All Classes Interface Summary Class Summary Exception Summary
| Class |
Description |
| AbstractGemmaEndpoint |
Abstracts out the security and a few constants.
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| AbstractSetListContainer |
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| AnchorTagUtil |
Used to generate hyperlinks to various things in Gemma.
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| AnnotationController |
Controller for methods involving annotation of experiments (and potentially other things); delegates to
OntologyService and the CharacteristicService.
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| ArrayDesignAddCommand |
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| ArrayDesignController |
Note: do not use parametrized collections as parameters for ajax methods in this class!
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| ArrayDesignFormController |
Controller for editing basic information about array designs.
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| ArrayDesignGroupingTag |
For display of information about array designs that subsume or are subsumed.
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| ArrayDesignHtmlUtil |
Yes, this is used by the ArrayDesignController, but should be phased out.
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| ArrayDesignIdentifierByNameEndpoint |
array design short name -> return matching array design identifier
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| ArrayDesignProbeMapperController |
A controller to run array design probe mapper either locally or in a space.
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| ArrayDesignPropertyEditor |
Used to convert ArrayDesigns from and into strings for display in forms.
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| ArrayDesignRepeatScanController |
A controller to run array design repeat scan either locally or in a space.
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| ArrayDesignRepeatScanTask |
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| ArrayDesignRepeatScanTaskCommand |
A command object to be used by spaces.
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| ArrayDesignRepeatScanTaskImpl |
An array design repeat scan spaces task
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| ArrayDesignUsedEndpoint |
Used for determining which array designs were used in a given expression experiment (EE)
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| ArrayDesignValueObjectExt |
Extended value object to carry more data to client.
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| AssayViewTag |
Used to display table of biomaterials and bioassays.
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| AuditController |
This is required solely for exposing auditables to remote services would try to marshall the abstract class
Auditable.
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| BaseController |
Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting
messages in the session.
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| BaseFormController |
Deprecated.
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| BatchInfoFetchController |
For populating "batch" information about experiments.
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| 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.
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| BioAssayController |
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| BioMaterialController |
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| BlatResultTrackController |
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| CacheMonitor |
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| CacheMonitorImpl |
Get statistics about and manage caches.
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| CharacteristicBrowserController |
NOTE: Logging messages from this service are important for tracking changes to annotations.
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| CharacteristicConverter |
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| ClassConverter |
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| ClientAbortExceptionResolver |
Resolves a ClientAbortException to an empty view.
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| CoexpressionSearchController |
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| CoexSearchTaskCommand |
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| CommonsMultipartFile |
Deprecated. |
| CommonsMultipartMonitoredResolver |
An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
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| CompositeSequenceController |
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| ConfigurationCookie |
Cookie class that also presents a commons configuration interface.
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| Constants |
Constant values used throughout the application.
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| 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.
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| ConstantsTei |
Implementation of TagExtraInfo for the constants tag, identifying the scripting object(s) to be
made visible.
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| ControllerUtils |
Created by tesarst on 09/03/17.
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| CustomRssViewer |
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| DatabaseEntryTag |
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| DEDVController |
Exposes methods for accessing underlying Design Element Data Vectors. eg: ajax methods for visualization
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| DEDVfromEEIDGeneIDEndpoint |
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.
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| DEDVRankEndpoint |
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.
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| DefaultHandlerExceptionResolver |
Custom exception resolver for Gemma.
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| DesignMatrixRowValueObject |
For the display of a summary table about experimental design.
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| DesignMatrixRowValueObject.Factory |
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| DifferentialExpressionAnalysisController |
A controller to run differential expression analysis either locally or in a space.
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| DifferentialExpressionAnalyzerInfo |
Used to carry information about the experimental design analysis settings to clients.
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| DifferentialExpressionProbeResultEndpoint |
Allows access to the differential expression analysis.
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| DifferentialExpressionSearchController |
A controller used to get differential expression analysis and meta analysis results.
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| DiffExMetaAnalyzerController |
A controller to analyze result sets either locally or in a space.
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| DiffExpressionSearchCommand |
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| DirectionConverter |
DWR converter for Direction type.
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| DoublePointConverter |
The 8 decimal precision of a double is just a waste of bandwidth in most cases.
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| Ee2AdUpdateJob |
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| Ee2cUpdateJob |
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| EmptyController |
This exists just to have an easy way to trick web pages into importing DWR-defined classes that are not in dwrServices.js.
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| EntityDelegator<T extends ubic.gemma.model.common.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.
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| EntityNotFoundException |
Signals that an entity was not found in the system.
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| ExceptionTag |
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| ExperimentalDesignController |
Main entry point to editing and viewing experimental designs.
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| ExperimentalFactorValueWebUIObject |
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| ExperimentAnnotationEndpoint |
Expression Experiments in Gemma contain annotations.
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| ExperimentDEDVEndpoint |
Allows access to all the Design Element Data Vectors (DEDV's) for a given Expression Experiment.
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| ExperimentIDbyTaxonEndpoint |
Given a Taxon (eg. "1" for Homo Sapien), will return all the Expression Experiment IDs that match the Taxon.
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| ExperimentIdEndpoint |
Given the short name of an Expression Experiment, will return the matching Expression Experiment ID
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| ExperimentNameEndpoint |
Used for getting the Short Name given an Expression Experiment ID eg: 793 --> GSE10470
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| ExperimentNumSamplesEndpoint |
Used for determining the number of samples (biomaterials) associated with a given expression experiment
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| ExperimentQCTag |
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| ExperimentSetListContainer |
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| ExpressionDataFileUploadController |
Replaces SimpleExpressionExperimentLoadController
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| ExpressionExperimentController |
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| ExpressionExperimentDataFetchCommand |
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| ExpressionExperimentDataFetchController |
For the download of data files from the browser.
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| ExpressionExperimentEditValueObject |
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| ExpressionExperimentExperimentalFactorValueObject |
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| ExpressionExperimentFormController |
Handle editing of expression experiments.
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| ExpressionExperimentLoadController |
Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
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| ExpressionExperimentQCController |
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| ExpressionExperimentQCUtils |
Helper functions for checking existence etc. of QC information.
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| ExpressionExperimentReportGenerationController |
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| ExpressionExperimentSetController |
For fetching and manipulating ExpressionExperimentSets.
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| ExpressionExperimentSetIDsEndpoint |
A service to return the full list of Expression Experiment Set IDs along with the corresponding name and experiment
ids it contains.
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| ExpressionExperimentUploadResponse |
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| ExpressionExperimentVisualizationCommand |
Expression experiment command object that wraps expression experiment visualization preferences.
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| ExpressionProfileDataObject |
A lightweight object to hold expression data for a single probe.
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| FactorProfile |
Represents data for displaying a factor (+ factor values) in a chart.
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| FailedMultipartHttpServletRequest |
Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
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| FeedReader |
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| FileUpload |
Command class to handle uploading of a file
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| FileUploadController |
Controller class to upload Files.
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| FileUploadUtil |
Utility methods for uploading files.
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| Gene2GOdescriptionEndpoint |
Given a collection of Gene ID, will return a collection of Gene Ontology IDs (ie.
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| Gene2GoTermEndpoint |
Given a collection of Gene IDs, will return a collection of Gene Ontology URIs for each gene.
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| Gene2ProbeEndpoint |
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.
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| GeneByNCBIIdEndpoint |
Given an NCBI ID, will return the matching Gemma gene id.
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| GeneCoexpressionEndpoint |
Allows access to the gene co-expression analysis.
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| GeneCoexpressionSearchEndpoint |
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| GeneController |
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| GeneDetailsByGeneIDEndpoint |
Given a collection of Gemma gene IDs, will return the matching NCBI Ids.
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| GeneExpressionProfile |
Expression data for one probe; designed for conveying small amounts of data to clients.
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| GeneIDbyTaxonEndpoint |
Given the Taxon (eg. "1" for Homo Sapiens), will return all the Gene IDs that match the taxon.
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| GeneIdEndpoint |
Given the official symbol and taxon of a gene, will return the matching gene ID.
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| GeneNameEndpoint |
Given a gene ID, will return the matching gene official symbol eg) 938103--> Grin1
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| GeneOverlapEndpoint |
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.
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| GenePickerController |
For 'live searches' from the web interface.
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| GeneralSearchController |
Note: do not use parametrized collections as parameters for ajax methods in this class!
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| GeneralSearchController.SearchResultValueObject<T extends ubic.gemma.model.common.IdentifiableValueObject<?>> |
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| GeneSetController |
Exposes GeneSetServices methods over ajax.
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| GeneSetListContainer |
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| GeneSymbolComparator |
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| GeoRecordBrowserController |
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| GOEvidenceCodeConverter |
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| GoTerm2GeneEndpoint |
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.
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| HibernateMonitor |
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| HibernateMonitorImpl |
Monitoring of Hibernate status.
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| HomePageController |
Responsible for display of the Gemma 2.0 home page.
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| IndexController |
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| JavascriptLogger |
Class to handle saving client-side javascript error messages and warnings to a server-side log.
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| JsonReaderResponse<T> |
Creates a response that can be consumed by an Ext.data.JsonReader.
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| JSONTableRenderer |
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| JsonUtil |
Utilities for writing JSON payloads to HttpServletResponse.
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| JSONView |
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| LabelValue |
A simple JavaBean to represent label-value pairs.
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| LinkAnalysisController |
A controller to pre-process expression data vectors.
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| ListBatchCommand |
Encapsulates information needed for generic list browsing.
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| MaintenanceModeController |
Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave
normally.
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| MessageUtil |
Provides methods for putting messages to the user in the session.
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| MessageUtilImpl |
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| MetaFile |
Wrapper for metadata file information for the frontend
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| MeterRegistryWebConfigurer |
Configured the environment='web' tag to the provided registry.
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| MinifierPostProcessor |
JAWR postprocessor to remove console.log and debugger breakpoint statements.
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| MonitoredDiskFileItem |
Commons FileItem that uses a MonitoredOutputStream
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| MonitoredDiskFileItemFactory |
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| MonitoredOutputStream |
OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
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| NewsItem |
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| OntologyController |
Provide minimal support for exposing Gemma ontology.
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| OutputStreamListener |
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| PhenotypeController |
Controller for phenotype
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| PreprocessController |
A controller to pre-process expression data (including updating diagnostics)
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| Probe2GeneEndpoint |
Used for determining what genes a probe assays for.
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| ProgressStatusService |
These methods are exposed to front-end.
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| ProgressStatusServiceImpl |
This class exposes methods for AJAX calls.
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| PubMedConfig |
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| PubMedQueryController |
Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
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| PubMedSearchCommand |
Supports seaching of pubmed references
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| QuantitationTypePropertyEditor |
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| ReCaptcha |
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| ReCaptchaException |
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| ReCaptchaResponse |
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| RssFeedController |
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| ScaleTypeConverter |
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| SecureMethodInvokingJobDetailFactoryBean |
Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
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| SecureQuartzJobBean |
A secure Quartz job bean that executes with a given security context.
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| SecurityController |
Manages data-level security (ie. can make data private).
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| SecurityInfoValueObject |
Carries extensive security information about an entity.
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| SequenceTypePropertyEditor |
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| ServiceUnavailableException |
Exception raised when a service is unavailable.
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| ServletMetricsFilter |
Metrics for servlet requests.
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| SessionListManager |
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| SessionListManagerImpl |
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| ShortBibliographicReferenceTag |
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| SidValueObject |
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| SignupController |
Controller to signup new users.
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| SimpleExpressionExperimentCommandValidation |
Stores information about the validation status of an attempted expression experiment load.
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| SimpleExpressionExperimentLoadTaskCommand |
Extends a SimpleExpressionExperimentMetaData with information about the file
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| SimplePageContext |
Deprecated. |
| SlackAppender |
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| StandardQuantitationTypeConverter |
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| StartupListener |
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.
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| StringPoint |
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| SvdController |
Run SVD on a data set.
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| SystemMonitorController |
Provide statistics about the system: hibernate, caches etc.
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| SystemStatsController |
System statistics
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| TaskCompletionController |
Exposes progress status service check result to the front end.
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| TaxonPropertyEditor |
Used to convert Taxon from and into strings for display in forms.
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| TextView |
Simply prints text to the client.
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| TwoChannelMissingValueController |
Run misssing value computation via web request.
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| UnhandledExceptionResolver |
Resolver used when no other resolver can intervene.
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| UploadInfo |
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| UploadListener |
This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
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| UserCounterListener |
Count active sessions
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| UserFormMultiActionController |
Controller to edit profile of users.
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| UserGroupValueObject |
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| UserListController |
For display and editing of users.
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| UserTracker |
Basic bean to hold number of sessions.
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| UserUpdateCommand |
Just like a regular user; but has 'new password' and 'confirm password' fields.
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| UserValueObject |
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| VisualizationValueObject |
Stores expression profile data from one expression experiment for plotting.
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| WebConstants |
Constant values used throughout the web portion of Gemma.
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| WhatsNewController |
Controller to provide information on "what's new" in the system
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| XmlView |
Model should contain a single value matching XML_PARAM
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