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

AbstractGemmaEndpoint - Class in ubic.gemma.web.services

Abstracts out the security and a few constants.

AbstractGemmaEndpoint() - Constructor for class ubic.gemma.web.services.AbstractGemmaEndpoint

AbstractSetListContainer - Class in ubic.gemma.web.persistence

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

add(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

add(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

addAlternateName(Long, String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

addAlternateName(Long, String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

addAuditEvent(EntityDelegator<? extends Auditable>, String, String, String) - Method in class ubic.gemma.web.remote.AuditController

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

addMessage(HttpServletRequest, String, Object[]) - Method in class ubic.gemma.web.controller.BaseController

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

addUserToGroup(String, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

afterPropertiesSet() - Method in class ubic.gemma.web.feed.FeedReader

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

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

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

AJAX-flavoured search.

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

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

AnchorTagUtil - Class in ubic.gemma.web.util

Used to generate hyperlinks to various things in Gemma.

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

annot(HttpServletRequest, HttpServletResponse) - 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

ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint

The local name of the expected request.

ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignUsedEndpoint

The local name of the expected request.

ArrayDesignAddCommand - Class in ubic.gemma.web.controller.expression.arrayDesign

ArrayDesignAddCommand() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand

ArrayDesignController - Interface in ubic.gemma.web.controller.expression.arrayDesign

Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

ArrayDesignControllerImpl - Class in ubic.gemma.web.controller.expression.arrayDesign

Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

ArrayDesignControllerImpl() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

ArrayDesignIdentifierByNameEndpoint - Class in ubic.gemma.web.services

array design short name -> return matching array design identifier

ArrayDesignIdentifierByNameEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint

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

ArrayDesignUsedEndpoint - Class in ubic.gemma.web.services

Used for determining which array designs were used in a given expression experiment (EE)

ArrayDesignUsedEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignUsedEndpoint

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

authenticate() - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

BibliographicReferenceController - Interface in ubic.gemma.web.controller.common.description.bibref

Note: do not use parameterized collections as parameters for ajax methods.

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

This controller is responsible for showing a list of all bibliographic references, as well sending the user to the pubMed.Detail.view when they click on a specific link in that list.

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

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 interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

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

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level? Is there security for ArrayDesigns? ids can be null

browse(ListBatchCommand, Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

buildBadResponse(Document, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

buildWrapper(Document, Collection<String>, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

Function to handle the constructing of output in xml format for returning the response to the client.

BUNDLE_KEY - Static variable in class ubic.gemma.web.util.Constants

The name of the ResourceBundle used in this application

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

calculateExternalDatabasesStatistics() - Method in class ubic.gemma.web.controller.PhenotypeController

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

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

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

createItem(String, String, boolean, String) - Method in class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory

createQueryStringFromMap(Map<String, String[]>, String) - Static method in class ubic.gemma.web.util.RequestUtil

Builds a query string from a given map of parameters

createWebApplicationContext(ServletContext) - Method in class ubic.gemma.web.listener.StartupListener

CustomRssViewer - Class in ubic.gemma.web.controller.common.rss

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

D

daily(HttpServletRequest, HttpServletResponse) - 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.

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

DEDVfromEEIDGeneIDEndpoint - Class in ubic.gemma.web.services

Given a list Experiment IDs and a list gene IDs will return design element data vectors (DEDV), all the genes that could have been responsible for that DEDV (only needs to contain 1 of the given genes) and the Expression Experiment that the data came from.

DEDVfromEEIDGeneIDEndpoint() - Constructor for class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint

DEDVRankEndpoint - Class in ubic.gemma.web.services

Given a collection of gene IDs, a collection of experiment IDs, and the method, the service will return a list of genes mapped to a list of space delimited ranks.

DEDVRankEndpoint() - Constructor for class ubic.gemma.web.services.DEDVRankEndpoint

DEFAULT_QC_IMAGE_SIZE_PX - Static variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

delete(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Delete an arrayDesign.

delete(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

delete(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

delete(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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

Exposed for AJAX calls.

deleteCookie(HttpServletResponse, Cookie, String) - Static method in class ubic.gemma.web.util.RequestUtil

Convenience method for deleting a cookie by name

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

AJAX

deleteGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

DELIMITER - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

For the display of a summary table about experimental design.

DesignMatrixRowValueObject(FactorValueVector, int) - Constructor for class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject

DesignMatrixRowValueObject.Factory - Class in ubic.gemma.web.controller.expression.experiment

detailedFactorAnalysis(Long, OutputStream) - 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

DifferentialExpressionProbeResultEndpoint - Class in ubic.gemma.web.services

Allows access to the differential expression analysis.

DifferentialExpressionProbeResultEndpoint() - Constructor for class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

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.expression.experiment.AssayViewTag

doEndTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

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

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

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

doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in interface ubic.gemma.web.controller.GeneralSearchController

doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl

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.common.auditAndSecurity.ExceptionTag

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

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

doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag

doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

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

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

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

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

E

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

Entry point for updates.

Ee2AdUpdateJob - Class in ubic.gemma.web.scheduler

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

Ee2cUpdateJob - Class in ubic.gemma.web.scheduler

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

EmptyController - Class in ubic.gemma.web.controller

This exists just to have an easy way to trick web pages into importing DWR-defined classes that are not in dwrServices.js.

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

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

encode(Object[]) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

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

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.Ee2AdUpdateJob

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

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

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

EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentIdEndpoint

The local name of the request/response.

EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentNameEndpoint

The local name of the expected request/response.

EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint

The local name of the expected request.

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

ExperimentAnnotationEndpoint - Class in ubic.gemma.web.services

Expression Experiments in Gemma contain annotations.

ExperimentAnnotationEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentAnnotationEndpoint

ExperimentDEDVEndpoint - Class in ubic.gemma.web.services

Allows access to all the Design Element Data Vectors (DEDV's) for a given Expression Experiment.

ExperimentDEDVEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentDEDVEndpoint

ExperimentIDbyTaxonEndpoint - Class in ubic.gemma.web.services

Given a Taxon (eg.

ExperimentIDbyTaxonEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint

ExperimentIdEndpoint - Class in ubic.gemma.web.services

Given the short name of an Expression Experiment, will return the matching Expression Experiment ID

ExperimentIdEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentIdEndpoint

ExperimentNameEndpoint - Class in ubic.gemma.web.services

Used for getting the Short Name given an Expression Experiment ID eg: 793 --> GSE10470

ExperimentNameEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentNameEndpoint

ExperimentNumSamplesEndpoint - Class in ubic.gemma.web.services

Used for determining the number of samples (biomaterials) associated with a given expression experiment

ExperimentNumSamplesEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentNumSamplesEndpoint

ExperimentQCTag - Class in ubic.gemma.web.taglib.expression.experiment

ExperimentQCTag() - 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

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

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

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

Handle editing of expression experiments.

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

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.

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

ExpressionExperimentSetIDsEndpoint - Class in ubic.gemma.web.services

A service to return the full list of Expression Experiment Set IDs along with the corresponding name and experiment ids it contains.

ExpressionExperimentSetIDsEndpoint() - Constructor for class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint

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

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

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

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

FeedReader - Class in ubic.gemma.web.feed

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

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Show array designs that match search criteria.

filter(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

filter(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController

filter(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

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

AJAX TODO --- include a search of subsets.

findAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

findBibliographicReference(String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController

Finds bibliographic reference with the given pubmed id.

findCandidateGenes(Long, boolean, Collection<Long>, String[]) - Method in class ubic.gemma.web.controller.PhenotypeController

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

findEvidenceByFilters(Long, Integer, String) - Method in class ubic.gemma.web.controller.PhenotypeController

findEvidenceOwners() - Method in class ubic.gemma.web.controller.PhenotypeController

Returns a collection of users who own evidence.

findExperimentCategory() - Method in class ubic.gemma.web.controller.PhenotypeController

Returns available efo category terms.

findExperimentOntologyValue(String, String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController

findExternalDatabaseName() - Method in class ubic.gemma.web.controller.PhenotypeController

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).

formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl

This is needed or you will have to specify a commandClass in the DispatcherServlet's context

forward(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

G

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

Deprecated.

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

Deprecated.

GENE_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneByNCBIIdEndpoint

The local name of the expected Request/Response.

GENE_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneIdEndpoint

The local name of the expected Request/Response.

GENE2GO_LOCAL_NAME - Static variable in class ubic.gemma.web.services.Gene2GoTermEndpoint

The local name of the expected request/response.

Gene2GOdescriptionEndpoint - Class in ubic.gemma.web.services

Given a collection of Gene ID, will return a collection of Gene Ontology IDs (ie.

Gene2GOdescriptionEndpoint() - Constructor for class ubic.gemma.web.services.Gene2GOdescriptionEndpoint

Gene2GoTermEndpoint - Class in ubic.gemma.web.services

Given a collection of Gene IDs, will return a collection of Gene Ontology URIs for each gene.

Gene2GoTermEndpoint() - Constructor for class ubic.gemma.web.services.Gene2GoTermEndpoint

Gene2ProbeEndpoint - Class in ubic.gemma.web.services

for a given Official Gene Symbol and Taxon ID will return all the probes IDs and their array design IDs that assay for that given gene.

Gene2ProbeEndpoint() - Constructor for class ubic.gemma.web.services.Gene2ProbeEndpoint

GeneByNCBIIdEndpoint - Class in ubic.gemma.web.services

Given an NCBI ID, will return the matching Gemma gene id.

GeneByNCBIIdEndpoint() - Constructor for class ubic.gemma.web.services.GeneByNCBIIdEndpoint

GeneCoexpressionEndpoint - Class in ubic.gemma.web.services

Allows access to the gene co-expression analysis.

GeneCoexpressionEndpoint() - Constructor for class ubic.gemma.web.services.GeneCoexpressionEndpoint

GeneCoexpressionSearchEndpoint - Class in ubic.gemma.web.services

GeneCoexpressionSearchEndpoint() - Constructor for class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

GeneController - Class in ubic.gemma.web.controller.genome.gene

GeneController() - Constructor for class ubic.gemma.web.controller.genome.gene.GeneController

GeneDetailsByGeneIDEndpoint - Class in ubic.gemma.web.services

Given a collection of Gemma gene IDs, will return the matching NCBI Ids.

GeneDetailsByGeneIDEndpoint() - Constructor for class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint

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

GeneIDbyTaxonEndpoint - Class in ubic.gemma.web.services

Given the Taxon (eg.

GeneIDbyTaxonEndpoint() - Constructor for class ubic.gemma.web.services.GeneIDbyTaxonEndpoint

GeneIdEndpoint - Class in ubic.gemma.web.services

Given the official symbol and taxon of a gene, will return the matching gene ID.

GeneIdEndpoint() - Constructor for class ubic.gemma.web.services.GeneIdEndpoint

GeneNameEndpoint - Class in ubic.gemma.web.services

Given a gene ID, will return the matching gene official symbol eg) 938103--> Grin1

GeneNameEndpoint() - Constructor for class ubic.gemma.web.services.GeneNameEndpoint

GeneOverlapEndpoint - Class in ubic.gemma.web.services

given a query gene id & collection of target gene ids will determine the overlapping Go terms (intersection) between each pair of Query Gene and Target Gene.

GeneOverlapEndpoint() - Constructor for class ubic.gemma.web.services.GeneOverlapEndpoint

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 - Interface in ubic.gemma.web.controller

Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

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

GeneralSearchControllerImpl - Class in ubic.gemma.web.controller

Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

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

generateCache(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController

generateSummary(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Build summary report for an array design

generateSummary(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

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

getAppURL(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil

Convenience method to get the application's URL based on request variables.

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

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

getArrayValues(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

getAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getAttribute(String, int) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getAttributeNamesInScope(int) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getAttributesScope(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getAuthenticatedUserCount() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

getAuthenticatedUserCount() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

getAuthenticatedUserNames() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

getAuthenticatedUserNames() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

getAvailableGroups() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

AJAX

getAvailableGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

getAvailablePrincipalSids() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

Return a list of principals that is users

getAvailablePrincipalSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

getAvailableSids() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

AJAX, but administrator-only!

getAvailableSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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.

getBioMaterialLink(BioMaterial, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil

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

getCookie(HttpServletRequest, String) - Static method in class ubic.gemma.web.util.RequestUtil

Convenience method to get a cookie by name

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

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

For the show-off graph that shows number of data sets per taxon.

getCsSummaries(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController

Exposed for AJAX calls (Probe browser) FIXME can probably remove soon since we should use getGeneCsSummaries? Might be another use for this

getCsSummaries(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Exposed for AJAX calls.

getCsSummaries(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

getDesignMatrix(ExpressionExperiment, boolean, boolean) - Static method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject.Factory

getDesignMatrixRows(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

AJAX

getDesignSummaries(ArrayDesign) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

getDesignSummaries(ArrayDesign) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

getDetails(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

getDetails(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

getELContext() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

getException() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

getExperimentalDesignLink(ExperimentalDesign, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil

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

getExpressionEvaluator() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

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

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

getExpressionExperimentLink(ExpressionExperiment, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil

getExpressionExperimentUrl(ExpressionExperiment, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil

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

getGeneABALink(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

getGroupMembers(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

getIsContinuous() - Method in class ubic.gemma.web.controller.visualization.FactorProfile

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

getLastSingleNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

basically Delegates to getSingleNodeValue and returns the just the last value.

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

Show all experiments

getLatestNews() - Method in class ubic.gemma.web.feed.FeedReader

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

getMessageUtil() - Method in class ubic.gemma.web.controller.BaseController

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

Deprecated.

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

getNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

getOptionalNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

Deprecated.

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

getOut() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

getPage() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

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

getQChtml() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

Used to include the html for the qc table in an ext panel (without using a tag) (This method should probably be in a service?)

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

getReportHtml(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

getRequest() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getRequestParameters(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil

getResponse() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

getSecurityInfo(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

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

getServletConfig() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getServletContext() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

getSession() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

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

getSingleNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

Function that handles the retrieval of xml input.

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

getSummaryForArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

getTaxaWithEvidence() - 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

getText(String, Object[], Locale) - Method in class ubic.gemma.web.controller.BaseController

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

Convenience method for getting a i18n key's value with arguments.

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

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

Convenient method for getting a i18n key's value with a single string argument.

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

getText(String, Locale) - Method in class ubic.gemma.web.controller.BaseController

getText(String, Locale) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

Convenience method for getting a i18n key's value.

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

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 interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController

getUsers() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl

getUsersData(String, boolean) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

AJAX

getUsersData(String, boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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.

getVariableResolver() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

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

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

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

GO2Gene_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GoTerm2GeneEndpoint

The local name of the expected request/response.

GOEvidenceCodeConverter - Class in ubic.gemma.web.remote

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

GoTerm2GeneEndpoint - Class in ubic.gemma.web.services

Given a Gene Ontology Term URI and a Taxon ID as input, will return a collection of gene IDs that match the GO Term and Taxon.

GoTerm2GeneEndpoint() - Constructor for class ubic.gemma.web.services.GoTerm2GeneEndpoint

H

handlePageException(Exception) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

handlePageException(Throwable) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

handleRequest(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController

handleRequest(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl

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

Handle case of text export of the results.

handleRequestInternal(HttpServletRequest) - 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

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

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

include(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

include(String, boolean) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

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

initialize(Servlet, ServletRequest, ServletResponse, String, boolean, int, boolean) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ArrayDesignUsedEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DEDVRankEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentAnnotationEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint

Reads the given requestElement, and sends the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentIdEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentNameEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneByNCBIIdEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint

Reads the given requestElement, and sends the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneIdEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneNameEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint

Reads the given requestElement, and sends a the response back.

invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint

Reads the given requestElement, and sends a the response back.

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

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

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

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 interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

load(Long) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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

loadAllenBrainImages(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

AJAX NOTE: this method updates the value object passed in

loadAllForExperiments() - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

loadAllForExperiments() - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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

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

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

loadArrayDesignsForShowAll(Long[]) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

loadArrayDesignsSummary() - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

loadArrayDesignsSummary() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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 interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

loadFromPubmedID(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

loadGeneDetails(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

loadGeneEvidence(Long, boolean, Collection<Long>, Long, String[]) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

AJAX used to show gene info in the phenotype tab FIXME Why is the taxonId a parameter, since we have the gene ID?

loadGenePhenotypes(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController

loadMultiple(Collection<Long>) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

loadMultiple(Collection<Long>) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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.

LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentAnnotationEndpoint

The local name of the expected request/response.

LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint

The local name of the expected Request/Response.

LOCAL_NAME - Static variable in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint

The local name of the expected request/response.

LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

The local name of the expected request/response.

LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneNameEndpoint

The local name of the expected Request/Response.

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

makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long, SortedSet<CharacteristicValueObject>, Double) - Method in class ubic.gemma.web.controller.PhenotypeController

makeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

makeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

makeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

makeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

makePrivate(EntityDelegator<? extends Securable>) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

makePrivate(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

makePublic(EntityDelegator<? extends Securable>) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

makePublic(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

manualAuthenticationService - Variable in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

MAX_RESULTS - Static variable in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

The maximum number of coexpression results to return per input gene; a value of zero will return all possible results (ie.

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

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

MinifierPostProcessor - Class in ubic.gemma.web.util

JAWR postprocessor to remove console.log and debugger breakpoint statements.

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

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

NAMESPACE_URI - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint

Namespace of both request and response.

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, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

onSubmit(HttpServletRequest, PubMedSearchCommand, BindingResult, SessionStatus) - Method in interface ubic.gemma.web.controller.common.description.bibref.PubMedQueryController

onSubmit(HttpServletRequest, PubMedSearchCommand, BindingResult, SessionStatus) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl

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

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

PhenotypeController - Class in ubic.gemma.web.controller

Controller for phenotype

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

postProcessBundle(BundleProcessingStatus, StringBuffer) - Method in class ubic.gemma.web.util.MinifierPostProcessor

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

Probe2GeneEndpoint - Class in ubic.gemma.web.services

Used for determining what genes a probe assays for.

Probe2GeneEndpoint() - Constructor for class ubic.gemma.web.services.Probe2GeneEndpoint

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

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

processFormSubmission(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in interface ubic.gemma.web.controller.GeneralSearchController

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

processPhenotypeAssociationForm(EvidenceValueObject<?>) - Method in class ubic.gemma.web.controller.PhenotypeController

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

PubMedQueryController - Interface in ubic.gemma.web.controller.common.description.bibref

Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

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

Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.

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

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

Supports seaching of pubmed references

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

Q

QuantitationTypePropertyEditor - Class in ubic.gemma.web.propertyeditor

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

R

readReport(InputStream) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

Looks to parse a previously generated xml report that was saved to disk.

readReport(String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

uses the default path of gemmaData/datafile/xml/ to look for reports.

readReport(String, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

reclaimRequestAttributes(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil

Returns request attributes from session to request

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

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

referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl

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.

release() - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

remove(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

removeAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

removeAttribute(String, int) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

removeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

removeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

removeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

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

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

removeUsersFromGroup(String[], String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

REQUEST - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint

RequestUtil - Class in ubic.gemma.web.util

RequestUtil utility class

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

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.ClientAbortExceptionResolver

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

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

RESPONSE - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint

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.

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(HttpServletRequest, String) - Method in class ubic.gemma.web.controller.BaseController

saveMessage(HttpServletRequest, String) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

Put a message into the session.

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

saveMessage(HttpServletRequest, String, Object[], String) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

Put a message into the session.

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

saveMessage(HttpServletRequest, String, Object, String) - Method in class ubic.gemma.web.controller.BaseController

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

Deprecated.

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

Put a message into the session.

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

saveMessage(HttpServletRequest, String, String) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

Put a message into the session.

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

saveMessage(HttpSession, String) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

Put a message into the session.

saveMessage(HttpSession, 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 interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController

Save or create the user.

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

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.

search(String, String) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController

search(SearchSettingsValueObject) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

search(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

searchBibRefs(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

searchBibRefs(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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.

searchOntologyForPhenotypes(String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController

Returns all phenotypes satisfied the given search criteria.

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 - Interface in ubic.gemma.web.controller.common.auditAndSecurity

Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

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

Manages data-level security (ie.

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

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

sendConfirmationEmail(HttpServletRequest, String, String, String, Map<String, Object>, String) - Method in class ubic.gemma.web.controller.BaseController

SequenceTypePropertyEditor - Class in ubic.gemma.web.propertyeditor

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

ServiceUnavailableException - Exception in ubic.gemma.web.util

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

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

setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint

Sets the "business service" to delegate to.

setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint

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.

setAttribute(String, Object) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

setAttribute(String, Object, int) - Method in class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

setAuditTrailService(AuditTrailService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

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

setBibliographicReferenceService(BibliographicReferenceService) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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

setBioAssayService(BioAssayService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

setBioMaterialService(BioMaterialService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

setBioMaterialService(BioMaterialService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

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

setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint

setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint

setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint

Sets the "business service" to delegate to.

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

setCookie(HttpServletResponse, String, String, String) - Static method in class ubic.gemma.web.util.RequestUtil

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

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

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

setDifferentialExpressionResultService(DifferentialExpressionResultService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

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

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

setEdit(String) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag

setEe(Long) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

The id of the EE to display QC info

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

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

setEeManagerId(String) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

setEEwithPvalue(ExpressionExperimentDetailsValueObject, 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

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.

setException(Exception) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag

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

setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint

setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint

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

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

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

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ArrayDesignUsedEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentAnnotationEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentIdEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentNameEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint

Sets the "business service" to delegate to.

setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

setExternalDatabaseService(ExternalDatabaseService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

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

setFactorValueService(FactorValueService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

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

setGeneCoexpressionSearchService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint

setGeneCoexpressionSearchService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

setGeneCoexpressionService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint

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

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

setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint

Sets the "business service" to delegate to.

setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint

Sets the "business service" to delegate to.

setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint

Sets the "business service" to delegate to.

setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint

Sets the "business service" to delegate to.

setGenes(Collection<GeneValueObject>) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile

setGeneService(GeneService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneByNCBIIdEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneIdEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneNameEndpoint

Sets the "business service" to delegate to.

setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint

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

setHasCorrDist(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setHasCorrMat(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setHasMeanVariance(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setHasNodeDegreeDist(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setHasPCA(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

setIsContinuous(Boolean) - Method in class ubic.gemma.web.controller.visualization.FactorProfile

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

setLocalName(String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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

setMailEngine(MailEngine) - Method in class ubic.gemma.web.controller.BaseController

setMailEngine(MailEngine) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

setManualAuthenticationService(ManualAuthenticationService) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

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.

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

setMessageSource(MessageSource) - Method in class ubic.gemma.web.controller.BaseController

setMessageUtil(MessageUtil) - Method in class ubic.gemma.web.controller.BaseController

setMessageUtil(MessageUtil) - Method in class ubic.gemma.web.controller.BaseFormController

Deprecated.

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

setNumFactors(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

How many factors (including batch etc) are available for PCA display?

setNumOutliersRemoved(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

setNumPossibleOutliers(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag

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

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

setOntologyService(OntologyService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController

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

setPersisterHelper(Persister) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

setPersisterHelper(Persister) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

setPlots(List<List<DoublePoint>>) - Method in class ubic.gemma.web.controller.visualization.FactorProfile

setPreprocessorService(PreprocessorService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController

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

setProcessedExpressionDataVectorService(ProcessedExpressionDataVectorService) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint

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

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

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.services.GeneCoexpressionSearchEndpoint

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

setShowStackTrace(Boolean) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag

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

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

settaxonService(TaxonService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint

Sets the "business service" to delegate to.

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint

Sets the "business service" to delegate to.

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneIdEndpoint

setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint

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

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! Use setProperty instead.

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

setWhatsNewService(WhatsNewService) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController

ShortBibliographicReferenceTag - Class in ubic.gemma.web.taglib

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

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

show(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController

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

show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController

show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController

show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController

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

showAllArrayDesigns() - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Show all array designs, or according to a list of IDs passed in.

showAllArrayDesigns() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

showAllBioAssays(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController

showAllExpressionExperiments(HttpServletRequest, HttpServletResponse) - 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(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

showAllForExperiments(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

showAllLinkSummaries(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

showAllPhenotypes(HttpServletRequest) - Method in class ubic.gemma.web.controller.PhenotypeController

showArrayDesign(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

showArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

showArrayDesignByName(String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

showArrayDesignByName(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

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

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.expression.experiment.ExperimentalDesignController

showCompositeSequences(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

Show (some of) the probes from an array.

showCompositeSequences(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

showExpressionExperiment(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 interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

shows a list of BioAssays for an expression experiment subset

showExpressionExperiments(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

showExpressionExperimentSet(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController

showForm(HttpServletRequest, HttpServletResponse, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl

Deprecated.

showGeneSet(HttpServletRequest) - 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(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController

showNeurocartaStatistics() - Method in class ubic.gemma.web.controller.PhenotypeController

showPhenotypeAssociationManager() - Method in class ubic.gemma.web.controller.PhenotypeController

showSubSet(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController

shows a list of BioAssays for an expression experiment subset

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

SimplePageContext - Class in ubic.gemma.web.taglib

Deprecated.

SimplePageContext(ServletContext) - Constructor for class ubic.gemma.web.taglib.SimplePageContext

Deprecated.

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 interface ubic.gemma.web.util.upload.OutputStreamListener

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

StartupListener - Class in ubic.gemma.web.listener

StartupListener class used to initialize the spring context and make it available to the servlet context, so filters that need the spring context can be configured.

StartupListener() - Constructor for class ubic.gemma.web.listener.StartupListener

stowRequestAttributes(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil

Stores request attributes in session

StringPoint - Class in ubic.gemma.web.remote

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

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

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

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.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.services - package ubic.gemma.web.services

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 interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController

update(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl

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

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 interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

updatePermission(SecurityInfoValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

updatePermissions(SecurityInfoValueObject[]) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController

updatePermissions(SecurityInfoValueObject[]) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl

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

AJAX.

updateReport(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

updateReport(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

updateReportById(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController

updateReportById(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

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

UploadListener(HttpServletRequest, long) - 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

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 - Interface in ubic.gemma.web.controller.common.auditAndSecurity

Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.

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

For display and editing of users.

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

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

validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation>) - Method in class ubic.gemma.web.controller.PhenotypeController

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, String, Boolean, Boolean, Boolean, Boolean, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

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

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

visualizePvalueDist(Long, Long, Long, String, Integer, OutputStream) - 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

weekly(HttpServletRequest, HttpServletResponse) - 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

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

writeReport(Element, Document, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint

This method should/can only be used when the wrapper is manually built in the specific endpoints (ie.

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"

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

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