All Classes

Class	Description
AbstractHeatmapTag<T extends Heatmap>
AbstractSetListContainer
AbstractStaticAssetTag	Base class for tags that refers to static assets.
AnnotationController	Controller for methods involving annotation of experiments (and potentially other things); delegates to OntologyService and the CharacteristicService.
ArrayDesignAddCommand
ArrayDesignController	Note: do not use parametrized collections as parameters for ajax methods in this class!
ArrayDesignFormController	Controller for editing basic information about array designs.
ArrayDesignGroupingTag	For display of information about array designs that subsume or are subsumed.
ArrayDesignHtmlUtil	Yes, this is used by the ArrayDesignController, but should be phased out.
ArrayDesignProbeMapperController	A controller to run array design probe mapper either locally or in a space.
ArrayDesignPropertyEditor	Used to convert ArrayDesigns from and into strings for display in forms.
ArrayDesignRepeatScanController	A controller to run array design repeat scan either locally or in a space.
ArrayDesignRepeatScanTask
ArrayDesignRepeatScanTaskCommand	A command object to be used by spaces.
ArrayDesignRepeatScanTaskImpl	An array design repeat scan spaces task
ArrayDesignValueObjectExt	Extended value object to carry more data to client.
AssayViewTag	Used to display table of biomaterials and bioassays.
AuditController	This is required solely for exposing auditables to remote services would try to marshall the abstract class Auditable.
BaseController	Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting messages in the session.
BaseFormController	Deprecated. SimpleFormController is deprecated, use annotations-based GET/POST mapping instead.
BatchInfoFetchController	For populating "batch" information about experiments.
BatchInfoRepopulationJob	Schedule job that populates batch information for all experiments that have been updated since the last run.
BibliographicReferenceController	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.
BioAssayController
BioMaterialController
BlatResultTrackController	See goldenPath help on custom track.
CacheMonitor
CacheMonitorImpl	Get statistics about and manage caches.
CharacteristicBrowserController	NOTE: Logging messages from this service are important for tracking changes to annotations.
CharacteristicConverter
CharacteristicTag
ClassConverter
ClientAbortExceptionResolver	Resolves a ClientAbortException to an empty view.
CoexpressionSearchController
CoexSearchTaskCommand
CommonsMultipartFile	Deprecated.
CommonsMultipartMonitoredResolver	An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
CompositeSequenceController
ConfigurationCookie	Cookie class that also presents a commons configuration interface.
Constants	Constant values used throughout the application.
ConstantsTag	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.
ConstantsTei	Implementation of TagExtraInfo for the constants tag, identifying the scripting object(s) to be made visible.
ControllerUtils	Created by tesarst on 09/03/17.
CustomRssViewer
DatabaseEntryTag
DEDVController	Exposes methods for accessing underlying Design Element Data Vectors. eg: ajax methods for visualization
DefaultHandlerExceptionResolver	Custom exception resolver for Gemma.
DesignMatrixRowValueObject	For the display of a summary table about experimental design.
DifferentialExpressionAnalysisController	A controller to run differential expression analysis either locally or in a space.
DifferentialExpressionAnalyzerInfo	Used to carry information about the experimental design analysis settings to clients.
DifferentialExpressionSearchController	A controller used to get differential expression analysis and meta analysis results.
DiffExMetaAnalyzerController	A controller to analyze result sets either locally or in a space.
DiffExpressionSearchCommand
DirectionConverter	DWR converter for Direction type.
DoublePointConverter	The 8 decimal precision of a double is just a waste of bandwidth in most cases.
Ee2AdUpdateJob
Ee2cUpdateJob
EntityDelegator<T extends Identifiable>	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.
EntityLinkTag	Tag that generates an HTML link for a given Identifiable entity.
EntityNotFoundException	Signals that an entity was not found in the system.
ExceptionTag
ExperimentalDesignController	Main entry point to editing and viewing experimental designs.
ExperimentalFactorValueWebUIObject
ExperimentQCTag
ExperimentSetListContainer
ExpressionDataFileUploadController	Replaces SimpleExpressionExperimentLoadController
ExpressionDataHeatmapTag
ExpressionExperimentController
ExpressionExperimentDataFetchCommand
ExpressionExperimentDataFetchController	For the download of data files from the browser.
ExpressionExperimentEditController	Handle advanced editing of expression experiments.
ExpressionExperimentEditController.ExpressionExperimentEditForm
ExpressionExperimentEditController.QuantitationTypeEditForm
ExpressionExperimentEditValueObject
ExpressionExperimentExperimentalFactorValueObject
ExpressionExperimentLoadController	Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
ExpressionExperimentQCController
ExpressionExperimentQCUtils	Helper functions for checking existence etc. of QC information.
ExpressionExperimentReportGenerationController
ExpressionExperimentSetController	For fetching and manipulating ExpressionExperimentSets.
ExpressionExperimentUploadResponse
ExpressionExperimentVisualizationCommand	Expression experiment command object that wraps expression experiment visualization preferences.
ExpressionProfileDataObject	A lightweight object to hold expression data for a single probe.
ExternalStaticAssetServer
FactorProfile	Represents data for displaying a factor (+ factor values) in a chart.
FactorValueTag
FailedMultipartHttpServletRequest	Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
FileUpload	Command class to handle uploading of a file
FileUploadController	Controller class to upload Files.
FileUploadUtil	Utility methods for uploading files.
GemmaClassicHomePageController	Deprecated.
GeneController
GeneExpressionProfile	Expression data for one probe; designed for conveying small amounts of data to clients.
GenePickerController	For 'live searches' from the web interface.
GeneralSearchController	Note: do not use parametrized collections as parameters for ajax methods in this class!
GeneralSearchController.SearchResultValueObject<T extends IdentifiableValueObject<?>>
GeneSetController	Exposes GeneSetServices methods over ajax.
GeneSetListContainer
GeneSymbolComparator
GeoRecordBrowserController
GOEvidenceCodeConverter
HibernateMonitor
HibernateMonitorImpl	Monitoring of Hibernate status.
HomePageController	Responsible for display of the Gemma 2.0 home page.
ImageTag	Write an <img/> tag.
IndexController
InitializeContext	Performs the standard context preparation from SpringContextUtils.prepareContext(ApplicationContext) as well as some more specific Web-related setups.
InternalStaticAssetServer
JavascriptLogger	Class to handle saving client-side javascript error messages and warnings to a server-side log.
JsonReaderResponse<T>	Creates a response that can be consumed by an Ext.data.JsonReader.
JSONTableRenderer
JsonUtil	Utilities for writing JSON payloads to HttpServletResponse.
JSONView
LabelValue	A simple JavaBean to represent label-value pairs.
LinkAnalysisController	A controller to pre-process expression data vectors.
ListBatchCommand	Encapsulates information needed for generic list browsing.
MaintenanceModeController	Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave normally.
MessageUtil	Provides methods for putting messages to the user in the session.
MessageUtilImpl
MetaFile	Wrapper for metadata file information for the frontend
MeterRegistryWebConfigurer	Configured the environment='web' tag to the provided registry.
MonitoredDiskFileItem	Commons FileItem that uses a MonitoredOutputStream
MonitoredDiskFileItemFactory
MonitoredOutputStream	OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
NewsItem
OntologyController	Provide minimal support for exposing Gemma ontology.
OutputStreamListener
PreprocessController	A controller to pre-process expression data (including updating diagnostics)
ProgressStatusService	These methods are exposed to front-end.
ProgressStatusServiceImpl	This class exposes methods for AJAX calls.
PubMedConfig
PubMedQueryController	Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
PubMedSearchCommand	Supports seaching of pubmed references
QuantitationTypePropertyEditor
ReCaptcha
ReCaptchaException
ReCaptchaResponse
RssFeedController
ScaleTypeConverter
ScriptTag	Write a <style/> tag.
SecureMethodInvokingJobDetailFactoryBean	Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
SecureQuartzJobBean	A secure Quartz job bean that executes with a given security context.
SecurityController	Manages data-level security (ie. can make data private).
SecurityInfoValueObject	Carries extensive security information about an entity.
SequenceTypePropertyEditor
ServiceUnavailableException	Exception raised when a service is unavailable.
ServletMetricsFilter	Metrics for servlet requests.
SessionListManager
SessionListManagerImpl
ShortBibliographicReferenceTag
SidValueObject
SignupController	Controller to signup new users.
SimpleExpressionExperimentCommandValidation	Stores information about the validation status of an attempted expression experiment load.
SimpleExpressionExperimentLoadTaskCommand	Extends a SimpleExpressionExperimentMetaData with information about the file
SimpleHttp
SingleCellSparsityHeatmapTag	Tag for displaying a single-cell sparsity heatmap.
SlackAppender
StandardQuantitationTypeConverter
StartupListener	Slight variant of ContextLoaderListener that logs the time taken to initialize the context.
StaticAssetResolver	Resolve static assets either froma InternalStaticAssetServer or from the webapp resources.
StaticAssetServer
StaticAssetServerConfig
StringPoint
StyleTag	write a <style/> tag.
SvdController	Run SVD on a data set.
SystemMonitorController	Provide statistics about the system: hibernate, caches etc.
SystemStatsController	System statistics
TagWriterUtils
TaskCompletionController	Exposes progress status service check result to the front end.
TaxonController
TaxonPropertyEditor	Used to convert Taxon from and into strings for display in forms.
TextView	Simply prints text to the client.
TwoChannelMissingValueController	Run misssing value computation via web request.
UnhandledExceptionResolver	Resolver used when no other resolver can intervene.
UploadInfo
UploadListener	This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
UserCounterListener	Count active sessions
UserFormMultiActionController	Controller to edit profile of users.
UserGroupValueObject
UserListController	For display and editing of users.
UserTracker	Basic bean to hold number of sessions.
UserUpdateCommand	Just like a regular user; but has 'new password' and 'confirm password' fields.
UserValueObject
VisualizationValueObject	Stores expression profile data from one expression experiment for plotting.
WebConstants	Constant values used throughout the web portion of Gemma.
WebEntityUrlBuilder	This builder has extras URL-generating capabilities for Web applications.
WhatsNewController	Controller to provide information on "what's new" in the system
XmlView	Model should contain a single value matching XML_PARAM