A B C D E F G H I J L M N O P Q R S T U V W X
All Classes All Packages

A

AbstractHeatmapTag<T extends Heatmap> - Class in ubic.gemma.web.taglib.expression.experiment

AbstractHeatmapTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag

AbstractSetListContainer - Class in ubic.gemma.web.persistence

AbstractSetListContainer() - Constructor for class ubic.gemma.web.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(Integer, 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.remote.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 interface ubic.gemma.web.job.progress.ProgressStatusService

Set up an email alert for this job; an email will be sent when it has finished (or failed).

addEmailAlert(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager

addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager

addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.web.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.persistence.SessionListManager

addGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager

addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

addProperty(String, Object) - Method in class ubic.gemma.web.util.ConfigurationCookie

addSessionGroup(SessionBoundExpressionExperimentSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController

AJAX adds the Expression Experiment group to the session

addSessionGroup(SessionBoundGeneSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController

* AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.

addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController

Deprecated.

addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController

Deprecated.

addSet(GemmaSessionBackedValueObject, boolean) - Method in class ubic.gemma.web.persistence.AbstractSetListContainer

Sets the reference (generates an id and assumes this group was made as a result of a modification for the type value) for the group then adds it to the session-bound list(s) for session-bound groups

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.controller.common.auditAndSecurity.SignupController

afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController

afterPropertiesSet() - Method in class ubic.gemma.web.util.CacheMonitorImpl

afterPropertiesSet() - Method in class ubic.gemma.web.util.StaticAssetResolver

ajaxLoginCheck(HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController

ajaxSearch(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.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.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

append(LoggingEvent) - Method in class ubic.gemma.web.logging.SlackAppender

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!

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

ArrayDesignPropertyEditor - Class in ubic.gemma.web.propertyeditor

Used to convert ArrayDesigns from and into strings for display in forms.

ArrayDesignPropertyEditor(ArrayDesignService) - Constructor for class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor

ArrayDesignRepeatScanController - Class in ubic.gemma.web.controller.analysis.sequence

A controller to run array design repeat scan either locally or in a space.

ArrayDesignRepeatScanController() - Constructor for class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController

ArrayDesignRepeatScanTask - Interface in ubic.gemma.web.tasks.analysis.sequence

ArrayDesignRepeatScanTaskCommand - Class in ubic.gemma.web.tasks.analysis.sequence

A command object to be used by spaces.

ArrayDesignRepeatScanTaskCommand(String, ArrayDesign) - Constructor for class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

NOTE: we can't pass in a we command as they are defined in the web module, which messes up the configuration.

ArrayDesignRepeatScanTaskCommand(ArrayDesign) - Constructor for class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

ArrayDesignRepeatScanTaskImpl - Class in ubic.gemma.web.tasks.analysis.sequence

An array design repeat scan spaces task

ArrayDesignRepeatScanTaskImpl() - Constructor for class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl

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

asUser() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

AuditController - Class in ubic.gemma.web.remote

This is required solely for exposing auditables to remote services would try to marshall the abstract class Auditable.

AuditController() - Constructor for class ubic.gemma.web.remote.AuditController

AUTH_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener

B

BaseController - Class in ubic.gemma.web.controller

Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting messages in the session.

BaseController() - Constructor for class ubic.gemma.web.controller.BaseController

BaseFormController - Class in ubic.gemma.web.controller

Deprecated.

SimpleFormController is deprecated, use annotations-based GET/POST mapping instead.

BaseFormController() - Constructor for class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

BatchInfoRepopulationJob - Class in ubic.gemma.web.scheduler.jobs

Schedule job that populates batch information for all experiments that have been updated since the last run.

BatchInfoRepopulationJob() - Constructor for class ubic.gemma.web.scheduler.jobs.BatchInfoRepopulationJob

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.CharacteristicBrowserController

browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

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

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.util.upload.OutputStreamListener

bytesRead(int) - Method in class ubic.gemma.web.util.upload.UploadListener

C

CacheMonitor - Interface in ubic.gemma.web.util

CacheMonitorImpl - Class in ubic.gemma.web.util

Get statistics about and manage caches.

CacheMonitorImpl() - Constructor for class ubic.gemma.web.util.CacheMonitorImpl

call() - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl

cancelJob(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService

Attempt to cancel the job.

cancelJob(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

canCurrentUserEditExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it

canCurrentUserEditGroup(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController

AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed

canCurrentUserEditGroup(GeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController

AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed

CASE_INSENSITIVE_ORDER - Static variable in class ubic.gemma.web.util.LabelValue

Comparator that can be used for a case insensitive sort of LabelValue objects.

CharacteristicBrowserController - Class in ubic.gemma.web.controller.common

NOTE: Logging messages from this service are important for tracking changes to annotations.

CharacteristicBrowserController() - Constructor for class ubic.gemma.web.controller.common.CharacteristicBrowserController

CharacteristicConverter - Class in ubic.gemma.web.remote

CharacteristicConverter() - Constructor for class ubic.gemma.web.remote.CharacteristicConverter

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.TaskCompletionController

checkResult(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService

checkResult(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

ClassConverter - Class in ubic.gemma.web.remote

ClassConverter() - Constructor for class ubic.gemma.web.remote.ClassConverter

CLASSIC_HOME_PAGE - Static variable in class ubic.gemma.web.controller.WebConstants

clazz - Variable in class ubic.gemma.web.taglib.ConstantsTag

The class to expose the variables from.

cleanupMultipart(MultipartHttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

clearAllCaches() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

Flush (clear) all caches.

clearAllCaches() - Method in interface ubic.gemma.web.util.CacheMonitor

Remove all items from all caches.

clearAllCaches() - Method in class ubic.gemma.web.util.CacheMonitorImpl

clearCache(String) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

Flush (clear) a cache.

clearCache(String) - Method in interface ubic.gemma.web.util.CacheMonitor

Remove all items from the cache with the given name.

clearCache(String) - Method in class ubic.gemma.web.util.CacheMonitorImpl

clearFactorValuesNeedsAttention(Long[], String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

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.util

Resolves a ClientAbortException to an empty view.

ClientAbortExceptionResolver() - Constructor for class ubic.gemma.web.util.ClientAbortExceptionResolver

close() - Method in class ubic.gemma.web.logging.SlackAppender

close() - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream

CoexpressionSearchController - Class in ubic.gemma.web.controller.coexpressionSearch

CoexpressionSearchController() - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController

CoexSearchTaskCommand - Class in ubic.gemma.web.controller.coexpressionSearch

CoexSearchTaskCommand(CoexpressionSearchCommand) - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand

CommonsMultipartFile - Class in ubic.gemma.web.util.upload

Deprecated.

CommonsMultipartFile(FileItem) - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

Create an instance wrapping the given FileItem.

CommonsMultipartMonitoredResolver - Class in ubic.gemma.web.util.upload

An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.

CommonsMultipartMonitoredResolver() - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

compare(Gene, Gene) - Method in class ubic.gemma.web.util.GeneSymbolComparator

compareTo(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject

compareTo(LabelValue) - Method in class ubic.gemma.web.util.LabelValue

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.

ConfigurationCookie - Class in ubic.gemma.web.util

Cookie class that also presents a commons configuration interface.

ConfigurationCookie(String) - Constructor for class ubic.gemma.web.util.ConfigurationCookie

Create a cookie with the given name.

ConfigurationCookie(Cookie) - Constructor for class ubic.gemma.web.util.ConfigurationCookie

Used when loading cookies from the user.

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

Created by tesarst on 09/03/17.

ControllerUtils() - Constructor for class ubic.gemma.web.controller.ControllerUtils

convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.CharacteristicConverter

convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.DirectionConverter

convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.GOEvidenceCodeConverter

convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.ScaleTypeConverter

convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.StandardQuantitationTypeConverter

convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.ClassConverter

convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.DoublePointConverter

copyUploadedFile(HttpServletRequest, String) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil

copyUploadedFile(MultipartFile, HttpServletRequest) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil

copyUploadedInputStream(InputStream) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil

count() - Method in class ubic.gemma.web.controller.common.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

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

createFactorValueCharacteristic(EntityDelegator<FactorValue>, CharacteristicValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

createGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

createItem(String, String, boolean, String) - Method in class ubic.gemma.web.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.common.auditAndSecurity.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. eg: ajax methods for visualization

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.util

Custom exception resolver for Gemma.

DefaultHandlerExceptionResolver() - Constructor for class ubic.gemma.web.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

deleteFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

deleteFactorValues(EntityDelegator<ExperimentalFactor>, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

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, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

determineAnalysisType(Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController

Ajax method.

determineEncoding(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

Determine the encoding for the given request.

diagnostics(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController

Only update the daignostics

DifferentialExpressionAnalysisController - Class in ubic.gemma.web.controller.diff

A controller to run differential expression analysis either locally or in a space.

DifferentialExpressionAnalysisController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController

DifferentialExpressionAnalyzerInfo - Class in ubic.gemma.web.controller.diff

Used to carry information about the experimental design analysis settings to clients.

DifferentialExpressionAnalyzerInfo() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo

DifferentialExpressionSearchController - Class in ubic.gemma.web.controller.diff

A controller used to get differential expression analysis and meta analysis results.

DifferentialExpressionSearchController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController

DiffExMetaAnalyzerController - Class in ubic.gemma.web.controller.diff

A controller to analyze result sets either locally or in a space.

DiffExMetaAnalyzerController() - Constructor for class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController

DiffExpressionSearchCommand - Class in ubic.gemma.web.controller.diff

DiffExpressionSearchCommand() - Constructor for class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

DirectionConverter - Class in ubic.gemma.web.remote

DWR converter for Direction type.

DirectionConverter() - Constructor for class ubic.gemma.web.remote.DirectionConverter

disableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

Exposed to AJAX

disableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor

Disable collection of statistics on the caches.

disableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl

doBackgroundCoexSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.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.util.upload.OutputStreamListener

done() - Method in class ubic.gemma.web.util.upload.UploadListener

doResolveException(HttpServletRequest, HttpServletResponse, Object, Exception) - Method in class ubic.gemma.web.util.ClientAbortExceptionResolver

doSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController

Important entry point - called by the CoexpressionSearchTask

doSearchQuickComplete(CoexpressionSearchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController

Do a search that fills in the edges among the genes already found.

doStartTag() - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag

doStartTag() - Method in class ubic.gemma.web.taglib.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.ScriptTag

doStartTagInternal() - Method in class ubic.gemma.web.taglib.StyleTag

DoublePointConverter - Class in ubic.gemma.web.remote

The 8 decimal precision of a double is just a waste of bandwidth in most cases.

DoublePointConverter() - Constructor for class ubic.gemma.web.remote.DoublePointConverter

downloadAnnotationFile(Long, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

downloadDEDV(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController

Handle case of text export of the results.

downloadFile(String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController

Regular spring MVC request to fetch a file that already has been generated.

downloadMetaFile(Long, Integer, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController

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.

dynamicAttributes - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag

E

editUser(String, String, String, String, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController

Entry point for updates.

Ee2AdUpdateJob - Class in ubic.gemma.web.scheduler.jobs

Ee2AdUpdateJob() - Constructor for class ubic.gemma.web.scheduler.jobs.Ee2AdUpdateJob

Ee2cUpdateJob - Class in ubic.gemma.web.scheduler.jobs

Ee2cUpdateJob() - Constructor for class ubic.gemma.web.scheduler.jobs.Ee2cUpdateJob

enableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

Exposed to AJAX

enableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor

Enable collection of statistics on the caches.

enableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl

EntityDelegator<T extends Identifiable> - Class in ubic.gemma.web.remote

Bean to expose for remote access via AJAX, when all that is needed is the ID and a way to know what the class is.

EntityDelegator() - Constructor for class ubic.gemma.web.remote.EntityDelegator

EntityDelegator(T) - Constructor for class ubic.gemma.web.remote.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 in ubic.gemma.web.util

Signals that an entity was not found in the system.

EntityNotFoundException(String) - Constructor for exception ubic.gemma.web.util.EntityNotFoundException

EntityNotFoundException(String, Throwable) - Constructor for exception ubic.gemma.web.util.EntityNotFoundException

equals(Object) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject

equals(Object) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

equals(Object) - Method in class ubic.gemma.web.util.LabelValue

error(String) - Method in interface ubic.gemma.web.util.upload.OutputStreamListener

error(String) - Method in class ubic.gemma.web.util.upload.UploadListener

ExceptionTag - Class in ubic.gemma.web.taglib.common.auditAndSecurity

ExceptionTag() - Constructor for class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag

executeAs(JobExecutionContext) - Method in class ubic.gemma.web.scheduler.jobs.BatchInfoRepopulationJob

executeAs(JobExecutionContext) - Method in class ubic.gemma.web.scheduler.jobs.Ee2AdUpdateJob

executeAs(JobExecutionContext) - Method in class ubic.gemma.web.scheduler.jobs.Ee2cUpdateJob

executeAs(JobExecutionContext) - Method in class ubic.gemma.web.scheduler.SecureQuartzJobBean

executeInternal(JobExecutionContext) - Method in class ubic.gemma.web.scheduler.SecureQuartzJobBean

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.persistence

ExperimentSetListContainer() - Constructor for class ubic.gemma.web.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

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.ExpressionExperimentEditForm - Class in ubic.gemma.web.controller.expression.experiment

ExpressionExperimentEditController.QuantitationTypeEditForm - 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

ExpressionExperimentQCUtils - Class in ubic.gemma.web.controller.expression.experiment

Helper functions for checking existence etc. of QC information.

ExpressionExperimentQCUtils() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils

ExpressionExperimentReportGenerationController - Class in ubic.gemma.web.controller

ExpressionExperimentReportGenerationController() - Constructor for class ubic.gemma.web.controller.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.util

ExternalStaticAssetServer(String) - Constructor for class ubic.gemma.web.util.ExternalStaticAssetServer

extractIds(String) - Static method in class ubic.gemma.web.controller.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.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.util.upload.FailedMultipartHttpServletRequest

FailedMultipartHttpServletRequest(HttpServletRequest, String) - Constructor for class ubic.gemma.web.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.util.upload

Utility methods for uploading files.

FileUploadUtil() - Constructor for class ubic.gemma.web.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.CharacteristicBrowserController

findCharacteristicsCustom(String, boolean, boolean, boolean, boolean, boolean, boolean, String) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController

findDetailMetaAnalysisById(Long) - Method in class ubic.gemma.web.controller.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.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

GemmaClassicHomePageController - Class in ubic.gemma.web.controller.common

Deprecated.

GemmaClassicHomePageController() - Constructor for class ubic.gemma.web.controller.common.GemmaClassicHomePageController

Deprecated.

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

Note: do not use parametrized collections as parameters for ajax methods in this class!

GeneralSearchController() - Constructor for class ubic.gemma.web.controller.GeneralSearchController

GeneralSearchController.SearchResultValueObject<T extends IdentifiableValueObject<?>> - Class in ubic.gemma.web.controller

generateCache() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.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.persistence

GeneSetListContainer() - Constructor for class ubic.gemma.web.persistence.GeneSetListContainer

GeneSymbolComparator - Class in ubic.gemma.web.util

GeneSymbolComparator() - Constructor for class ubic.gemma.web.util.GeneSymbolComparator

GeoRecordBrowserController - Class in ubic.gemma.web.controller.expression.experiment

GeoRecordBrowserController() - Constructor for class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController

get(String, String) - Static method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp

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

getAdminUser() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getAllExperimentSets() - Method in interface ubic.gemma.web.persistence.SessionListManager

getAllExperimentSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getAllGeneSets() - Method in interface ubic.gemma.web.persistence.SessionListManager

getAllGeneSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getAllGeneSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager

getAllGeneSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getAllParentsAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

getAllSessionBoundGroups() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer

getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

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

getArrayDesign() - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

getArrayDesignMismatchProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

getArrayDesignName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

getArrayDesigns(Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

getAsText() - Method in class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor

getAsText() - Method in class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor

getAsText() - Method in class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor

getAsText() - Method in class ubic.gemma.web.propertyeditor.TaxonPropertyEditor

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.util.ExternalStaticAssetServer

getBaseUrl() - Method in class ubic.gemma.web.util.InternalStaticAssetServer

getBaseUrl() - Method in interface ubic.gemma.web.util.StaticAssetServer

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.

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

getBioMaterialsForEE(Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

getBioProcessAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

getBody() - Method in class ubic.gemma.web.feed.NewsItem

getBoolean(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getBytes() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getBytesRead() - Method in class ubic.gemma.web.util.upload.UploadInfo

getCacheStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

getCancelView(HttpServletRequest) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

Override this to control which cancelView is used.

getCancelView(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController

getCategoryTerms() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController

getClassDelegatingFor() - Method in class ubic.gemma.web.remote.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

getConfirmNewPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getContentType() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getContentType() - Method in class ubic.gemma.web.view.JSONView

getContextUploadPath() - Static method in class ubic.gemma.web.util.upload.FileUploadUtil

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?

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

getDate() - Method in class ubic.gemma.web.feed.NewsItem

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.common.auditAndSecurity.UserUpdateCommand

getDescription(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

AJAX call

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.diff.DifferentialExpressionSearchController

AJAX entry which returns results on a non-meta analysis basis.

getDifferentialExpression(Long, double, Integer) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController

AJAX entry which returns results on a non-meta analysis basis.

getDifferentialExpressionWithoutBatch(Long, double, Integer) - Method in class ubic.gemma.web.controller.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.remote.ListBatchCommand

getDisplayName() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile

getDouble(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getEeId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject

getEeIds() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

getEeQuery() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

getEeSetId() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

getEeSetName() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

getEevo() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject

getEmail() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getEmail() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

getEnabled() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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

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.util.upload.FailedMultipartHttpServletRequest

getEvents(EntityDelegator<? extends Auditable>) - Method in class ubic.gemma.web.remote.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

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.persistence.SessionListManager

getExperimentIdsInSet(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getExperimentSetById(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager

Get the session-bound group using the group's id

getExperimentSetById(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getExperimentsInSet(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager

getExperimentsInSet(Long) - Method in class ubic.gemma.web.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

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.diff.DifferentialExpressionAnalyzerInfo

getFactors() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

getFactors(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController

AJAX entry.

getFactorTypes() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

getFactorValue(Long, String) - Method in class ubic.gemma.web.controller.OntologyController

getFactorValueAnnotation(Long, Long, String) - Method in class ubic.gemma.web.controller.OntologyController

getFactorValueMap() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

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

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

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.util.upload.UploadInfo

getFileItem() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

Return the underlying org.apache.commons.fileupload.FileItem instance.

getForm() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController

getFormat() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

getFullName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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.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.

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.persistence.SessionListManager

Get the session-bound group using the group's id

getGeneSetById(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getGenesInGroup(Long) - Method in interface ubic.gemma.web.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.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

getId() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getId() - Method in class ubic.gemma.web.remote.EntityDelegator

getInputStream() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getInt(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

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

getIsNormalized() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm

getIsRatio() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm

getIsRecomputedFromRawData() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm

getJobs() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getKeys() - Method in class ubic.gemma.web.util.ConfigurationCookie

getLabel() - Method in class ubic.gemma.web.util.LabelValue

getLastName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getLatestExperiments() - Method in class ubic.gemma.web.controller.common.rss.RssFeedController

Show all experiments

getLaunchInstruction() - Method in class ubic.gemma.web.util.ExternalStaticAssetServer

getLaunchInstruction() - Method in class ubic.gemma.web.util.InternalStaticAssetServer

getLaunchInstruction() - Method in interface ubic.gemma.web.util.StaticAssetServer

Obtain launch instructions if the server is not running.

getLimit() - Method in class ubic.gemma.web.remote.ListBatchCommand

getList(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getLocalPath() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload

getLong(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

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.remote.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.persistence.SessionListManager

getModifiedExperimentSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getModifiedExperimentSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager

getModifiedExperimentSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getModifiedGeneSets() - Method in interface ubic.gemma.web.persistence.SessionListManager

getModifiedGeneSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getModifiedGeneSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager

getModifiedGeneSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

getMultipartContentType(String) - Method in class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest

getMultipartHeaders(String) - Method in class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest

getName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getName() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

getName() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getNewPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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

getOldPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getOntology() - Method in class ubic.gemma.web.controller.OntologyController

getOriginalFilename() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getOriginalFileName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

getOutputFile(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController

getOutputStream() - Method in class ubic.gemma.web.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.UserUpdateCommand

getPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

getPasswordHint() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

getPhase() - Method in class ubic.gemma.web.util.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 interface ubic.gemma.web.job.progress.ProgressStatusService

Get the latest information about how a job is doing.

getProgressStatus(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

getProperties(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getProperty(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getPValue() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile

getQuantitationType() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

getQuantitationTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

getQuantitationTypeProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

getQuantitationTypes() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject

getRank() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile

getRecords() - Method in class ubic.gemma.web.remote.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

getRole() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

Deprecated.

use UserValueObject.getGroups() instead

getSampleNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject

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.

getSearchCriteria() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

getSearchOptions() - Method in class ubic.gemma.web.controller.coexpressionSearch.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.diff.DiffExpressionSearchCommand

getServerFilePath() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

getSessionBoundModifiedGroups() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer

getShort(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getSize() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

getSort() - Method in class ubic.gemma.web.remote.ListBatchCommand

getStart() - Method in class ubic.gemma.web.remote.ListBatchCommand

getStats() - Method in interface ubic.gemma.web.util.HibernateMonitor

getStats() - Method in class ubic.gemma.web.util.HibernateMonitorImpl

getStats(boolean, boolean, boolean) - Method in interface ubic.gemma.web.util.HibernateMonitor

Log some statistics.

getStats(boolean, boolean, boolean) - Method in class ubic.gemma.web.util.HibernateMonitorImpl

getStats(Locale) - Method in interface ubic.gemma.web.util.CacheMonitor

Obtain the cache statistics in HTML format.

getStats(Locale) - Method in class ubic.gemma.web.util.CacheMonitorImpl

getStatus() - Method in class ubic.gemma.web.util.upload.UploadInfo

getStorageDescription() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile

Deprecated.

Return a description for the storage location of the multipart content.

getString(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

getSubmittedTask(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService

getSubmittedTask(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

getSubmittedTasks() - Method in interface ubic.gemma.web.job.progress.ProgressStatusService

getSubmittedTasks() - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

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.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

getTaskId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse

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.diff.DiffExpressionSearchCommand

getTaxonName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

getTeaser() - Method in class ubic.gemma.web.feed.NewsItem

getTerm(String) - Method in class ubic.gemma.web.controller.OntologyController

getThreshold() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

getTitle() - Method in class ubic.gemma.web.feed.NewsItem

getTotalRecords() - Method in class ubic.gemma.web.remote.JsonReaderResponse

getTotalSize() - Method in class ubic.gemma.web.util.upload.UploadInfo

getType() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo

getTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile

getUploadPath() - Static method in class ubic.gemma.web.util.upload.FileUploadUtil

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.UserUpdateCommand

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

getValue() - Method in class ubic.gemma.web.util.LabelValue

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.CharacteristicBrowserController

getView() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryController

getViewNameForRequest(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController

GOEvidenceCodeConverter - Class in ubic.gemma.web.remote

GOEvidenceCodeConverter() - Constructor for class ubic.gemma.web.remote.GOEvidenceCodeConverter

H

handleRequestInternal(String, String, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

handleRequestInternal(HttpServletRequest) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

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.common.auditAndSecurity.UserUpdateCommand

hashCode() - Method in class ubic.gemma.web.util.LabelValue

hasNodeDegreeDistFile(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils

hasPvalueDistFiles(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils

heatmap - Variable in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag

Heatmap to render.

HibernateMonitor - Interface in ubic.gemma.web.util

HibernateMonitorImpl - Class in ubic.gemma.web.util

Monitoring of Hibernate status.

HibernateMonitorImpl() - Constructor for class ubic.gemma.web.util.HibernateMonitorImpl

holds(Class<?>) - Method in class ubic.gemma.web.remote.EntityDelegator

Check if the entity delegator holds the given type.

HOME_PAGE - Static variable in class ubic.gemma.web.controller.WebConstants

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

HOST - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha

htmlEscape(String) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag

htmlEscape(String) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag

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.persistence.SessionListManager

incrementAndGetLargestExperimentSetSessionId() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

incrementAndGetLargestGeneSetSessionId() - Method in interface ubic.gemma.web.persistence.SessionListManager

incrementAndGetLargestGeneSetSessionId() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

incrementAndGetLargestSessionId() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer

incrementSessions() - Static method in class ubic.gemma.web.listener.UserTracker

index(IndexerTaskCommand) - Method in class ubic.gemma.web.controller.IndexController

IndexController - Class in ubic.gemma.web.controller

IndexController() - Constructor for class ubic.gemma.web.controller.IndexController

initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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.util

InternalStaticAssetServer(Path, Path, String, boolean, Path) - Constructor for class ubic.gemma.web.util.InternalStaticAssetServer

invoke() - Method in class ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean

isAlive() - Method in class ubic.gemma.web.util.ExternalStaticAssetServer

isAlive() - Method in class ubic.gemma.web.util.InternalStaticAssetServer

isAlive() - Method in interface ubic.gemma.web.util.StaticAssetServer

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.util.InternalStaticAssetServer

isAvailable() - Method in class ubic.gemma.web.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.diff.DiffExpressionSearchCommand

isEmpty() - Method in class ubic.gemma.web.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.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.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

isRunning() - Method in class ubic.gemma.web.util.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.remote.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.util

Class to handle saving client-side javascript error messages and warnings to a server-side log.

JavascriptLogger() - Constructor for class ubic.gemma.web.util.JavascriptLogger

JsonReaderResponse<T> - Class in ubic.gemma.web.remote

Creates a response that can be consumed by an Ext.data.JsonReader.

JsonReaderResponse(String) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse

Creates an unJsonReaderResponse.successful JsonReaderResponse with null JsonReaderResponse.records.

JsonReaderResponse(Collection<T>, long) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse

Use for remote paging applications.

JsonReaderResponse(List<T>) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse

Creates a successful JsonReaderResponse with the provided objectsToConvertToRecords.

JSONTableRenderer - Class in ubic.gemma.web.view

JSONTableRenderer() - Constructor for class ubic.gemma.web.view.JSONTableRenderer

JsonUtil - Class in ubic.gemma.web.util

Utilities for writing JSON payloads to HttpServletResponse.

JsonUtil() - Constructor for class ubic.gemma.web.util.JsonUtil

JSONView - Class in ubic.gemma.web.view

JSONView() - Constructor for class ubic.gemma.web.view.JSONView

JSONView(String) - Constructor for class ubic.gemma.web.view.JSONView

L

LabelValue - Class in ubic.gemma.web.util

A simple JavaBean to represent label-value pairs.

LabelValue() - Constructor for class ubic.gemma.web.util.LabelValue

Default constructor.

LabelValue(String, String) - Constructor for class ubic.gemma.web.util.LabelValue

Construct an instance with the supplied property values.

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.remote

Encapsulates information needed for generic list browsing.

ListBatchCommand() - Constructor for class ubic.gemma.web.remote.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(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.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

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 - Variable in class ubic.gemma.web.controller.BaseController

log - Static variable in class ubic.gemma.web.controller.BaseFormController

Deprecated.

log - Static variable in class ubic.gemma.web.controller.ControllerUtils

log - Static variable in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController

log - Static variable in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController

logger - Static variable in class ubic.gemma.web.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

markOutlier(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController

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.remote.JsonReaderResponse

MESSAGES_ATTRIBUTE - Static variable in class ubic.gemma.web.util.MessageUtilImpl

messageSource - Variable in class ubic.gemma.web.controller.BaseController

messageUtil - Variable in class ubic.gemma.web.controller.BaseController

messageUtil - Variable in class ubic.gemma.web.controller.BaseFormController

Deprecated.

MessageUtil - Interface in ubic.gemma.web.util

Provides methods for putting messages to the user in the session.

MessageUtilImpl - Class in ubic.gemma.web.util

MessageUtilImpl() - Constructor for class ubic.gemma.web.util.MessageUtilImpl

MetaFile - Class in ubic.gemma.web.controller.expression.experiment

Wrapper for metadata file information for the frontend

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.util.upload

Commons FileItem that uses a MonitoredOutputStream

MonitoredDiskFileItem(String, String, boolean, String, int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItem

MonitoredDiskFileItemFactory - Class in ubic.gemma.web.util.upload

MonitoredDiskFileItemFactory(int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory

MonitoredDiskFileItemFactory(OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory

MonitoredOutputStream - Class in ubic.gemma.web.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.util.upload.MonitoredOutputStream

N

newFileUpload(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

Create a factory for disk-based file items with a listener we can check for progress.

NewsItem - Class in ubic.gemma.web.feed

NewsItem() - Constructor for class ubic.gemma.web.feed.NewsItem

numFactors(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils

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

Provide minimal support for exposing Gemma ontology.

OntologyController() - Constructor for class ubic.gemma.web.controller.OntologyController

OutputStreamListener - Interface in ubic.gemma.web.util.upload

P

PATH - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha

pcaFactors(Long, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

pcaScree(Long, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

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

processErrors(HttpServletRequest, HttpServletResponse, Object, BindException, String) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

Convenience method to get the user object from the session

processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

Default behavior for FormControllers - redirect to the successView when the cancel button has been pressed.

processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController

ProgressStatusService - Interface in ubic.gemma.web.job.progress

These methods are exposed to front-end.

ProgressStatusServiceImpl - Class in ubic.gemma.web.job.progress

This class exposes methods for AJAX calls.

ProgressStatusServiceImpl() - Constructor for class ubic.gemma.web.job.progress.ProgressStatusServiceImpl

PubMedConfig - Class in ubic.gemma.web.controller.common.description.bibref

PubMedConfig() - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedConfig

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

pubMedXMLFetcher(String) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedConfig

Q

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

QuantitationTypePropertyEditor - Class in ubic.gemma.web.propertyeditor

QuantitationTypePropertyEditor(Collection<QuantitationType>) - Constructor for class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor

R

recalculateBatchConfound(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

recalculateBatchEffect(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

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 in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha

ReCaptchaException(String) - Constructor for exception ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException

ReCaptchaException(String, Throwable) - Constructor for exception 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.remote.JsonReaderResponse

redirectToHomePage(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.HomePageController

redo(Long, Long) - Method in class ubic.gemma.web.controller.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.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.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.CharacteristicBrowserController

removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager

removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl

removeExperimentTag(Collection<Long>, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController

removeGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager

removeGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.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.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.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(List<Object>) - Method in class ubic.gemma.web.view.JSONTableRenderer

render(Map<String, ?>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.JSONView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.TextView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.XmlView

requiresLayout() - Method in class ubic.gemma.web.logging.SlackAppender

resetHibernateStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

resetPassword(String, String, HttpServletRequest, 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.util.HibernateMonitor

Clear all statistics.

resetStats() - Method in class ubic.gemma.web.util.HibernateMonitorImpl

resolveException(HttpServletRequest, HttpServletResponse, Object, Exception) - Method in class ubic.gemma.web.util.UnhandledExceptionResolver

resolveMultipart(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

resolveUrl(String) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag

resolveUrl(String) - Method in class ubic.gemma.web.util.StaticAssetResolver

Resolve a URL to a static asset.

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.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. -- uses default settings

run(Long) - Method in class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController

AJAX entry point.

run(Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController

AJAX entry point when running completely automatically.

run(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController

AJAX entry point.

run(Long) - Method in class ubic.gemma.web.controller.ExpressionExperimentReportGenerationController

runAll() - Method in class ubic.gemma.web.controller.ExpressionExperimentReportGenerationController

runCustom(Long, Collection<Long>, boolean, Long) - Method in class ubic.gemma.web.controller.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

S

saveMessage(String) - Method in interface ubic.gemma.web.util.MessageUtil

Put a message into the session.

saveMessage(String) - Method in class ubic.gemma.web.util.MessageUtilImpl

saveMessage(String, Object[], String) - Method in interface ubic.gemma.web.util.MessageUtil

Put a message into the session.

saveMessage(String, Object[], String) - Method in class ubic.gemma.web.util.MessageUtilImpl

saveMessage(String, Object, String) - Method in interface ubic.gemma.web.util.MessageUtil

Put a message into the session.

saveMessage(String, Object, String) - Method in class ubic.gemma.web.util.MessageUtilImpl

saveMessage(String, String) - Method in interface ubic.gemma.web.util.MessageUtil

Put a message into the session.

saveMessage(String, String) - Method in class ubic.gemma.web.util.MessageUtilImpl

saveResultSets(Collection<Long>, String, String) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController

saveUser(UserValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListController

ScaleTypeConverter - Class in ubic.gemma.web.remote

ScaleTypeConverter() - Constructor for class ubic.gemma.web.remote.ScaleTypeConverter

scheduleDiffExpSearchTask(Long, ExpressionExperimentSetValueObject, GeneSetValueObject) - Method in class ubic.gemma.web.controller.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.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.GeneralSearchController.SearchResultValueObject

SecureMethodInvokingJobDetailFactoryBean - Class in ubic.gemma.web.scheduler

Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).

SecureMethodInvokingJobDetailFactoryBean(SecurityContext) - Constructor for class ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean

SecureQuartzJobBean - Class in ubic.gemma.web.scheduler

A secure Quartz job bean that executes with a given security context.

SecureQuartzJobBean() - Constructor for class ubic.gemma.web.scheduler.SecureQuartzJobBean

SecurityController - Class in ubic.gemma.web.controller.common.auditAndSecurity

Manages data-level security (ie. can make data private).

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

SequenceTypePropertyEditor - Class in ubic.gemma.web.propertyeditor

SequenceTypePropertyEditor() - Constructor for class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor

ServiceUnavailableException - Exception in ubic.gemma.web.util

Exception raised when a service is unavailable.

ServiceUnavailableException(String) - Constructor for exception ubic.gemma.web.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

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.persistence

SessionListManagerImpl - Class in ubic.gemma.web.persistence

SessionListManagerImpl() - Constructor for class ubic.gemma.web.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.

setAdminUser(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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.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

setArrayDesign(ArrayDesign) - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

setArrayDesignMatchesDataFile(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

setArrayDesignMismatchProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

setArrayDesignName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController

setAsText(String) - Method in class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor

setAsText(String) - Method in class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor

setAsText(String) - Method in class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor

setAsText(String) - Method in class ubic.gemma.web.propertyeditor.TaxonPropertyEditor

Allow us to convert from either an id or the scientific name.

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.ExpressionExperimentEditValueObject

setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag

setBioProcessAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

setBody(String) - Method in class ubic.gemma.web.feed.NewsItem

setBytesRead(long) - Method in class ubic.gemma.web.util.upload.UploadInfo

setCacheMonitor(CacheMonitor) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

setCanEdit(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject

setChannel(String) - Method in class ubic.gemma.web.logging.SlackAppender

setCitation(BibliographicReference) - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag

setClassDelegatingFor(String) - Method in class ubic.gemma.web.remote.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

setConfirmNewPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setContentDisposition(String) - Method in class ubic.gemma.web.view.TextView

setCount(int) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

setCssClass(String) - Method in class ubic.gemma.web.taglib.ImageTag

setCssStyle(String) - Method in class ubic.gemma.web.taglib.ImageTag

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

setDate(Date) - Method in class ubic.gemma.web.feed.NewsItem

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.common.auditAndSecurity.UserUpdateCommand

setDimension(BioAssayDimension) - Method in class ubic.gemma.web.taglib.EntityLinkTag

setDir(String) - Method in class ubic.gemma.web.remote.ListBatchCommand

setDirty(boolean) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.EntityLinkTag

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.ImageTag

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.ScriptTag

setDynamicAttribute(String, String, Object) - Method in class ubic.gemma.web.taglib.StyleTag

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.diff.DiffExpressionSearchCommand

setEeQuery(String) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

setEeSetId(Long) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

setEeSetName(String) - Method in class ubic.gemma.web.controller.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.UserUpdateCommand

setEmail(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

setEnabled(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

setEnabled(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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

setError(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse

setErrorCategory(String) - Method in class ubic.gemma.web.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.util.UnhandledExceptionResolver

Set the view to use for reporting unhandled exception.

setExperimentalDesignId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

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.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

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.diff.DifferentialExpressionAnalyzerInfo

setFactors(List<String>) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

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.util.upload.UploadInfo

setFilter(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

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.diff.DiffExpressionSearchCommand

setGeneIds(Collection<Long>) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject

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

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

setHibernateMonitor(HibernateMonitor) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController

setId(Long) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setId(Long) - Method in class ubic.gemma.web.remote.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

setIsNormalized(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

setIsRecomputedFromRawData(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditController.QuantitationTypeEditForm

setJobs(Set<JobInfo>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setLabel(String) - Method in class ubic.gemma.web.util.LabelValue

setLastName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setLimit(Integer) - Method in class ubic.gemma.web.remote.ListBatchCommand

setLocalPath(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload

setMaskMissing(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

setMaxUploadSize(long) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

Set the maximum allowed size (in bytes) before uploads are refused. -1 indicates no limit (the default).

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.remote.JsonReaderResponse

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.common.auditAndSecurity.UserUpdateCommand

setName(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

setNewPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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

setNumRows(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

setOldPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setOriginalFileName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

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

setPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setPasswordEncoder(PasswordEncoder) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController

setPasswordHint(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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

setProperty(String, Object) - Method in class ubic.gemma.web.util.ConfigurationCookie

setPubliclyReadable(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject

setPValue(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile

setQuantitationType(QuantitationType) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

setQuantitationTypeId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

setQuantitationTypeIsValid(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

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

setQuantitationTypeService(QuantitationTypeService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController

setRank(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile

setRecaptchaTester(ReCaptcha) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController

setRecords(List<T>) - Method in class ubic.gemma.web.remote.JsonReaderResponse

setSampleNames(List<String>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject

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.coexpressionSearch.CoexSearchTaskCommand

setSearchString(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand

setSelectedFactors(Collection<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

setServerFilePath(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

setServletContext(ServletContext) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver

setShared(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject

setShortNameIsUnique(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

setSort(String) - Method in class ubic.gemma.web.remote.ListBatchCommand

setSrc(String) - Method in class ubic.gemma.web.taglib.AbstractStaticAssetTag

setStart(Integer) - Method in class ubic.gemma.web.remote.ListBatchCommand

setStatus(String) - Method in class ubic.gemma.web.util.upload.UploadInfo

setStatusCode(int) - Method in class ubic.gemma.web.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.remote.JsonReaderResponse

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.diff.DiffExpressionSearchCommand

setTaxonName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

setTeaser(String) - Method in class ubic.gemma.web.feed.NewsItem

setThreshold(Double) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

setTitle(String) - Method in class ubic.gemma.web.feed.NewsItem

setTitle(String) - Method in class ubic.gemma.web.taglib.EntityLinkTag

setToken(String) - Method in class ubic.gemma.web.logging.SlackAppender

setTotalRecords(long) - Method in class ubic.gemma.web.remote.JsonReaderResponse

setTotalSize(long) - Method in class ubic.gemma.web.util.upload.UploadInfo

setType(String) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo

setUpFactorProfiles(LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject

Initialize the factor profiles.

setUserManager(UserManager) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController

setUserName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

setUserName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject

setValidateOnly(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

setValue(String) - Method in class ubic.gemma.web.util.ConfigurationCookie

Don't use this method if you can help it!

setValue(String) - Method in class ubic.gemma.web.util.LabelValue

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, Long) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController

show(Long, Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

show(HttpServletRequest) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

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() - 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) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

showAllSubSets(String, Long) - 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

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.GemmaClassicHomePageController

Deprecated.

showHomePage() - Method in class ubic.gemma.web.controller.common.HomePageController

showMetaAnalysisManager() - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController

showSubSet(Long, Long) - 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, HttpServletRequest, HttpServletResponse) - 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

SimpleExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

SimpleHttp - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha

SimpleHttp() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp

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

SlackAppender - Class in ubic.gemma.web.logging

SlackAppender() - Constructor for class ubic.gemma.web.logging.SlackAppender

Used in log4j.properties via reflection.

SlackAppender(Slack) - Constructor for class ubic.gemma.web.logging.SlackAppender

StandardQuantitationTypeConverter - Class in ubic.gemma.web.remote

StandardQuantitationTypeConverter() - Constructor for class ubic.gemma.web.remote.StandardQuantitationTypeConverter

start() - Method in class ubic.gemma.web.util.InternalStaticAssetServer

start() - Method in interface ubic.gemma.web.util.upload.OutputStreamListener

start() - Method in class ubic.gemma.web.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.util

Resolve static assets either froma InternalStaticAssetServer or from the webapp resources.

StaticAssetResolver() - Constructor for class ubic.gemma.web.util.StaticAssetResolver

staticAssetServer() - Method in class ubic.gemma.web.util.StaticAssetServerConfig

StaticAssetServer - Interface in ubic.gemma.web.util

StaticAssetServerConfig - Class in ubic.gemma.web.util

StaticAssetServerConfig() - Constructor for class ubic.gemma.web.util.StaticAssetServerConfig

stop() - Method in class ubic.gemma.web.util.InternalStaticAssetServer

stop(Runnable) - Method in class ubic.gemma.web.util.InternalStaticAssetServer

StringPoint - Class in ubic.gemma.web.remote

StyleTag - Class in ubic.gemma.web.taglib

write a <style/> tag.

StyleTag() - Constructor for class ubic.gemma.web.taglib.StyleTag

success - Variable in class ubic.gemma.web.remote.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

Exposes progress status service check result to the front end.

TaskCompletionController() - Constructor for class ubic.gemma.web.controller.TaskCompletionController

TaxonController - Class in ubic.gemma.web.controller.expression.experiment

TaxonController() - Constructor for class ubic.gemma.web.controller.expression.experiment.TaxonController

TaxonPropertyEditor - Class in ubic.gemma.web.propertyeditor

Used to convert Taxon from and into strings for display in forms.

TaxonPropertyEditor(TaxonService) - Constructor for class ubic.gemma.web.propertyeditor.TaxonPropertyEditor

TEXT_PARAM - Static variable in class ubic.gemma.web.view.TextView

Name of parameter used to retrieve the text from the model.

TextView - Class in ubic.gemma.web.view

Simply prints text to the client.

TextView() - Constructor for class ubic.gemma.web.view.TextView

Create a text view for text/plain content.

TextView(String) - Constructor for class ubic.gemma.web.view.TextView

toggleUsability(String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController

toString() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

toString() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand

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

toString() - Method in class ubic.gemma.web.remote.EntityDelegator

toString() - Method in class ubic.gemma.web.util.LabelValue

totalRecords - Variable in class ubic.gemma.web.remote.JsonReaderResponse

transferTo(File) - Method in class ubic.gemma.web.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.context - package ubic.gemma.web.context

ubic.gemma.web.controller - package ubic.gemma.web.controller

ubic.gemma.web.controller.analysis.expression.coexpression.links - package ubic.gemma.web.controller.analysis.expression.coexpression.links

ubic.gemma.web.controller.analysis.preprocess - package ubic.gemma.web.controller.analysis.preprocess

ubic.gemma.web.controller.analysis.sequence - package ubic.gemma.web.controller.analysis.sequence

ubic.gemma.web.controller.coexpressionSearch - package ubic.gemma.web.controller.coexpressionSearch

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.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.diff - package ubic.gemma.web.controller.diff

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.monitoring - package ubic.gemma.web.controller.monitoring

ubic.gemma.web.controller.visualization - package ubic.gemma.web.controller.visualization

ubic.gemma.web.feed - package ubic.gemma.web.feed

ubic.gemma.web.job.progress - package ubic.gemma.web.job.progress

ubic.gemma.web.listener - package ubic.gemma.web.listener

ubic.gemma.web.logging - package ubic.gemma.web.logging

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.persistence - package ubic.gemma.web.persistence

ubic.gemma.web.propertyeditor - package ubic.gemma.web.propertyeditor

ubic.gemma.web.remote - package ubic.gemma.web.remote

ubic.gemma.web.scheduler - package ubic.gemma.web.scheduler

ubic.gemma.web.scheduler.jobs - package ubic.gemma.web.scheduler.jobs

This packages contains Quartz job definitions.

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.tasks.analysis.sequence - package ubic.gemma.web.tasks.analysis.sequence

ubic.gemma.web.util - package ubic.gemma.web.util

ubic.gemma.web.util.upload - package ubic.gemma.web.util.upload

ubic.gemma.web.view - package ubic.gemma.web.view

UnhandledExceptionResolver - Class in ubic.gemma.web.util

Resolver used when no other resolver can intervene.

UnhandledExceptionResolver() - Constructor for class ubic.gemma.web.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

updateCharacteristics(Collection<AnnotationValueObject>) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController

Update characteristics associated with entities.

updateCounts() - Method in class ubic.gemma.web.controller.common.GemmaClassicHomePageController

Deprecated.

updateExperimentalFactors(ExperimentalFactorValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager

updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.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

updateGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager

updateGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.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.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.util.upload

UploadInfo() - Constructor for class ubic.gemma.web.util.upload.UploadInfo

UploadInfo(int, long, long, String) - Constructor for class ubic.gemma.web.util.upload.UploadInfo

UploadListener - Class in ubic.gemma.web.util.upload

This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).

UploadListener(HttpServletRequest) - Constructor for class ubic.gemma.web.util.upload.UploadListener

URL - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha

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

UserUpdateCommand - Class in ubic.gemma.web.controller.common.auditAndSecurity

Just like a regular user; but has 'new password' and 'confirm password' fields.

UserUpdateCommand() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand

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, Integer, Integer, Integer, Boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

visualizeMeanVariance(Long, Double, Boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

visualizeProbeCorrDist(Long, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

visualizePvalueDist(Long, Long, Long, Integer, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

visualizeSingleCellDataBoxplot(Long, Long, Long, Long[], String, Long, Long, 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, Integer, Integer, Integer, Boolean, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

W

WebConstants - Class in ubic.gemma.web.controller

Constant values used throughout the web portion of Gemma.

WebConstants() - Constructor for class ubic.gemma.web.controller.WebConstants

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.common.auditAndSecurity.WhatsNewController

WhatsNewController - Class in ubic.gemma.web.controller.common.auditAndSecurity

Controller to provide information on "what's new" in the system

WhatsNewController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController

write(byte[]) - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream

write(byte[], int, int) - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream

write(int) - Method in class ubic.gemma.web.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.util.JsonUtil

writeErrorToResponse(Exception, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil

writeErrorToResponse(AuthenticationException, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil

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

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.

writeToDebugLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger

Write to log with severity = "debug"

writeToErrorLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger

Write to log with severity = "error"

writeToFatalLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger

Write to log with severity = "fatal"

writeToInfoLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger

Write to log with severity = "info"

writeToLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger

Defaults to writing to log with severity = "info"

writeToResponse(JSONObject, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil

writeToWarnLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.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

X

XML_PARAM - Static variable in class ubic.gemma.web.view.XmlView

Name of the parameter that is used to retrieve the xml from the model.

XmlView - Class in ubic.gemma.web.view

Model should contain a single value matching XML_PARAM

XmlView() - Constructor for class ubic.gemma.web.view.XmlView

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