analysis.expression.coexpression - package ubic.gemma.web.controller.analysis.expression.coexpression
ubic.gemma.web.controller.analysis.expression.coexpression.links - package ubic.gemma.web.controller.analysis.expression.coexpression.links
ubic.gemma.web.controller.analysis.expression.diff - package ubic.gemma.web.controller.analysis.expression.diff
ubic.gemma.web.controller.analysis.preprocess - package ubic.gemma.web.controller.analysis.preprocess
ubic.gemma.web.controller.analysis.report - package ubic.gemma.web.controller.analysis.report
ubic.gemma.web.controller.analysis.sequence - package ubic.gemma.web.controller.analysis.sequence
ubic.gemma.web.controller.common - package ubic.gemma.web.controller.common
ubic.gemma.web.controller.common.auditAndSecurity - package ubic.gemma.web.controller.common.auditAndSecurity
ubic.gemma.web.controller.common.auditAndSecurity.recaptcha - package ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ubic.gemma.web.controller.common.description - package ubic.gemma.web.controller.common.description
ubic.gemma.web.controller.common.description.bibref - package ubic.gemma.web.controller.common.description.bibref
ubic.gemma.web.controller.common.rss - package ubic.gemma.web.controller.common.rss
ubic.gemma.web.controller.dwr - package ubic.gemma.web.controller.dwr
ubic.gemma.web.controller.expression.arrayDesign - package ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.bioAssay - package ubic.gemma.web.controller.expression.bioAssay
ubic.gemma.web.controller.expression.biomaterial - package ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.controller.expression.designElement - package ubic.gemma.web.controller.expression.designElement
ubic.gemma.web.controller.expression.experiment - package ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.genome - package ubic.gemma.web.controller.genome
ubic.gemma.web.controller.genome.gene - package ubic.gemma.web.controller.genome.gene
ubic.gemma.web.controller.job - package ubic.gemma.web.controller.job
ubic.gemma.web.controller.monitoring - package ubic.gemma.web.controller.monitoring
ubic.gemma.web.controller.ontology - package ubic.gemma.web.controller.ontology
ubic.gemma.web.controller.persistence - package ubic.gemma.web.controller.persistence
ubic.gemma.web.controller.search - package ubic.gemma.web.controller.search
ubic.gemma.web.controller.util - package ubic.gemma.web.controller.util
ubic.gemma.web.controller.util.upload - package ubic.gemma.web.controller.util.upload
ubic.gemma.web.controller.util.view - package ubic.gemma.web.controller.util.view
ubic.gemma.web.controller.visualization - package ubic.gemma.web.controller.visualization
ubic.gemma.web.listener - package ubic.gemma.web.listener
ubic.gemma.web.metrics - package ubic.gemma.web.metrics
ubic.gemma.web.metrics.binder.servlet - package ubic.gemma.web.metrics.binder.servlet
ubic.gemma.web.service - package ubic.gemma.web.service
ubic.gemma.web.taglib - package ubic.gemma.web.taglib
ubic.gemma.web.taglib.arrayDesign - package ubic.gemma.web.taglib.arrayDesign
ubic.gemma.web.taglib.common.auditAndSecurity - package ubic.gemma.web.taglib.common.auditAndSecurity
ubic.gemma.web.taglib.expression.experiment - package ubic.gemma.web.taglib.expression.experiment
ubic.gemma.web.util - package ubic.gemma.web.util
UnhandledExceptionResolver - Class in ubic.gemma.web.controller.util: Resolver used when no other resolver can intervene.
UnhandledExceptionResolver() - Constructor for class ubic.gemma.web.controller.util.UnhandledExceptionResolver
unmarkOutlier(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
unmatchAllBioAssays(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Completely reset the pairing of bioassays to biomaterials, so they are no longer paired.
update(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
update(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
update(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
updateBasics(UpdateEEDetailsCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
updateBioMaterials(BioMaterialValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
updateCharacteristics(Collection<AnnotationValueObject>) - Method in class ubic.gemma.web.controller.common.description.CharacteristicBrowserController: Update characteristics associated with entities.
updateExperimentalFactors(ExperimentalFactorValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
updateExpressionExperiment(Long, ExpressionExperimentEditController.ExpressionExperimentEditForm, BindingResult, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController
updateFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: AJAX
updateGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.controller.persistence.SessionListManager
updateGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.controller.persistence.SessionListManagerImpl
updateMembers(Long, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the given group (permission permitting) with the given list of memberIds.
updateMembers(Long, Collection<Long>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
updateNameDesc(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
updateNameDesc(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
updatePermission(SecurityInfoValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
updatePermissions(SecurityInfoValueObject[]) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
updatePubMed(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX.
updateReport(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
updateReportById(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
updateSessionGroup(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX updates a session group
updateSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the session group.
updateSessionGroups(Collection<SessionBoundGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Deprecated.
updateSet(GemmaSessionBackedValueObject) - Method in class ubic.gemma.web.controller.persistence.AbstractSetListContainer
updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the session group and user database groups.
updateUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the session group and user database groups.
upload(InputStream) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController: Ajax.
UploadInfo - Class in ubic.gemma.web.controller.util.upload
UploadInfo() - Constructor for class ubic.gemma.web.controller.util.upload.UploadInfo
UploadInfo(int, long, long, String) - Constructor for class ubic.gemma.web.controller.util.upload.UploadInfo
UploadListener - Class in ubic.gemma.web.controller.util.upload: This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
UploadListener(HttpServletRequest) - Constructor for class ubic.gemma.web.controller.util.upload.UploadListener
URL - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
userAgentAnalyzer() - Method in class ubic.gemma.web.util.UserAgentAnalyzerConfig
UserAgentAnalyzerConfig - Class in ubic.gemma.web.util
UserAgentAnalyzerConfig() - Constructor for class ubic.gemma.web.util.UserAgentAnalyzerConfig
UserCounterListener - Class in ubic.gemma.web.listener: Count active sessions
UserCounterListener() - Constructor for class ubic.gemma.web.listener.UserCounterListener
useResizeTrick - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Use the resize trick to render the heatmap by generating one pixel per cell and scaling it with CSS.
UserFormMultiActionController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller to edit profile of users.
UserFormMultiActionController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
UserGroupValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
UserGroupValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
UserListController - Class in ubic.gemma.web.controller.common.auditAndSecurity: For display and editing of users.
UserListController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserListController
UserTracker - Class in ubic.gemma.web.listener: Basic bean to hold number of sessions.
UserTracker() - Constructor for class ubic.gemma.web.listener.UserTracker
UserValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
UserValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
UserValueObject(User) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

V

validate(SimpleExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
validateRequest(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
var - Variable in class ubic.gemma.web.taglib.ConstantsTag: The single variable to expose.
VisualizationValueObject - Class in ubic.gemma.web.controller.visualization: Stores expression profile data from one expression experiment for plotting.
VisualizationValueObject() - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, Collection<GeneValueObject>, Double, Collection<DifferentialExpressionValueObject>) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, List<GeneValueObject>, Collection<Long>) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, List<GeneValueObject>, Collection<Long>, Double) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
visualizeCorrMat(Long, double, boolean, boolean, boolean, boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeHeatmap(Long, Long, int, int, Integer, boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeMeanVariance(Long, double, boolean, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeProbeCorrDist(Long, double, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizePvalueDist(Long, Long, Long, Integer, double, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeSingleCellDataBoxplot(Long, Long, Long, Long[], String, String, Long, double, String, boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeSingleCellSparsityHeatmap(Long, String, Integer, boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeSubSetHeatmap(Long, int, int, Integer, boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

W

WebEntityUrlBuilder - Class in ubic.gemma.web.util: This builder has extras URL-generating capabilities for Web applications.
WebEntityUrlBuilder(String, ServletContext) - Constructor for class ubic.gemma.web.util.WebEntityUrlBuilder
weekly() - Method in class ubic.gemma.web.controller.analysis.report.WhatsNewController
WhatsNewController - Class in ubic.gemma.web.controller.analysis.report: Controller to provide information on "what's new" in the system
WhatsNewController() - Constructor for class ubic.gemma.web.controller.analysis.report.WhatsNewController
write(byte[]) - Method in class ubic.gemma.web.controller.util.upload.MonitoredOutputStream
write(byte[], int, int) - Method in class ubic.gemma.web.controller.util.upload.MonitoredOutputStream
write(int) - Method in class ubic.gemma.web.controller.util.upload.MonitoredOutputStream
writeAttributes(Map<String, Object>, boolean, TagWriter) - Static method in class ubic.gemma.web.taglib.TagWriterUtils
writeBooleanAttribute(String, boolean, TagWriter) - Static method in class ubic.gemma.web.taglib.TagWriterUtils
writeEigenGenes(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
writeErrorToResponse(int, String, HttpServletResponse) - Static method in class ubic.gemma.web.controller.util.JsonUtil
writeErrorToResponse(Exception, HttpServletResponse) - Static method in class ubic.gemma.web.controller.util.JsonUtil: Write an error message to the response based on the exception type.
writeGenes(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
writeHeatmap(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
writeHeatmapImage(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag: Write the heatmap image.
writeHeatmapImage(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
writeHeatmapImage(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
writeHeatmapYLabelsAndImage(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
writeHeatmapYLabelsAndImage(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
writeOptionalAttributes(TagWriter) - Method in class ubic.gemma.web.taglib.AbstractHtmlElementTag
writeQc(TagWriter, String) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
writeSrcAttribute(TagWriter) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag: Write a URL attribute for a static asset.
writeSuccessToResponse(HttpServletResponse) - Static method in class ubic.gemma.web.controller.util.JsonUtil: Write a simple JSON object with a "success" key set to true to the response.
writeToDebugLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Write to log with severity = "debug"
writeToErrorLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Write to log with severity = "error"
writeToFatalLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Write to log with severity = "fatal"
writeToInfoLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Write to log with severity = "info"
writeToLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Defaults to writing to log with severity = "info"
writeToResponse(JSONObject, HttpServletResponse) - Static method in class ubic.gemma.web.controller.util.JsonUtil
writeToWarnLog(String, String, String, String, String) - Method in class ubic.gemma.web.controller.common.JavascriptLogger: Write to log with severity = "warn"
writeXLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
writeXLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
writeXLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
writeYLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag
writeYLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag
writeYLabels(TagWriter) - Method in class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag

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