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! Type information is lost
during proxy creation so DWR can't figure out what type of collection the method should take.
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| ArrayDesignControllerImpl |
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.
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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 |
Note: do not use parameterized collections as parameters for ajax methods.
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| BibliographicReferenceControllerImpl |
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.
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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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| 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 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.
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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.
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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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| GemmaClassicHomePageController |
Deprecated. |
| 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.
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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! Type information is lost
during proxy creation so DWR can't figure out what type of collection the method should take.
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| GeneralSearchController.SearchResultValueObject<T extends IdentifiableValueObject<?>> |
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| GeneralSearchControllerImpl |
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.
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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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| PubMedQueryController |
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 |
Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
|
| 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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| RequestUtil |
RequestUtil utility class
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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 |
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.
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| SecurityControllerImpl |
Manages data-level security (ie.
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| SecurityInfoValueObject |
Carries extensive security information about an entity.
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| SequenceTypePropertyEditor |
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| ServiceUnavailableException |
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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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| SimpleHttp |
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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 |
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.
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| UserListControllerImpl |
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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