All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
| Class |
Description |
| AbaGene |
|
| ABALinkOutValueObject |
Value Object for transporting details needed from other websites to provide convenient links to them in gemma
|
| AbstractAnalyzer |
Analyzer base class.
|
| AbstractArg<T> |
Base class for non Object-specific functionality argument types, that can be malformed on input (E.g an argument
representing a number was a non-numeric string in the request).
|
| AbstractArrayArg<T> |
Class representing an API argument that should be an array.
|
| AbstractAsyncFactoryBean<T> |
|
| AbstractAuditable |
An entity which can have an audit trail attached to it.
|
| AbstractCLI |
Base Command Line Interface.
|
| AbstractCLIContextCLI |
Spring configuration for CLI.
|
| AbstractCriteriaFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> |
Created by tesarst on 07/03/17.
|
| AbstractCuratableValueObject<C extends Curatable> |
Created by tesarst on 07/03/17.
|
| AbstractDao<T extends Identifiable> |
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
|
| AbstractDescribable |
|
| AbstractDesignElementDataVectorDao<T extends DesignElementDataVector> |
|
| AbstractDesignElementDataVectorService<T extends DesignElementDataVector> |
|
| AbstractDifferentialExpressionAnalyzer |
An abstract differential expression analyzer to be extended
|
| AbstractEntityArg<T,O extends Identifiable,S extends FilteringService<O>> |
Interface representing and API call argument that can represent various identifiers of different types.
|
| AbstractEntityArgService<T extends Identifiable,S extends FilteringService<T>> |
|
| AbstractEntityArrayArg<O extends Identifiable,S extends FilteringService<O>> |
|
| AbstractExceptionMapper<E extends Throwable> |
|
| AbstractFetcher |
|
| AbstractFileService<T> |
Provide base implementation for all sorts of file services that serialize data in tabular format.
|
| AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractFilteringVoEnabledDao.FilterablePropertyMeta |
Meta-information for a filterable property.
|
| AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractGemmaEndpoint |
Abstracts out the security and a few constants.
|
| AbstractGeoService |
|
| AbstractMatrixRowPairAnalysis |
|
| AbstractMeterRegistryConfigurer |
|
| AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
|
| AbstractPersister |
|
| AbstractPersister.Caches |
Various caches to refer back to not-yet persisted entities (and thus not easily obtainable from the persistence
context).
|
| AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractService<O extends Identifiable> |
Base for all services handling DAO access.
|
| AbstractSetListContainer |
|
| AbstractSpringAwareCLI |
Subclass this to create command line interface (CLI) tools that need a Spring context.
|
| AbstractTask<C extends TaskCommand> |
|
| AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| AccessDeniedExceptionMapper |
Map Spring Security's AccessDeniedException to a 403 Forbidden response.
|
| AclAdvice |
For permissions modification to be triggered, the method name must match certain patterns, which include "create", or
"remove".
|
| AclAfterCollectionCompSeqByArrayDesignFilter |
For this particular AfterInvocationProvider, composite sequence authorization is determined based on the secured
array design acl.
|
| AclAfterCollectionDataVectorByExpressionExperimentFilter |
Filter collections of DesignElementDataVectors or DataVectorValueObjects based on the permissions of the associated
ExpressionExperiment(s).
|
| AclAfterCompSeqByArrayDesignFilter |
|
| AclCriteriaUtils |
Utilities for integrating ACLs with Hibernate Criteria API. |
| AclQueryUtils |
Utilities for integrating ACL into Query. |
| AffyChipTypeExtractor |
Extract the chip type from Affymetrix CEL files.
|
| AffyDataFromCelCli |
Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
|
| AffyPowerToolsProbesetSummarize |
|
| AffyProbeCollapseCli |
Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
|
| AffyProbeNameFilter |
|
| AffyProbeNameFilter.Pattern |
|
| AffyProbeReader |
Reads Affymetrix Probe files, including exon arrays.
|
| AffyScanDateExtractor |
Extract the scan date from Affymetrix CEL files.
|
| AgilentScanDateExtractor |
Because agilent makes slides that work with any scanner, the formats are not that predictable.
|
| AlignmentBasedGeneMappingEvent |
Signifies a mapping based on sequence alignment performed by the system.
|
| AllenBrainAtlasService |
|
| AllenBrainAtlasServiceImpl |
Acts as a convenient front end to the Allen Brain Atlas REST (web) services Used the ABAApi.java as the original
template for this Service (found in ABA demo code).
|
| AlreadyExistsInSystemException |
Can be thrown when an attempt is made to load data into the system that already exists.
|
| AlternateName |
|
| AlternateName.Factory |
|
| Analysis |
An analysis of one or more Investigations.
|
| AnalysisDao<T extends SingleExperimentAnalysis> |
|
| AnalysisResult |
|
| AnalysisResultSet<R extends AnalysisResult> |
An abstract class representing a related set of generic analysis results, part of an analysis.
|
| AnalysisResultSetDao<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
|
| AnalysisResultSetService<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
|
| AnalysisResultSetsWebService |
|
| AnalysisResultSetValueObject<K extends AnalysisResult,R extends AnalysisResultSet<K>> |
|
| AnalysisResultValueObject<A extends AnalysisResult> |
|
| AnalysisSelectionAndExecutionService |
|
| AnalysisSelectionAndExecutionServiceImpl |
A differential expression analysis tool that executes the appropriate analysis based on the number of experimental
factors and factor values, as well as the block design.
|
| AnalysisService<T extends Analysis> |
Provides basic services for dealing with analyses
|
| AnalysisSuitabilityEvent |
Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
|
| AnalysisUtilService |
|
| AnalysisUtilServiceImpl |
Utility methods for dealing with analyses.
|
| AnalysisValueObject<T extends Analysis> |
|
| AnalyticsApplicationEventListener |
|
| AnalyticsProvider |
Interface for analytics providers.
|
| AnalyticsRequestEventListener |
Request event listener that publishes an event when a request is finished.
|
| AnchorTagUtil |
Used to generate hyperlinks to various things in Gemma.
|
| AnnotationAssociation |
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather
than our own sequence analysis.
|
| AnnotationAssociation.Factory |
|
| AnnotationAssociationDao |
|
| AnnotationAssociationDaoImpl |
|
| AnnotationAssociationService |
|
| AnnotationAssociationServiceImpl |
|
| AnnotationBasedGeneMappingEvent |
To signify the array design was mapped from an external source, not by our own sequence analysis.
|
| AnnotationController |
Controller for methods involving annotation of experiments (and potentially other things); delegates to
OntologyService and the CharacteristicService.
|
| AnnotationEvent |
|
| AnnotationsWebService |
RESTful interface for annotations.
|
| AnnotationsWebService.AnnotationSearchResultValueObject |
|
| AnnotationValueObject |
|
| ArchiveFetcher |
Interface defining a class that downloads archives and unpacks them.
|
| Arg<T> |
|
| ArgUtils |
Utilities for working with Arg. |
| ArrayDesign |
Represents an assembly of design elements that are assayed all at once.
|
| ArrayDesign.Factory |
|
| ArrayDesignAddCommand |
|
| ArrayDesignAlternativePopulateCli |
This only needs to be re-run when the mappings change.
|
| ArrayDesignAnalysisEvent |
An event involving the analysis of an ArrayDesign
|
| ArrayDesignAnnotationFileCli |
Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for
the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or
merged into another AD.
|
| ArrayDesignAnnotationService |
Methods to generate annotations for array designs, based on information already in the database.
|
| ArrayDesignAnnotationService.OutputType |
|
| ArrayDesignAnnotationServiceImpl |
|
| ArrayDesignAuditTrailCleanupCli |
work in progress
|
| ArrayDesignBioSequenceDetachCli |
Remove all associations that this array design has with BioSequences.
|
| ArrayDesignBlatCli |
Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
|
| 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.
|
| 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.
|
| ArrayDesignDao |
Created by tesarst on 13/03/17.
|
| ArrayDesignDaoImpl |
|
| ArrayDesignFormController |
Controller for editing basic information about array designs.
|
| ArrayDesignGeneMappingEvent |
The mapping of probes to genes for an ArrayDesign
|
| 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.
|
| ArrayDesignIdentifierByNameEndpoint |
array design short name -> return matching array design identifier
|
| ArrayDesignMapResultService |
|
| ArrayDesignMapResultServiceImpl |
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
|
| ArrayDesignMapSummaryCli |
CLI for ArrayDesignMapSummaryService
|
| ArrayDesignMergeCli |
make new array design based on others
Keep map of relation between new design elements and old ones
Store relationship with mergees
Separate operations:
For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
|
| ArrayDesignMergeEvent |
|
| ArrayDesignMergeHelperService |
|
| ArrayDesignMergeHelperServiceImpl |
|
| ArrayDesignMergeService |
Make new array design based on others
Keep map of relation between new design elements and old ones
Store relationship with mergees
|
| ArrayDesignMergeServiceImpl |
|
| ArrayDesignParser |
Deprecated. |
| ArrayDesignPersister |
This class handles persisting array designs.
|
| ArrayDesignProbeCleanupCLI |
Delete design elements (probes) that are invalid for one reason or another.
|
| ArrayDesignProbeMapperCli |
Process the blat results for an array design to map them onto genes.
|
| ArrayDesignProbeMapperController |
A controller to run array design probe mapper either locally or in a space.
|
| ArrayDesignProbeMapperService |
|
| ArrayDesignProbeMapperServiceImpl |
For an array design, generate gene product mappings for the sequences.
|
| ArrayDesignProbeMapperTaskImpl |
A probe mapper spaces task .
|
| ArrayDesignProbeMapTaskCommand |
A command object to be used by spaces.
|
| ArrayDesignProbeRenamerCli |
Deprecated.
|
| ArrayDesignProbeRenamingEvent |
Signifies that the probes were renamed from their original values.
|
| ArrayDesignPropertyEditor |
Used to convert ArrayDesigns from and into strings for display in forms.
|
| ArrayDesignRepeatAnalysisEvent |
|
| ArrayDesignRepeatScanCli |
Runs repeatmasker on array designs.
|
| 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
|
| ArrayDesignReportService |
|
| ArrayDesignReportServiceImpl |
|
| ArrayDesignSequenceAlignmentService |
|
| ArrayDesignSequenceAlignmentServiceImpl |
Aligns sequences from array designs to the genome, using blat, and persists the blat results.
|
| ArrayDesignSequenceAnalysisEvent |
The sequence alignment analysis of an ArrayDesign
|
| ArrayDesignSequenceAssociationCli |
Attach sequences to array design, fetching from BLAST database if requested.
|
| ArrayDesignSequenceManipulatingCli |
Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something
with it.
|
| ArrayDesignSequenceProcessingService |
|
| ArrayDesignSequenceProcessingServiceImpl |
Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
|
| ArrayDesignSequenceRemoveEvent |
Used to indicate that all associations that this array design has with BioSequences have been removed.
|
| ArrayDesignSequenceUpdateEvent |
The updating of the sequences associated with an ArrayDesign
|
| ArrayDesignService |
|
| ArrayDesignServiceImpl |
|
| ArrayDesignsForExperimentCache |
Used to hold information for matching to a new experiment, during persisting.
|
| ArrayDesignSubsumeCheckEvent |
|
| ArrayDesignSubsumptionTesterCli |
Test two array designs to see if one subsumes the other, and if so update their information.
|
| ArrayDesignUsedEndpoint |
Used for determining which array designs were used in a given expression experiment (EE)
|
| ArrayDesignValueObject |
Value object for quickly displaying varied information about Array Designs.
|
| ArrayDesignValueObjectExt |
Extended value object to carry more data to client.
|
| ArrayExpressUtil |
|
| AssayViewTag |
Used to display table of biomaterials and bioassays.
|
| AsyncFactoryBean<T> |
|
| AsyncFactoryBeanUtils |
Utilities for manipulating async factory beans.
|
| Auditable |
Created by tesarst on 07/03/17.
|
| AuditableObject |
|
| AuditAction |
|
| AuditAdvice |
Manage audit trails on objects.
|
| AuditController |
This is required solely for exposing auditables to remote services would try to marshall the abstract class
Auditable.
|
| AuditEvent |
An event in the life of an object.
|
| AuditEvent.Factory |
|
| AuditEventDao |
|
| AuditEventDaoImpl |
|
| AuditEventService |
|
| AuditEventServiceImpl |
|
| AuditEventType |
|
| AuditEventValueObject |
|
| AuditTrail |
The trail of events (create or update) that occurred in an objects lifetime.
|
| AuditTrail.Factory |
|
| AuditTrailDao |
|
| AuditTrailDaoImpl |
|
| AuditTrailService |
Create and manipulate audit trails.
|
| AuditTrailServiceImpl |
|
| AuthenticationBasedUserIdRetrievalStrategy |
Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
|
| AuthenticationExceptionMapper |
Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
|
| AutomatedAnnotationEvent |
Deprecated.
|
| BaseCodeOntologySearchException |
|
| BaseController |
Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting
messages in the session.
|
| BaseDao<T> |
Interface that supports basic CRUD operations.
|
| BaseExpressionDataMatrix<T> |
Base class for ExpressionDataMatrix implementations.
|
| BaseFormController |
Implementation of SimpleFormController that contains convenience methods for subclasses.
|
| BaseImmutableService<O extends Identifiable> |
Base service class for an immutable entity.
|
| BaselineSelection |
Utilities for deciding if a factor value is a baseline condition.
|
| BaseReadOnlyService<O extends Identifiable> |
Interface for read-only services.
|
| BaseScanDateExtractor |
|
| BaseService<O extends Identifiable> |
Interface that supports basic CRUD operations.
|
| BaseValueObject |
|
| BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| BasicLineMapParser<K,T> |
A line parser that produces a Map instead of a Collection.
|
| BasicLineParser<T> |
A simple LineParser implementation that doesn't do anything.
|
| BatchConfound |
Represents a summary of a batch effect confound.
|
| BatchConfoundUtils |
Test if an experimental design is confounded with batches.
|
| BatchCorrectionEvent |
|
| BatchEffectDetails |
provide some basic information about the properties and strength of a batch effect, if any.
|
| BatchEffectPopulationCli |
For bulk processing of batch-info-fetching.
|
| BatchInfoFetchController |
For populating "batch" information about experiments.
|
| BatchInfoFetchTask |
|
| BatchInfoFetchTaskCommand |
|
| BatchInfoFetchTaskImpl |
Task to try to get 'batch' information about an experiment.
|
| BatchInfoParser |
Parse information on batch from raw data files.
|
| BatchInfoPopulationException |
Used to indicate a problem with the population of batch information for a given
ExpressionExperiment. |
| BatchInfoPopulationHelperService |
|
| BatchInfoPopulationHelperServiceImpl |
|
| BatchInfoPopulationService |
Retrieve batch information from the data source, if possible, and populate it into experiments.
|
| BatchInfoPopulationServiceImpl |
Retrieve batch information from the data source, if possible, and populate it into experiments.
|
| BatchInformationFetchingEvent |
Indicates that batch information was obtained
|
| BatchProblemsUpdateEvent |
|
| BeanInitializationTimeMonitor |
Hook into the bean post-processing lifecycle and report the worst offenders.
|
| BeanNameGenerator |
Our \@Service etc.
|
| BibliographicPhenotypesValueObject |
|
| BibliographicReference |
|
| BibliographicReference.Factory |
|
| BibliographicReferenceController |
Note: do not use parameterized collections as parameters for ajax methods.
|
| 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.
|
| BibliographicReferenceDao |
|
| BibliographicReferenceDaoImpl |
|
| BibliographicReferenceService |
|
| BibliographicReferenceServiceImpl |
Implementation of BibliographicReferenceService.
|
| BibliographicReferenceValueObject |
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists
in web
|
| BibRefAnnotation |
|
| BibRefUpdaterCli |
Refreshes the information in all the bibliographic references in the system.
|
| BioAssay |
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
|
| BioAssay.Factory |
|
| BioAssayController |
|
| BioAssayDao |
|
| BioAssayDaoImpl |
|
| BioAssayDimension |
Stores the order of BioAssays referred to in DataVectors.
|
| BioAssayDimension.Factory |
|
| BioAssayDimensionDao |
|
| BioAssayDimensionDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
|
| BioAssayDimensionService |
|
| BioAssayDimensionServiceImpl |
Spring Service base class for BioAssayDimensionService, provides access to all services and entities
referenced by this service.
|
| BioAssayDimensionValueObject |
|
| BioAssayOutlierProcessingTask |
|
| BioAssayOutlierProcessingTaskCommand |
|
| BioAssayOutlierProcessingTaskImpl |
Handle 'flagging' a sample as an outlier.
|
| BioAssayService |
|
| BioAssayServiceImpl |
|
| BioAssaySet |
Represents a set of BioAssays.
|
| BioAssayValueObject |
|
| BiomartEnsembleNcbiParser |
Parser for BioMart file.
|
| BiomartEnsemblNcbiFetcher |
BioMart is a query-oriented data management system.
|
| BiomartEnsemblNcbiObjectGenerator |
Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble
protein id.
|
| BioMaterial |
In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA,
proteins, etc...
|
| BioMaterial.Factory |
|
| BioMaterialController |
|
| BioMaterialDao |
|
| BioMaterialDaoImpl |
|
| BioMaterialMappingUpdate |
To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.
|
| BioMaterialService |
|
| BioMaterialServiceImpl |
|
| BioMaterialValueObject |
|
| BioSequence |
The sequence of a biological polymer such as a protein or DNA.
|
| BioSequence.Factory |
|
| BioSequence2GeneProduct |
An association between a BioSequence and a Gene Product.
|
| BioSequenceCleanupCli |
Goes through the biosequences for array designs in the database and removes duplicates.
|
| BioSequenceDao |
|
| BioSequenceDaoImpl |
|
| BioSequenceService |
|
| BioSequenceServiceImpl |
Spring Service base class for BioSequenceService, provides access to
all services and entities referenced by this service.
|
| BioSequenceValueObject |
|
| BlacklistCli |
Add entries to the blacklist
|
| BlacklistedEntity |
|
| BlacklistedEntityDao |
|
| BlacklistedEntityDaoImpl |
|
| BlacklistedEntityService |
|
| BlacklistedEntityServiceImpl |
|
| BlacklistedExperiment |
TODO Document Me
|
| BlacklistedPlatform |
|
| BlacklistedValueObject |
|
| Blat |
|
| BlatAssociation |
|
| BlatAssociation.Factory |
|
| BlatAssociationDao |
|
| BlatAssociationDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
BlatAssociation.
|
| BlatAssociationScorer |
Given a set of BlatAssociations that might be redundant, clean them up and score them.
|
| BlatAssociationService |
|
| BlatAssociationServiceImpl |
Spring Service base class for BlatAssociationService, provides access to all services and entities
referenced by this service.
|
| BlatResult |
Represents the result of a BLAT search.
|
| BlatResult.Factory |
|
| BlatResult2Psl |
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
|
| BlatResultDao |
|
| BlatResultDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.sequenceAnalysis.BlatResult.
|
| BlatResultParser |
Loader to handle results generated by Jim Kent's Blat.
|
| BlatResultService |
|
| BlatResultServiceImpl |
Spring Service base class for BlatResultService, provides access to all services and entities referenced
by this service.
|
| BlatResultTrackController |
|
| BlatResultValueObject |
|
| BooleanVectorValueObject |
This is used to represent missing value data.
|
| BrowsingDao<T> |
Support for paging through the data.
|
| BusinessKey |
Methods to test business-key-related issues on objects.
|
| CacheControl |
|
| CacheControlHeaderDecorator |
|
| CacheControls |
|
| CachedFilteringDao<O extends Identifiable> |
|
| CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| CacheMonitor |
|
| CacheMonitorImpl |
Get statistics about and manage caches.
|
| CacheUtils |
Created by tesarst on 04/04/17.
|
| CacheUtils.Lock |
|
| ChannelUtils |
Determine if a quantitation type (by name) represents background or signal.
|
| Characteristic |
Instances of this are used to describe other entities.
|
| Characteristic.Factory |
|
| CharacteristicBasicValueObject |
|
| CharacteristicBrowserController |
NOTE: Logging messages from this service are important for tracking changes to annotations.
|
| CharacteristicConverter |
|
| CharacteristicDao |
|
| CharacteristicDao.CharacteristicUsageFrequency |
|
| CharacteristicDaoImpl |
|
| CharacteristicService |
|
| CharacteristicServiceImpl |
|
| CharacteristicUpdateCommand |
|
| CharacteristicUpdateTask |
|
| CharacteristicUpdateTaskImpl |
This handles characteristic updates from the client: experiment tags, characteristic browser
|
| CharacteristicValueObject |
ValueObject wrapper for a Characteristic
|
| Chromosome |
Immutable representation of a chromosome
|
| ChromosomeDao |
|
| ChromosomeDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.Chromosome.
|
| ChromosomeFeature |
Some part of a chromosome
|
| ChromosomeLocation |
|
| ChromosomeService |
|
| ChromosomeServiceImpl |
Spring Service base class for ChromosomeService, provides access to all services
and entities referenced by this service.
|
| ChromosomeUtil |
|
| CitationValueObject |
Represents a BibliographicReference as a citation string (which is really super light value object).
|
| ClassConverter |
|
| CLI |
Interface for CLI tools.
|
| ClientIdRetrievalStrategy |
Strategy for retrieving a client ID.
|
| CoexpCorrelationDistribution |
|
| CoexpCorrelationDistribution.Factory |
|
| CoexpressionAnalysis |
A coexpression analysis of one experiment.
|
| CoexpressionAnalysis.Factory |
|
| CoexpressionAnalysisDao |
|
| CoexpressionAnalysisDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.
|
| CoexpressionAnalysisService |
Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
|
| CoexpressionAnalysisServiceImpl |
|
| CoexpressionCache |
Cache for coexpression results.
|
| CoexpressionCacheImpl |
Configures the cache for gene2gene coexpression.
|
| CoexpressionCacheValueObject |
Used to cache results; these objects are unmodifiable, and contains the coexpression data for one query gene and one
result gene, in all experiments.
|
| CoexpressionDao |
|
| CoexpressionDaoImpl |
Manages and queries coexpression 'links' between genes.
|
| CoexpressionMetaValueObject |
|
| CoexpressionNodeDegreeDao |
|
| CoexpressionNodeDegreeDaoImpl |
|
| CoexpressionSearchCommand |
|
| CoexpressionSearchController |
|
| CoexpressionService |
A key service for working with coexpression at a fairly low level.
|
| CoexpressionServiceImpl |
|
| CoexpressionSummaryValueObject |
|
| CoexpressionValueObject |
Lightweight/convenient object for manipulating coexpression for a pair of genes.
|
| CoexpressionValueObjectExt |
A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
|
| CoexSearchTaskCommand |
|
| ComBat<R,C> |
|
| CommentedEvent |
An event indicating a comment was added to the auditable.
|
| CommonPersister |
Persister for ubic.gemma.model.common package classes.
|
| CommonQueries |
Contains methods to perform 'common' queries that are needed across DAOs.
|
| CommonsMultipartFile |
Deprecated. |
| CommonsMultipartMonitoredResolver |
An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
|
| CompositeClientIdRetrievalStrategy |
Composite strategy for retrieving client ID.
|
| CompositeSearchSource |
A search source constituted of multiple other sources.
|
| CompositeSearchSource.SearchFunction<T extends Identifiable> |
|
| CompositeSequence |
A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
|
| CompositeSequence.Factory |
|
| CompositeSequenceArg<T> |
Mutable argument type base class for Composite Sequence arguments.
|
| CompositeSequenceArgService |
|
| CompositeSequenceArrayArg |
|
| CompositeSequenceController |
|
| CompositeSequenceDao |
|
| CompositeSequenceDaoImpl |
|
| CompositeSequenceGeneMapperService |
|
| CompositeSequenceIdArg |
Composite Sequence argument for CS ID.
|
| CompositeSequenceMapSummary |
This is a convenience object to hold the results of CompositeSequence mapping results.
|
| CompositeSequenceMapValueObject |
|
| CompositeSequenceNameArg |
Composite Sequence argument for CS name.
|
| CompositeSequenceParser |
Parse the "old" array description format.
|
| CompositeSequenceService |
|
| CompositeSequenceServiceImpl |
|
| CompositeSequenceValueObject |
|
| Compound |
|
| Compound.Factory |
|
| CompoundDao |
|
| CompoundDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.biomaterial.Compound.
|
| CompoundService |
|
| CompoundServiceImpl |
Spring Service base class for CompoundService, provides access to all services and entities referenced
by this service.
|
| 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.
|
| Contact |
Representing a person or organization that can be contacted about, or is the source of, data in the system.
|
| Contact.Factory |
|
| ContactDao |
|
| ContactDaoImpl |
|
| ContactService |
|
| ContactServiceImpl |
|
| ContrastResult |
Represents a contrast between "conditions".
|
| ContrastResult.Factory |
|
| ContrastResultValueObject |
Represents a contrast result.
|
| ContrastsValueObject |
Stores selected details of the contrasts for a single DifferentialExpressionResult
|
| ContrastVO |
Helper object, not for general use.
|
| ControllerUtils |
Created by tesarst on 09/03/17.
|
| Converter<S,T> |
Defines a class that can convert objects from one type to another.
|
| CorsFilter |
Filter for adding CORS headers to the RESTful API responses.
|
| CountObsoleteTermsCli |
|
| CtdDatabaseImporterCli |
Deprecated. |
| Curatable |
Created by tesarst on 06/03/17.
|
| CuratableDao<C extends Curatable> |
Created by tesarst on 13/03/17.
|
| CuratableService<C extends Curatable,VO extends AbstractCuratableValueObject<C>> |
Interface for curatable services.
|
| CurationDetails |
Class encapsulating all the curation information for Curatable objects.
|
| CurationDetailsEvent |
|
| CurationNoteUpdateEvent |
Indicates that previous validation is being invalidated
|
| CustomModelResolver |
Resolve Arg parameters' schema. |
| CustomModelResolverRegistrationListener |
Registers our customized ModelResolver.
|
| CustomRssViewer |
|
| DataAddedEvent |
Indicates that a data type (for a specific QuantitationType, possibly new) was added.
|
| DataAnalysisEvidence |
Deprecated. |
| DatabaseBackedGeneSetValueObject |
|
| DatabaseEntry |
A reference to a record in a database.
|
| DatabaseEntry.Factory |
|
| DatabaseEntryArg<T> |
Mutable argument type base class for DatabaseEntry API.
|
| DatabaseEntryArgService |
|
| DatabaseEntryArrayArg |
|
| DatabaseEntryDao |
|
| DatabaseEntryDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
DatabaseEntry.
|
| DatabaseEntryIdArg |
Long argument type for DatabaseEntry API, referencing the Taxon ID.
|
| DatabaseEntryService |
|
| DatabaseEntryServiceImpl |
Spring Service base class for DatabaseEntryService, provides access to all services and entities
referenced by this service.
|
| DatabaseEntryStringArg |
String argument type for DatabaseEntry API, Can also be null.
|
| DatabaseEntryTag |
|
| DatabaseEntryValueObject |
ValueObject for database entry
|
| DatabaseSearchSource |
Search source for direct database results.
|
| DatabaseSearchSourceUtils |
|
| DatabaseType |
|
| DatabaseViewGenerator |
|
| DatabaseViewGeneratorCLI |
Simple driver of DatabaseViewGenerator.
|
| DatabaseViewGeneratorImpl |
Generates textual views of the database so other people can use the data.
|
| DataFileFetcher |
ArrayExpress stores files in an FTP site as tarred-gzipped archives.
|
| DataReplacedEvent |
Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the
system.
|
| DatasetArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
|
| DatasetArgService |
|
| DatasetArrayArg |
|
| DatasetCombiner |
Class to handle cases where there are multiple GEO dataset for a single actual experiment.
|
| DatasetFetcher |
Retrieve GEO GDS files from the NCBI FTP server.
|
| DatasetIdArg |
Long argument type for dataset API, referencing the Dataset ID.
|
| DatasetStringArg |
String argument type for dataset API, referencing the Dataset short name.
|
| DatasetsWebService |
RESTful interface for datasets.
|
| DatasetsWebService.AnnotationWithUsageStatisticsValueObject |
This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
|
| DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject |
|
| DatasetsWebService.CategoryWithUsageStatisticsValueObject |
|
| DatasetsWebService.ExpressionExperimentWithSearchResultValueObject |
|
| DatasetsWebService.OntologyTermValueObject |
|
| DatasetsWebService.TaxonWithUsageStatisticsValueObject |
|
| DatasetsWebService.UsageStatistics |
|
| DataUpdater |
|
| DataUpdaterImpl |
Update or fill in the data associated with an experiment.
|
| DataVector |
An abstract class representing a one-dimensional vector of data about some aspect of an experiment.
|
| DataVectorValueObject |
|
| DEDVController |
Exposes methods for accessing underlying Design Element Data Vectors.
|
| 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.
|
| 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.
|
| DefaultHighlighter |
|
| DeleteDiffExCli |
Delete differential expression analsyes on a per-experiment basis.
|
| DeleteEvidenceCLI |
When we need to remove all evidence from an external database, usually to reimport them after
|
| DeleteExperimentsCli |
Delete one or more experiments from the system.
|
| Describable |
|
| DescribableComparator |
|
| DesignElementDataVector |
|
| DesignElementDataVectorDao<T extends DesignElementDataVector> |
|
| DesignMatrixRowValueObject |
For the display of a summary table about experimental design.
|
| DesignMatrixRowValueObject.Factory |
|
| DgaDatabaseImporterCli |
Deprecated. |
| DifferentialExpressionAnalysis |
An analysis of changes in expression levels across experimental conditions
|
| DifferentialExpressionAnalysis.Factory |
|
| DifferentialExpressionAnalysisCli |
|
| DifferentialExpressionAnalysisConfig |
Holds the settings used for differential expression analysis, and defines some defaults.
|
| DifferentialExpressionAnalysisController |
A controller to run differential expression analysis either locally or in a space.
|
| DifferentialExpressionAnalysisDao |
|
| DifferentialExpressionAnalysisEvent |
Indicates the experiment was the subject of a differential expression analysis.
|
| DifferentialExpressionAnalysisHelperService |
Service methods to do database-related work for differential expression analysis
|
| DifferentialExpressionAnalysisHelperServiceImpl |
Transactional methods for dealing with differential expression analyses.
|
| DifferentialExpressionAnalysisRemoveTaskCommand |
Specialized command object for removing analysis results.
|
| DifferentialExpressionAnalysisResult |
Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one
factor.
|
| DifferentialExpressionAnalysisResult.Factory |
|
| DifferentialExpressionAnalysisResultComparator |
|
| DifferentialExpressionAnalysisResultComparator.Factory |
|
| DifferentialExpressionAnalysisResultSetValueObject |
|
| DifferentialExpressionAnalysisResultSetVisualizationValueObject |
This class contains data for a column in metaheatmap visualization.
|
| DifferentialExpressionAnalysisResultValueObject |
|
| DifferentialExpressionAnalysisService |
|
| DifferentialExpressionAnalysisServiceImpl |
|
| DifferentialExpressionAnalysisTask |
|
| DifferentialExpressionAnalysisTaskCommand |
A command object to be used by spaces.
|
| DifferentialExpressionAnalysisTaskImpl |
A differential expression analysis spaces task
|
| DifferentialExpressionAnalysisUtil |
A helper class for the differential expression analyzers.
|
| DifferentialExpressionAnalysisValueObject |
Summary of a differential expression analysis
|
| DifferentialExpressionAnalyzerInfo |
Used to carry information about the experimental design analysis settings to clients.
|
| DifferentialExpressionAnalyzerService |
|
| DifferentialExpressionAnalyzerServiceImpl |
Differential expression service to run the differential expression analysis (and persist the results using the
appropriate data access objects).
|
| DifferentialExpressionAnalyzerServiceImpl.AnalysisType |
Defines the different types of analyses our linear modeling framework supports:
GENERICLM - generic linear regression (interactions are omitted, but this could change)
OSTTEST - one sample t-test
OWA - one-way ANOVA
TTEST - two sample t-test
TWO_WAY_ANOVA_WITH_INTERACTION
TWO_WAY_ANOVA_NO_INTERACTION
|
| DifferentialExpressionEvidence |
Deprecated. |
| DifferentialExpressionEvidence.Factory |
|
| DifferentialExpressionEvidenceDao |
|
| DifferentialExpressionEvidenceDaoImpl |
|
| DifferentialExpressionFileUtils |
|
| DifferentialExpressionGenesConditionsValueObject |
Represents a complete set of data for a differential expression query over a set of genes x conditions (resultSets x
contrasts).
|
| DifferentialExpressionMetaAnalysisValueObject |
A value object with meta analysis results.
|
| DifferentialExpressionProbeResultEndpoint |
Allows access to the differential expression analysis.
|
| DifferentialExpressionResultCache |
Cache for differential expression results.
|
| DifferentialExpressionResultCacheImpl |
Cache for data from differential expression result queries.
|
| DifferentialExpressionResultDao |
|
| DifferentialExpressionResultDaoImpl |
This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of
working with DifferentialExpressionResults).
|
| DifferentialExpressionResultService |
Main entry point to retrieve differential expression data.
|
| DifferentialExpressionResultServiceImpl |
|
| DifferentialExpressionSearchController |
A controller used to get differential expression analysis and meta analysis results.
|
| DifferentialExpressionSearchTask |
Created with IntelliJ IDEA.
|
| DifferentialExpressionSearchTaskCommand |
Created with IntelliJ IDEA.
|
| DifferentialExpressionSearchTaskImpl |
Encapsulates the search for differential expression results, for a set of genes and experiments (which can be
grouped)
|
| DifferentialExpressionSuitabilityEvent |
Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.
|
| DifferentialExpressionValueObject |
Represents the results for one probe.
|
| DiffExAnalyzer |
|
| DiffExMetaAnalyzerController |
A controller to analyze result sets either locally or in a space.
|
| DiffExMetaAnalyzerService |
Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially
store the results.
|
| DiffExMetaAnalyzerServiceImpl |
|
| DiffExMetaAnalyzerTask |
|
| DiffExMetaAnalyzerTaskCommand |
A command object to be used by spaces.
|
| DiffExMetaAnalyzerTaskImpl |
A differential expression meta-analysis space task
|
| DiffExpressionEvidenceValueObject |
|
| DiffExpressionSearchCommand |
|
| DiffExpressionSelectedFactorCommand |
A command object with a selected factor and associated experiment.
|
| DiffExprGeneSearchResult |
Value object for differential expression result for one result - corresponds to the
DifferentialExpressionAnalysisResults for one gene in one ResultSet (combined for multiple probes), but represents
only the "selected" analysisResult.
|
| DiffExResultSetSummaryValueObject |
Summary of a result set.
|
| Direction |
Represents the direction of a change e.g.
|
| DirectionConverter |
DWR converter for Direction type.
|
| DoesNotNeedAttentionEvent |
An event that occurs when a curator has validated the entity and indicated that it is "approved".
|
| DoublePointConverter |
The 8 decimal precision of a double is just a waste of bandwidth in most cases.
|
| DoubleVectorValueObject |
Simple wrapper for a double[] that is derived from a DesignElementDataVector.
|
| DummyMailSender |
Mock mail sender for testing.
|
| DumpsValueObject |
|
| EhCache24Metrics |
Metrics for Ehcache 2.4 series.
|
| Eigenvalue |
|
| Eigenvalue.Factory |
|
| Eigenvector |
A right singular vector (a.k.a.
|
| Eigenvector.Factory |
|
| EmailNotificationContext |
author: anton date: 10/02/13
|
| EmptyController |
This exists just to have an easy way to trick web pages into importing DWR-defined classes that are not in dwrServices.js.
|
| EmptyExpressionMatrix |
Used to make a 'dummy matrix' that has the column information populated.
|
| Ensembl2NcbiValueObject |
Value object that represents a file record line from BioMart as configured with query parameters.
|
| EntityArgService<T extends Identifiable,S extends FilteringService<T>> |
|
| EntityDelegator |
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.
|
| EntityNotFoundException |
Deprecated. |
| EntityNotFoundException |
|
| EntityNotFoundException |
Signals that an entity was not found in the system.
|
| EntityNotFoundExceptionMapper |
Deprecated. |
| EntityUtils |
|
| ESearchException |
|
| ESearchXMLParser |
|
| EutilFetch |
|
| EutilFetch.Mode |
|
| EvidenceFilter |
Used to filter values received depending on taxon and privacy chosen
|
| EvidenceImporterAbstractCLI |
Deprecated. |
| EvidenceImporterCLI |
Class used to load evidence into Phenocarta.
|
| EvidenceSecurityValueObject |
|
| EvidenceSourceValueObject |
|
| EvidenceValueObject<E extends PhenotypeAssociation> |
Parent class of all evidence value objects
|
| ExceptionMapperUtils |
|
| ExceptionTag |
|
| ExcludeArg<T> |
|
| ExecutingTask |
Task Lifecycle Hooks ProgressUpdateAppender -
|
| ExecutingTask.TaskLifecycleHandler |
|
| ExperimentalDesign |
|
| ExperimentalDesign.Factory |
|
| ExperimentalDesignController |
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.
|
| ExperimentalDesignControllerImpl |
Main entry point to editing and viewing experimental designs.
|
| ExperimentalDesignDao |
|
| ExperimentalDesignDaoImpl |
|
| ExperimentalDesignImportCli |
|
| ExperimentalDesignImporter |
Parse a description of ExperimentalFactors from a file, and associate it with a given ExpressionExperiment.
|
| ExperimentalDesignImporterImpl |
See interface for docs.
|
| ExperimentalDesignService |
|
| ExperimentalDesignServiceImpl |
Spring Service base class for ubic.gemma.model.expression.experiment.ExperimentalDesignService, provides
access to all services and entities referenced by this service.
|
| ExperimentalDesignUpdatedEvent |
Describes an event that involved a change of assignment of factor value to bio material, or other changes in the
experimental design.
|
| ExperimentalDesignUtils |
|
| ExperimentalDesignViewCli |
|
| ExperimentalDesignVisualizationService |
|
| ExperimentalDesignVisualizationServiceImpl |
Tools for visualizing experimental designs.
|
| ExperimentalDesignWriter |
|
| ExperimentalDesignWriterCLI |
Writes out the experimental design for a given experiment.
|
| ExperimentalEvidence |
Deprecated. |
| ExperimentalEvidence.Factory |
|
| ExperimentalEvidenceDao |
|
| ExperimentalEvidenceDaoImpl |
|
| ExperimentalEvidenceValueObject |
|
| ExperimentalFactor |
ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
|
| ExperimentalFactor.Factory |
|
| ExperimentalFactorDao |
|
| ExperimentalFactorDaoImpl |
|
| ExperimentalFactorService |
|
| ExperimentalFactorServiceImpl |
|
| ExperimentalFactorValueObject |
|
| ExperimentAnnotationEndpoint |
Expression Experiments in Gemma contain annotations.
|
| ExperimentCoexpressionLink |
Represents coexpression at the level of experiment, referinng to links stored as Gene2GeneCoexpression.
|
| ExperimentDEDVEndpoint |
Allows access to all the Design Element Data Vectors (DEDV's) for a given Expression Experiment.
|
| ExperimentExpressionLevelsValueObject |
|
| ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject |
|
| ExperimentExpressionLevelsValueObject.VectorElementValueObject |
|
| ExperimentIDbyTaxonEndpoint |
Given a Taxon (eg.
|
| ExperimentIdEndpoint |
Given the short name of an Expression Experiment, will return the matching Expression Experiment ID
|
| ExperimentNameEndpoint |
Used for getting the Short Name given an Expression Experiment ID eg: 793 --> GSE10470
|
| ExperimentNumSamplesEndpoint |
Used for determining the number of samples (biomaterials) associated with a given expression experiment
|
| ExperimentPlatformSwitchHelperService |
Use to finish final transactional step in updating platform
|
| ExperimentPlatformSwitchHelperServiceImpl |
|
| ExperimentQCTag |
|
| ExperimentSetListContainer |
|
| ExpLevelConsolidationArg |
Class representing an API argument that should be one of the expression level consolidation options.
|
| ExpressionAnalysis |
An analysis of one or more ExpressionExperiments
|
| ExpressionAnalysisResultSet |
A group of results for an ExpressionExperiment.
|
| ExpressionAnalysisResultSet.Factory |
|
| ExpressionAnalysisResultSetArg |
Represents an expression analysis result set identifier.
|
| ExpressionAnalysisResultSetArgService |
|
| ExpressionAnalysisResultSetDao |
|
| ExpressionAnalysisResultSetDaoImpl |
|
| ExpressionAnalysisResultSetFileService |
|
| ExpressionAnalysisResultSetFileServiceImpl |
|
| ExpressionAnalysisResultSetService |
|
| ExpressionAnalysisResultSetServiceImpl |
|
| ExpressionDataBooleanMatrix |
Matrix of booleans mapped from an ExpressionExperiment.
|
| ExpressionDataCorrMatCli |
Create correlation visualizations for expression experiments
|
| ExpressionDataDoubleMatrix |
A data structure that holds a reference to the data for a given expression experiment.
|
| ExpressionDataDoubleMatrixUtil |
Perform various computations on ExpressionDataMatrices (usually in-place).
|
| ExpressionDataFileService |
|
| ExpressionDataFileServiceImpl |
Supports the creation and location of 'flat file' versions of data in the system, for download by users.
|
| ExpressionDataFileUploadController |
Replaces SimpleExpressionExperimentLoadController
|
| ExpressionDataIntegerMatrix |
Warning, not fully tested.
|
| ExpressionDataMatrix<T> |
Represents a matrix of data from an expression experiment.
|
| ExpressionDataMatrixBuilder |
Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the
processed data, preferred data, background, etc.
|
| ExpressionDataMatrixColumnSort |
Methods to organize ExpressionDataMatrices by column (or at least provide the ordering).
|
| ExpressionDataMatrixRowElement |
Encapsulates information about the row 'label' for a ExpressionDataMatrix.
|
| ExpressionDataMatrixService |
Tools for easily getting data matrices for analysis in a consistent way.
|
| ExpressionDataMatrixServiceImpl |
Tools for easily getting data matrices for analysis in a consistent way.
|
| ExpressionDataMatrixWriterCLI |
Prints preferred data matrix to a file.
|
| ExpressionDataStringMatrix |
|
| ExpressionDataSVD |
Perform SVD on an expression data matrix, E = U S V'.
|
| ExpressionDataWriterUtils |
|
| ExpressionExperiment |
|
| ExpressionExperiment.Factory |
|
| ExpressionExperimentAnalysisEvent |
An event involving an ExpressionExperiment
|
| ExpressionExperimentBatchCorrectionService |
|
| ExpressionExperimentBatchCorrectionServiceImpl |
Methods for correcting batch effects.
|
| ExpressionExperimentBibRefFinder |
|
| ExpressionExperimentController |
|
| ExpressionExperimentDao |
Created by tesarst on 13/03/17.
|
| ExpressionExperimentDaoImpl |
|
| ExpressionExperimentDataFetchCommand |
|
| ExpressionExperimentDataFetchController |
For the download of data files from the browser.
|
| ExpressionExperimentDataFileGeneratorCli |
|
| ExpressionExperimentDetailsValueObject |
|
| ExpressionExperimentEditValueObject |
|
| ExpressionExperimentExperimentalFactorValueObject |
|
| ExpressionExperimentFilter |
Methods to handle filtering expression experiments for analysis.
|
| ExpressionExperimentFormController |
Handle editing of expression experiments.
|
| ExpressionExperimentLoadController |
Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
|
| ExpressionExperimentLoadTask |
|
| ExpressionExperimentLoadTaskCommand |
|
| ExpressionExperimentLoadTaskImpl |
|
| ExpressionExperimentManipulatingCLI |
Base class for CLIs that needs one or more expression experiment as an input.
|
| ExpressionExperimentMetaFileType |
|
| ExpressionExperimentPlatformSwitchCli |
Switch the array design used to the merged one.
|
| ExpressionExperimentPlatformSwitchEvent |
The event that this expressionexperiment has had its array design switched (typically to a 'merged' one.
|
| ExpressionExperimentPlatformSwitchService |
Switch an expression experiment from one array design to another.
|
| ExpressionExperimentPrePersistService |
Sets up the array designs before saving an experiment.
|
| ExpressionExperimentPrePersistServiceImpl |
Sets up the array designs, put the designelements in the data vectors.
|
| ExpressionExperimentPrimaryPubCli |
Update the primary publication for experiments.
|
| ExpressionExperimentQCController |
|
| ExpressionExperimentQCUtils |
Helper functions for checking existence etc.
|
| ExpressionExperimentReportGenerationController |
|
| ExpressionExperimentReportService |
Methods for reading and creating reports on ExpressinExperiments.
|
| ExpressionExperimentReportServiceImpl |
Handles creation, serialization and/or marshaling of reports about expression experiments.
|
| ExpressionExperimentReportTask |
Handles delegation of report generation (to the space, or run locally)
|
| ExpressionExperimentReportTaskCommand |
|
| ExpressionExperimentReportTaskImpl |
|
| ExpressionExperimentSearchService |
|
| ExpressionExperimentSearchServiceImpl |
Handles searching for experiments and experiment sets
|
| ExpressionExperimentService |
|
| ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm |
|
| ExpressionExperimentServiceImpl |
|
| ExpressionExperimentSet |
A grouping of expression studies.
|
| ExpressionExperimentSet.Factory |
|
| ExpressionExperimentSetController |
For fetching and manipulating ExpressionExperimentSets.
|
| ExpressionExperimentSetDao |
|
| ExpressionExperimentSetDaoImpl |
|
| ExpressionExperimentSetIDsEndpoint |
A service to return the full list of Expression Experiment Set IDs along with the corresponding name and experiment
ids it contains.
|
| ExpressionExperimentSetService |
|
| ExpressionExperimentSetServiceImpl |
Spring Service base class for ubic.gemma.model.analysis.expression.ExpressionExperimentSetService,
provides access to all services and entities referenced by this service.
|
| ExpressionExperimentSetValueObject |
|
| ExpressionExperimentSetValueObjectHelper |
|
| ExpressionExperimentSetValueObjectHelperImpl |
This class will handle population of ExpressionExperimentSetValueObjects.
|
| ExpressionExperimentSubSet |
A subset of samples from an ExpressionExperiment
|
| ExpressionExperimentSubSet.Factory |
|
| ExpressionExperimentSubSetDao |
|
| ExpressionExperimentSubSetDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.
|
| ExpressionExperimentSubSetService |
|
| ExpressionExperimentSubSetServiceImpl |
|
| ExpressionExperimentSubsetValueObject |
|
| ExpressionExperimentUploadResponse |
|
| ExpressionExperimentValueObject |
|
| ExpressionExperimentVectorManipulatingService |
|
| ExpressionExperimentVectorMergeEvent |
Indicates that the "Vector merging" has been done on the associated experiment.
|
| ExpressionExperimentVisualizationCommand |
Expression experiment command object that wraps expression experiment visualization preferences.
|
| ExpressionPersister |
|
| ExpressionProfileDataObject |
A lightweight object to hold expression data for a single probe.
|
| ExternalDatabase |
|
| ExternalDatabase.Factory |
|
| ExternalDatabaseAdderCli |
Add a new external database, but requires editing the code to do so.
|
| ExternalDatabaseDao |
|
| ExternalDatabaseDaoImpl |
|
| ExternalDatabaseEvidenceImporterAbstractCLI |
Deprecated. |
| ExternalDatabases |
|
| ExternalDatabaseService |
|
| ExternalDatabaseServiceImpl |
|
| ExternalDatabaseStatisticsValueObject |
|
| ExternalDatabaseUpdaterCli |
|
| ExternalDatabaseUtils |
Provides convenience methods to provide ExternalDatabases and DatabaseEntries for common cases, such as Genbank.
|
| ExternalDatabaseValueObject |
|
| ExternalFileGeneLoaderCLI |
CLI for loading genes from a non NCBI files.
|
| ExternalFileGeneLoaderService |
|
| ExternalFileGeneLoaderServiceImpl |
Class to provide functionality to load genes from a tab delimited file.
|
| FactorAssociatedAnalysisResultSet<R extends AnalysisResult> |
|
| FactorProfile |
Represents data for displaying a factor (+ factor values) in a chart.
|
| FactorType |
|
| FactorValue |
The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
|
| FactorValue.Factory |
|
| FactorValueArg<A> |
Represents an API arguments that maps to a FactorValue by its ID or name. |
| FactorValueArrayArg |
|
| FactorValueBasicValueObject |
Each factorvalue can be associated with multiple characteristics (or with a measurement).
|
| FactorValueComparator |
|
| FactorValueDao |
|
| FactorValueDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.experiment.FactorValue.
|
| FactorValueDeletion |
This interface needed to be extracted for factor value deletions in
order to be able to make the methods transactional
|
| FactorValueDeletionImpl |
Handles deletions of a factor values.
|
| FactorValueIdArg |
|
| FactorValueService |
|
| FactorValueServiceImpl |
Spring Service base class for FactorValueService, provides access
to all services and entities referenced by this service.
|
| FactorValueValueArg |
Deprecated. |
| FactorValueValueObject |
Deprecated.
|
| FactorValueVector |
|
| FailedBatchInformationFetchingEvent |
Indicates that the attempt to get batch information failed due to an error.
|
| FailedBatchInformationMissingEvent |
Use to indicate that the batch information has been successfully looked for, but is not available, so we shouldn't
look again.
|
| FailedDataReplacedEvent |
Represents a failed data replace.
|
| FailedDifferentialExpressionAnalysisEvent |
|
| FailedLinkAnalysisEvent |
|
| FailedMeanVarianceUpdateEvent |
|
| FailedMissingValueAnalysisEvent |
|
| FailedMultipartHttpServletRequest |
Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
|
| FailedPCAAnalysisEvent |
|
| FailedProcessedVectorComputationEvent |
|
| FailedSampleCorrelationAnalysisEvent |
|
| FailedToComputeSingularValueDecomposition |
|
| FastaCmd |
Interface representing a class that can retrieve sequences from Blast databases.
|
| FastaParser |
FASTA sequence file parser.
|
| FASTQHeadersPresentButNotUsableException |
Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.
|
| FeedReader |
|
| Fetcher |
Interface for classes that can fetch files from a remote location and copy them to a specified location.
|
| FileFormatException |
Use to indicate a file format error.
|
| FileService<T> |
Interface for a service that serialize entities.
|
| FileUpload |
Command class to handle uploading of a file
|
| FileUploadController |
Controller class to upload Files.
|
| FileUploadUtil |
Utility methods for uploading files.
|
| Filter |
Holds the necessary information to filter an entity with a property, operator and right-hand side value.
|
| Filter.Operator |
|
| FilterArg<O extends Identifiable> |
Represent a filter argument designed to generate a Filters from user input. |
| FilterArg.Filter |
Represents the internal value of a FilterArg. |
| FilterArgBaseListener |
This class provides an empty implementation of FilterArgListener,
which can be extended to create a listener which only needs to handle a subset
of the available methods. |
| FilterArgLexer |
|
| FilterArgListener |
This interface defines a complete listener for a parse tree produced by
FilterArgParser. |
| FilterArgParser |
|
| FilterArgParser.ClauseContext |
|
| FilterArgParser.CollectionContext |
|
| FilterArgParser.CollectionOperatorContext |
|
| FilterArgParser.DisjunctionContext |
|
| FilterArgParser.FilterContext |
|
| FilterArgParser.OperatorContext |
|
| FilterArgParser.ScalarContext |
|
| FilterArgParser.SubClauseContext |
|
| FilterConfig |
Holds settings for filtering.
|
| FilterCriteriaUtils |
|
| FilteredAndPaginatedResponseDataObject<T> |
|
| FilteredResponseDataObject<T> |
|
| FilteringDao<O extends Identifiable> |
Interface for filtering-capable DAO.
|
| FilteringException |
|
| FilteringService<O extends Identifiable> |
Interface for filtering-capable services.
|
| FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Interface for VO-enabled DAO with filtering capabilities.
|
| FilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Interface VO-enabled service with filtering capabilities.
|
| FilterQueryUtils |
|
| Filters |
Represents a conjunction of disjunctions of Filter. |
| FiltersUtils |
|
| FreeTextExpressionExperimentResultsValueObject |
|
| FreeTextGeneResultsValueObject |
*
|
| FtpArchiveFetcher |
Fetcher that can fetch archives (e.g., tar.gz) and unpack them.
|
| FtpFetcher |
Download files by FTP.
|
| Geeq |
Represents quality information about a data set.
|
| GeeqAdminValueObject |
Represents administrative geeq information.
|
| GeeqCli |
Generate or update GEEQ scores
|
| GeeqDao |
|
| GeeqDaoImpl |
|
| GeeqEvent |
|
| GeeqService |
|
| GeeqService.ScoreMode |
Modes for filling GEEQ scores.
|
| GeeqServiceImpl |
|
| GeeqValueObject |
Represents publicly available geeq information
|
| GemmaClassicHomePageController |
Deprecated. |
| GemmaCLI |
Generic command line for Gemma.
|
| GemmaCLI.CommandGroup |
|
| GemmaOntologyService |
Ontology created for Gemma.
|
| GemmaSessionBackedValueObject |
|
| GemmaWebOnly |
Indicate that a property is exclusively used for Gemma Web.
|
| Gene |
Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
|
| Gene.Factory |
|
| Gene2CsStatus |
Used to store information about what happened when the GENE2CS table was updated.
|
| Gene2GeneAssociation |
Entity representing a relationship between two genes.
|
| Gene2GeneCoexpression |
Represents coexpression of a pair of genes.
|
| Gene2GeneIdAssociation |
Entity representing a relationship between two genes identified by ID, rather than by the Gene entity (for efficiency
reasons).
|
| Gene2GOAssociation |
|
| Gene2GOAssociation.Factory |
|
| Gene2GOAssociationDao |
|
| Gene2GOAssociationDaoImpl |
|
| Gene2GOAssociationService |
|
| Gene2GOAssociationServiceImpl |
|
| Gene2GOdescriptionEndpoint |
Given a collection of Gene ID, will return a collection of Gene Ontology IDs (ie.
|
| Gene2GoTermEndpoint |
Given a collection of Gene IDs, will return a collection of Gene Ontology URIs for each gene.
|
| Gene2OntologyEntryAssociation |
|
| Gene2OntologyEntryAssociationImpl |
|
| 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.
|
| GeneAlias |
|
| GeneAlias.Factory |
|
| GeneAliasDao |
|
| GeneAliasDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.gene.GeneAlias.
|
| GeneAnyIdArg<T> |
Base class for GeneArg representing any of the identifiers of a Gene.
|
| GeneArg<T> |
Mutable argument type base class for Gene API.
|
| GeneArgService |
|
| GeneArrayArg |
|
| GeneByNCBIIdEndpoint |
Given an NCBI ID, will return the matching Gemma gene id.
|
| GeneCoexpressedGenes |
Important: this is slightly misnamed, since it potentially includes links that have support of zero.
|
| GeneCoexpressionEndpoint |
Allows access to the gene co-expression analysis.
|
| GeneCoexpressionNodeDegree |
Represents the coexpression node degree for a gene summarized across experiments, at each level of support.
|
| GeneCoexpressionNodeDegree.Factory |
|
| GeneCoexpressionNodeDegreeValueObject |
Represents a GeneCoexpressionNodeDegree
|
| GeneCoexpressionSearchEndpoint |
|
| GeneCoexpressionSearchService |
Provides access to Gene2Gene links.
|
| GeneCoexpressionSearchServiceImpl |
|
| GeneCoexpressionTestedIn |
Tracks the datasets in which coexpression for a gene has been tested.
|
| GeneController |
|
| GeneCoreService |
core service for Gene
|
| GeneDao |
|
| GeneDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Gene.
|
| GeneDetailsByGeneIDEndpoint |
Given a collection of Gemma gene IDs, will return the matching NCBI Ids.
|
| GeneDifferentialExpressionMetaAnalysis |
Represents an analysis that combines the results of other analyses of differential expression.
|
| GeneDifferentialExpressionMetaAnalysis.Factory |
|
| GeneDifferentialExpressionMetaAnalysisDetailValueObject |
|
| GeneDifferentialExpressionMetaAnalysisResult |
|
| GeneDifferentialExpressionMetaAnalysisResult.Factory |
|
| GeneDifferentialExpressionMetaAnalysisResultValueObject |
|
| GeneDifferentialExpressionMetaAnalysisSummaryValueObject |
|
| GeneDifferentialExpressionService |
|
| GeneDifferentialExpressionServiceImpl |
|
| GeneDiffExMetaAnalysisDao |
|
| GeneDiffExMetaAnalysisDaoImpl |
|
| GeneDiffExMetaAnalysisHelperService |
|
| GeneDiffExMetaAnalysisHelperServiceImpl |
* @author frances
|
| GeneDiffExMetaAnalysisService |
|
| GeneDiffExMetaAnalysisServiceImpl |
|
| GeneEnsemblIdArg |
Long argument type for Gene API, referencing the Gene Ensembl ID.
|
| GeneEvidenceValueObject |
Deprecated. |
| GeneExpressionProfile |
Expression data for one probe; designed for conveying small amounts of data to clients.
|
| GeneIDbyTaxonEndpoint |
Given the Taxon (eg.
|
| GeneIdEndpoint |
Given the official symbol and taxon of a gene, will return the matching gene ID.
|
| GeneMappingSummary |
This is a convenience value object to hold a BlatResult and its associated gene products and genes.
|
| GeneMultifunctionalityPopulationService |
Populate/update the gene multifunctionality information in the system.
|
| GeneMultifunctionalityPopulationServiceImpl |
Compute gene multifunctionality and store it in the database.
|
| GeneNameEndpoint |
Given a gene ID, will return the matching gene official symbol eg) 938103--> Grin1
|
| GeneNcbiIdArg |
Long argument type for Gene API, referencing the Gene NCBI ID.
|
| GeneOntologyService |
|
| GeneOntologyServiceImpl |
Holds a complete copy of the GeneOntology.
|
| GeneOntologyServiceImpl.GOAspect |
|
| GeneOntologyTermValueObject |
|
| 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.
|
| GenePickerController |
For 'live searches' from the web interface.
|
| GeneProduct |
|
| GeneProduct.Factory |
|
| GeneProductDao |
|
| GeneProductDaoImpl |
|
| GeneProductService |
|
| GeneProductServiceImpl |
|
| GeneProductValueObject |
|
| 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.
|
| GeneralSearchController.SearchResultValueObject<T extends IdentifiableValueObject<?>> |
|
| 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.
|
| GeneralType |
|
| GenericCuratableDao |
Service that simplifies operation with curatable entities of unknown types.
|
| GenericCuratableDaoImpl |
|
| GenericEvidence |
Deprecated. |
| GenericEvidence.Factory |
|
| GenericEvidenceDao |
|
| GenericEvidenceDaoImpl |
|
| GenericEvidenceValueObject |
|
| GenericExperiment |
Deprecated. |
| GenericExperiment.Factory |
|
| GenericExperimentDao |
|
| GenericExperimentDaoImpl |
|
| GenericGenelistDesignGenerator |
Create (or update) an array design based on the current set of transcripts for a taxon.
|
| GenericMeterRegistryConfigurer |
Attach all the given MeterBinder to the registry.
|
| GenericScanFileDateExtractor |
Looks through text file looking for a date near the top of the file in a reasonable format.
|
| GenericStreamConsumer |
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
|
| GenericValueObjectConverter<O extends Identifiable,VO extends IdentifiableValueObject<?>> |
Generic value object converter.
|
| GeneSearchService |
Service for searching genes (and gene sets)
|
| GeneSearchServiceImpl |
Service for searching genes (and gene sets)
|
| GeneService |
|
| GeneServiceImpl |
|
| GeneSet |
A grouping of genes that share a common relationship
|
| GeneSet.Factory |
|
| GeneSetController |
Exposes GeneSetServices methods over ajax.
|
| GeneSetDao |
The interface for managing groupings of genes.
|
| GeneSetDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.gene.GeneSet.
|
| GeneSetListContainer |
|
| GeneSetMember |
|
| GeneSetMember.Factory |
|
| GeneSetMemberDaoImpl |
|
| GeneSetSearch |
|
| GeneSetSearchImpl |
|
| GeneSetService |
Service for managing gene sets
|
| GeneSetServiceImpl |
Service for managing gene sets
|
| GeneSetValueObject |
Represents a Gene group gene set
|
| GeneSetValueObjectHelper |
* @author tvrossum
|
| GeneSetValueObjectHelperImpl |
This class will handle population of GeneSetValueObjects.
|
| GeneSymbolArg |
String argument type for Gene API.
|
| GeneSymbolComparator |
|
| GeneTestedInCache |
Cache of the 'tested-in' information for genes.
|
| GeneTestedInCacheImpl |
|
| GeneValueObject |
|
| GeneWebService |
RESTful interface for genes.
|
| GenomePersister |
|
| GeoBrowser |
Gets records from GEO and compares them to Gemma.
|
| GeoBrowserService |
|
| GeoBrowserServiceImpl |
This is marked as Lazy since we don't use it outside Gemma Web, so it won't be loaded unless it's needed. |
| GeoChannel |
Represents data for one channel on a microarray in GEO.
|
| GeoChannel.ChannelMolecule |
|
| GeoConstants |
Constants used to help decipher GEO data files.
|
| GeoContact |
|
| GeoConverter |
|
| GeoConverterImpl |
Convert GEO domain objects into Gemma objects.
|
| GeoData |
Abstract class from which other GEO objects are descended.
|
| GeoDataset |
A GEO-curated dataset.
|
| GeoDataset.ExperimentType |
|
| GeoDataset.PlatformType |
|
| GeoDataset.SampleType |
|
| GeoDataset.ValueType |
|
| GeoDomainObjectGenerator |
Handle fetching and parsing GEO files.
|
| GeoDomainObjectGeneratorLocal |
GEO object generator that works on local files.
|
| GeoException |
|
| GeoFamilyParser |
Class for parsing GSE and GDS files from NCBI GEO.
|
| GeoFetcher |
|
| GeoGrabberCli |
Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further
screening.
|
| GeoParseResult |
This simply holds the results obtained from parsing.
|
| GeoPlatform |
Bean describing a microarray platform in GEO
|
| GeoRecord |
Used to contain GEO summary information from the 'Browse' views.
|
| GeoRecordBrowserController |
|
| GeoReplication |
Represents a group of samples that were replicated.
|
| GeoReplication.ReplicationType |
Permitted types of replication.
|
| GeoSample |
Represents a sample (GSM) in GEO.
|
| GeoSample.LibraryStrategy |
|
| GeoSampleCorrespondence |
Holds information about GEO samples that "go together" across datasets (GDS), because they came from the same sample
(or so we infer)
|
| GeoSeries |
Represents a set of GEO samples that were submitted together.
|
| GeoSeries.SeriesType |
|
| GeoService |
|
| GeoServiceImpl |
Non-interactive fetching, processing and persisting of GEO data.
|
| GeoSubset |
Represents a subset of samples.
|
| GeoUtil |
|
| GeoValues |
Class to store the expression data prior to conversion.
|
| GeoVariable |
A GeoVariable represents variables which were investigated.
|
| GeoVariable.VariableType |
Permitted descriptions of terms.
|
| getOntologyTermFormatter |
|
| GOEvidenceCode |
This enumeration was originally based on GO, but is used for all entities that have evidenciary aspects; Thus it has
been expanded to include: Terms from RGD (rat genome database)
IED = Inferred from experimental data
IAGP = Inferred from association of genotype and phenotype
IPM = Inferred from phenotype manipulation
QTM = Quantitative Trait Measurement
And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have
computed
See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
|
| GOEvidenceCodeConverter |
|
| GOGroupValueObject |
|
| GoldenPath |
Perform useful queries against GoldenPath (UCSC) databases.
|
| GoldenPathQuery |
|
| GoldenPathSequenceAnalysis |
Using the Goldenpath databases for comparing sequence alignments to gene locations.
|
| GoMetric |
|
| GoMetric.Metric |
|
| GoMetricImpl |
|
| GoogleAnalytics4Provider |
Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API. |
| 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.
|
| GroupAuthority |
Authority for groups (kind of like a "user role", but for group-based authorization)
|
| GroupAuthority.Factory |
|
| GroupAuthorityImpl |
|
| GwasDatabaseImporterCli |
Deprecated. |
| GZIP |
Used to annotate endpoints that will have their payload compressed with GZIPOutputStream
unconditionally. |
| GzipHeaderDecorator |
Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP. |
| H2Dialect |
|
| Hibernate4Metrics |
Metrics for Hibernate 4.
|
| Hibernate4QueryMetrics |
Query metrics for Hibernate 4.
|
| HibernateMonitor |
|
| HibernateMonitorImpl |
Monitoring of Hibernate status.
|
| HibernateSearchException |
|
| HibernateSearchSource |
Search source based on Hibernate Search.
|
| Highlighter |
Custom highlighter for search results.
|
| HikariCPMetrics |
|
| HitListSize |
The number of probes meeting a given q-value threshold in the result set.
|
| HitListSize.Factory |
|
| HomePageController |
Responsible for display of the Gemma 2.0 home page.
|
| HomologeneFetcher |
Grabs urls like ftp:///ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
|
| HomologeneService |
|
| HomologeneServiceFactory |
|
| HomologeneServiceImpl |
Reads in the homologene list as specified in the Gemmea.properties file.
|
| HttpArchiveFetcherInterface |
Interface for downloading via http files and unarchiving them
|
| HttpFetcher |
A generic class for fetching files via HTTP and writing them to a local file system.
|
| HumanCoexpressionSupportDetailsImpl |
|
| HumanExperimentCoexpressionLinkImpl |
|
| HumanGeneCoExpression |
|
| HumanGeneCoExpression.Factory |
|
| HumanGeneCoExpressionImpl |
|
| IdArray |
Represents a set of IDs for entities (e.g., genes or experiments), stored in a bitSet.
|
| IdArrayValueObject |
|
| Identifiable |
Created by tesarst on 31/05/17.
|
| IdentifiableValueObject<O extends Identifiable> |
Base implementations for value objects representing persistent objects
|
| IgnoreAudit |
Mark a DAO method as ignored for auditing.
|
| IlluminaProbeReader |
Parse an Illumina "manifest.txt" file (tab-delimited).
|
| Image |
allen brain Atlas Image class.
|
| ImageSeries |
Represents the ImageSeries information returned from the AIBS brain atlas
|
| IncludedResultSetInfoValueObject |
|
| IndexController |
|
| IndexerService |
Indexer service.
|
| IndexerServiceImpl |
|
| IndexerTask |
Created with IntelliJ IDEA.
|
| IndexerTaskCommand |
|
| IndexerTaskImpl |
|
| IndexGemmaCLI |
|
| InferredQuantitationMismatchException |
Exception raised when the quantitation of an ExpressionDataMatrix does not agree with the one inferred. |
| InsufficientDataException |
Used to indicate that analysis was skipped, not necessarily an error.
|
| InsufficientProbesException |
|
| InsufficientSamplesException |
|
| Investigation |
An abstract concept of a scientific study
|
| JacksonConfig |
Configure the various beans injected in Swagger's components relating to Jackson's JSON serialization.
|
| JavascriptLogger |
Class to handle saving client-side javascript error messages and warnings to a server-side log.
|
| JobInfo |
|
| JobInfo.Factory |
|
| JsonFileService<T> |
Interface for service that provides JSON serialization.
|
| JsonMappingExceptionMapper |
Mapper that creates a well composed error body response out of a JsonMappingException.
|
| JsonReaderResponse<T> |
Creates a response that can be consumed by an Ext.data.JsonReader.
|
| JSONTableRenderer |
|
| JsonUtil |
Utilities for writing JSON payloads to HttpServletResponse.
|
| JSONView |
|
| Keyword |
|
| Keyword.Factory |
|
| LabelValue |
A simple JavaBean to represent label-value pairs.
|
| LikelyNonPublicGeoRecordException |
|
| LimitArg |
Argument used to represent a limit.
|
| LimitedResponseDataObject<T> |
Represents a payload with a limited number of results.
|
| LinearModelAnalyzer |
Handles fitting linear models with continuous or fixed-level covariates.
|
| LineMapParser<K,T> |
The difference between this class and BasicLineMapParser is more flexibility in how keys are provided.
|
| LineParser<T> |
A Parser that processes its input line-by-line.
|
| LinkAnalysis |
Handles the actual coexpression analysis, once handed data that has been prepared.
|
| LinkAnalysisCli |
Commandline tool to conduct link (coexpression) analysis.
|
| LinkAnalysisConfig |
Holds parameters needed for LinkAnalysis.
|
| LinkAnalysisConfig.NormalizationMethod |
|
| LinkAnalysisConfig.SingularThreshold |
Configures whether only one of the two thresholds should be used.
|
| LinkAnalysisController |
A controller to pre-process expression data vectors.
|
| LinkAnalysisEvent |
Computing coexpression links for an expression experiment
|
| LinkAnalysisPersister |
Handles the persistence phase of a Link analysis.
|
| LinkAnalysisPersisterImpl |
Handles moving gene coexpression links from memory into the database; updates related meta-data.
|
| LinkAnalysisService |
|
| LinkAnalysisServiceImpl |
Running link analyses through the spring context; will persist the results if the configuration says so.
|
| LinkAnalysisTaskCommand |
Command object for Link analysis
|
| LinkAnalysisTaskImpl |
|
| LinkCreator |
Helper class to use for generating the link objects for persistence.
|
| ListBatchCommand |
Encapsulates information needed for generic list browsing.
|
| ListUtils |
Utilities and algorithms for List. |
| LiteratureEvidence |
Deprecated. |
| LiteratureEvidence.Factory |
|
| LiteratureEvidenceDao |
|
| LiteratureEvidenceDaoImpl |
|
| LiteratureEvidenceValueObject |
|
| LoadEvidenceForClassifier |
Retrieve information used for classifying Phenocarta evidence quality.
|
| LoadExpressionDataCli |
Simple command line to load expression experiments, either singly or in batches defined on the command line or in a
file.
|
| LoadSimpleExpressionDataCli |
Command Line tools for loading the expression experiment in flat files
|
| LocalDatasetFetcher |
Used for testing, but might have other uses, to fetch GEO data from local files instead of the GEO website.
|
| LocalFile |
Not a persistent entity
|
| LocalFile.Factory |
|
| LocalSeriesFetcher |
A fetcher that only looks locally for "family" files (GPLXXX_family, GSEXXX_family).
|
| Log4jConfigurer |
|
| LoggingConfigurer |
Simple interface for configuring logging levels.
|
| MailEngine |
|
| MailEngineImpl |
|
| MailUtils |
|
| MailUtilsImpl |
|
| MaintenanceModeController |
Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave
normally.
|
| MakeExperimentPrivateCli |
|
| MakeExperimentsPublicCli |
Make data sets public.
|
| MakePrivateEvent |
|
| MakePublicEvent |
|
| MalformedArgException |
Specialized error for malformed Arg
The recommended HTTP status for this exception is 400 Bad Request. |
| MalformedArgExceptionMapper |
|
| ManualAnnotationEvent |
|
| MatrixRowPairAnalysis |
|
| MatrixWriter |
|
| MeanVarianceRelation |
|
| MeanVarianceRelation.Factory |
|
| MeanVarianceService |
Responsible for returning the coordinates of the experiment's Mean-Variance relationship.
|
| MeanVarianceServiceHelper |
|
| MeanVarianceServiceImpl |
Manage the mean-variance relationship.
|
| MeanVarianceUpdateEvent |
|
| Measurement |
|
| Measurement.Factory |
|
| MeasurementKind |
|
| MeasurementType |
|
| MeasurementValueObject |
|
| MediaTypeUtils |
Utilities for MediaType.
|
| MedicalSubjectHeading |
|
| MedicalSubjectHeading.Factory |
|
| MeshTermFetcherCli |
Deprecated.
|
| MessageUtil |
Provides methods for putting messages to the user in the session.
|
| MessageUtilImpl |
|
| MetaFile |
Wrapper for metadata file information for the frontend
|
| MeterRegistryCliConfigurer |
This configurer adds two tags: environment='cli' and user to the given meter registry.
|
| MeterRegistryEhcacheConfigurer |
Add metrics from each available Ehcache in the given CacheManager to the supplied meter registry. |
| MeterRegistryWebConfigurer |
Configured the environment='web' tag to the provided registry.
|
| MetricsApplicationEventListener |
|
| MinifierPostProcessor |
JAWR postprocessor to remove console.log and debugger breakpoint statements.
|
| MissingResult |
Represents a gene that was not tested.
|
| MissingValueAnalysisEvent |
Computing missing values for an expression experiment
|
| MondoOntologyService |
MONDO ontology.
|
| MonitoredDiskFileItem |
Commons FileItem that uses a MonitoredOutputStream
|
| MonitoredDiskFileItemFactory |
|
| MonitoredOutputStream |
OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
|
| MouseCoexpressionSupportDetailsImpl |
|
| MouseExperimentCoexpressionLinkImpl |
|
| MouseGeneCoExpression |
|
| MouseGeneCoExpression.Factory |
|
| MouseGeneCoExpressionImpl |
|
| Multifunctionality |
|
| Multifunctionality.Factory |
|
| MultifunctionalityCli |
|
| MySQL57InnoDBDialect |
|
| NCBIGene2Accession |
See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
|
| NcbiGene2AccessionParser |
Class to parse the NCBI gene2accession files.
|
| NCBIGene2GOAssociationLoader |
|
| NCBIGene2GOAssociationLoaderCLI |
Load GO -> gene associations from NCBI.
|
| NCBIGene2GOAssociationParser |
This parses GO annotations from NCBI.
|
| NcbiGeneConverter |
Convert NCBIGene2Accession objects into Gemma Gene objects with associated GeneProducts.
|
| NcbiGeneData |
Simple helper data structure that stores an NcbiGeneInfo and its associated
NcbiGene2Accession elements.
|
| NcbiGeneDomainObjectGenerator |
Combines information from the gene2accession and gene_info files from NCBI Gene.
|
| NcbiGeneEnsemblFileParser |
|
| NCBIGeneFileFetcher |
Class to download files for NCBI gene.
|
| NcbiGeneHistory |
Represents the information from the "gene_history" file from NCBI (for one gene's history).
|
| NcbiGeneHistoryParser |
Parse the NCBI "gene_history" file.
|
| NCBIGeneInfo |
See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
|
| NCBIGeneInfo.GeneType |
See http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn unknown (0)
, 36
|
| NCBIGeneInfo.NomenclatureStatus |
|
| NcbiGeneInfoParser |
Class to parse the gene_info file from NCBI Gene.
|
| NcbiGeneLoader |
Load or update information about genes from the NCBI Gene database.
|
| NcbiGeneLoaderCLI |
Command line interface to gene parsing and loading
|
| NCBIUtil |
|
| NeedsAttentionEvent |
Indicates that previous validation is being invalidated
|
| NetDatasourceUtil |
Helper methods to get FTP connection.
|
| NewsItem |
|
| NonPersistentNonOrderedCoexpLink |
Wrapper object used to track and eliminate duplicates.
|
| NonRetainedResult |
Represents a gene that was tested, but the result wasn't significant.
|
| NoRowsLeftAfterFilteringException |
This is a special kind of preprocessing exception that occurs when filtering the expression data matrix result in no
rows left.
|
| NotFoundExceptionMapper |
This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject
entity. |
| NotTroubledStatusFlagEvent |
This event type resets the trouble flag of curation details of a curatable object.
|
| ObjectMapperResolver |
|
| OffsetArg |
Argument used to represent an offset.
|
| OmimDatabaseImporterCli |
Deprecated. |
| OntologyController |
Provide minimal support for exposing Gemma ontology.
|
| OntologySearchSource |
|
| OntologyService |
|
| OntologyServiceFactory<T extends OntologyService> |
|
| OntologyServiceImpl |
Has a static method for finding out which ontologies are loaded into the system and a general purpose find method
that delegates to the many ontology services.
|
| OntologyUtils |
Utilities for working with ontologies.
|
| OpenApiUtils |
Utilities for interacting with OpenAPI at runtime.
|
| OrderVectorsByDesignCli |
Use to change the order of the values to match the experimental design.
|
| OtherCoexpressionSupportDetailsImpl |
|
| OtherExperimentCoexpressionLinkImpl |
|
| OtherGeneCoExpression |
|
| OtherGeneCoExpression.Factory |
|
| OtherGeneCoExpressionImpl |
|
| OutlierAnalysisEvent |
|
| OutlierDetails |
Container for details about a proposed outlier
|
| OutlierDetectionService |
|
| OutlierDetectionServiceImpl |
Methods to (attempt to) detect outliers in data sets.
|
| OutlierFlaggingService |
|
| OutlierFlaggingServiceImpl |
Service for removing sample(s) from an expression experiment.
|
| OutlierFoundAnalysisEvent |
|
| OutliersNotFoundAnalysisEvent |
|
| OutputStreamListener |
|
| PaginatedResponseDataObject<T> |
Represents paginated results with offset and limit.
|
| Parser<T> |
Interface for classes that allow parsing of files and streams.
|
| ParserAndLoaderTools |
Utilities to be used by parsers and loaders.
|
| ParsingStreamConsumer<T> |
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
|
| PatoOntologyService |
|
| PCAAnalysisEvent |
|
| PearsonMetrics |
A correlation analysis for a given data set, designed for selection of values based on criteria set by the user.
|
| PermissionChangeEvent |
Represents a change in permissions
|
| Persister |
Interface defining the ability to create domain objects in bulk or singly.
|
| PersisterHelper |
|
| PersisterHelperImpl |
A service that knows how to persist Gemma-domain objects.
|
| Person |
Deprecated.
|
| PersonDao |
Deprecated.
|
| PersonDaoImpl |
Deprecated.
|
| PhenotypeAssociation |
Deprecated. |
| PhenotypeAssociationConstants |
Deprecated. |
| PhenotypeAssociationDao |
|
| PhenotypeAssociationDaoImpl |
deals with all basic queries used by Neurocarta
|
| PhenotypeAssociationManagerService |
Deprecated. |
| PhenotypeAssociationManagerServiceImpl |
Deprecated. |
| PhenotypeAssociationPublication |
Deprecated. |
| PhenotypeAssociationPublication.Factory |
|
| PhenotypeAssociationService |
|
| PhenotypeAssociationServiceImpl |
Service responsible for low level operations, used by PhenotypeAssociationManagerServiceImpl
|
| PhenotypeAssoManagerServiceHelper |
Deprecated. |
| PhenotypeAssoManagerServiceHelperImpl |
Deprecated. |
| PhenotypeAssoOntologyHelper |
Deprecated. |
| PhenotypeAssoOntologyHelperImpl |
Deprecated. |
| PhenotypeAssPubValueObject |
|
| PhenotypeController |
Controller for phenotype
|
| PhenotypeGroupValueObject |
|
| PhenotypeMappingType |
Deprecated. |
| PhenotypeValueObject |
|
| PhenotypeWebService |
Deprecated. |
| PhysicalLocation |
|
| PhysicalLocation.Factory |
|
| PhysicalLocationValueObject |
A very simple value object to represent a physical location
|
| PlatformArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
|
| PlatformArgService |
|
| PlatformArrayArg |
|
| PlatformFetcher |
Fetch GEO "GPLXXX_family.soft.gz" files
|
| PlatformIdArg |
Long argument type for platform API, referencing the platform ID.
|
| PlatformStringArg |
String argument type for platform API, referencing the Platform short name.
|
| PlatformsWebService |
RESTful interface for platforms.
|
| Pointcuts |
General-purpose pointcuts to recognize CRUD operations etc.
|
| PolymerType |
|
| PreprocessController |
A controller to pre-process expression data (including updating diagnostics)
|
| PreprocessExperimentTask |
A "processed expression data vector create" task
|
| PreprocessingException |
Allows us to catch preprocessing errors and handle them correctly.
|
| PreprocessorService |
Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.
|
| PreprocessorServiceImpl |
|
| PreprocessTaskCommand |
Command object for processing data vectors.
|
| PreprocessTaskImpl |
|
| PrimitiveType |
|
| PrincipalComponentAnalysis |
|
| PrincipalComponentAnalysis.Factory |
|
| PrincipalComponentAnalysisDao |
|
| PrincipalComponentAnalysisDaoImpl |
|
| PrincipalComponentAnalysisService |
|
| PrincipalComponentAnalysisServiceImpl |
|
| Probe2GeneEndpoint |
Used for determining what genes a probe assays for.
|
| ProbeLoading |
Only stored for some of the probes (e.g.
|
| ProbeLoading.Factory |
|
| ProbeMapper |
|
| ProbeMapperConfig |
Holds parameters for how mapping should be done.
|
| ProbeMapperImpl |
Provides methods for mapping sequences to genes and gene products.
|
| ProbeMapUtils |
|
| ProbeSequenceParser |
Parse probes from a tabular file.
|
| ProcessedDataComputeCLI |
Prepare the "processed" expression data vectors, and can also do batch correction.
|
| ProcessedDataVectorCache |
Cache of data vectors
|
| ProcessedDataVectorCacheImpl |
Configures the cache for data vectors.
|
| ProcessedExpressionDataVector |
Represents the processed data that is used for actual analyses.
|
| ProcessedExpressionDataVector.Factory |
|
| ProcessedExpressionDataVectorDao |
|
| ProcessedExpressionDataVectorDao.RankMethod |
|
| ProcessedExpressionDataVectorDaoImpl |
|
| ProcessedExpressionDataVectorService |
|
| ProcessedExpressionDataVectorServiceImpl |
|
| ProcessedVectorComputationEvent |
Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an
Expression Experiment
|
| ProgressData |
|
| ProgressStatusService |
These methods are exposed to front-end.
|
| ProgressStatusServiceImpl |
This class exposes methods for AJAX calls.
|
| ProgressUpdateAppender |
This appender is used by remote tasks to send progress notifications to the webapp.
|
| ProgressUpdateAppender.ProgressUpdateCallback |
Callback used to emit progress updates.
|
| ProgressUpdateAppender.ProgressUpdateContext |
|
| PropertyMapping |
Represents a mapping between a query/criteria property and some original property space.
|
| PropertyMappingUtils |
|
| Protocol |
|
| Protocol.Factory |
|
| ProtocolDao |
|
| ProtocolDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Protocol.
|
| ProtocolService |
|
| ProtocolServiceImpl |
|
| PubMedLoaderCli |
Load PubMed files from XML files -- not used routinely!
|
| 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.
|
| PubMedSearch |
Search PubMed for terms, retrieve document records.
|
| PubMedSearchCommand |
Supports seaching of pubmed references
|
| PubMedSearcher |
Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
|
| PubMedService |
Manage the loading of large numbers of pubmed entries into the database.
|
| PubMedXMLFetcher |
Class that can retrieve pubmed records (in XML format) via HTTP.
|
| PubMedXMLParser |
Simple class to parse XML in the format defined by
ncbi. |
| PvalueDistribution |
|
| PvalueDistribution.Factory |
|
| QuantileNormalizer<R,C> |
Perform quantile normalization on a matrix, as described in:
|
| QuantitationMismatchException |
|
| QuantitationMismatchPreprocessingException |
|
| QuantitationType |
|
| QuantitationType.Factory |
|
| QuantitationTypeArg<T> |
|
| QuantitationTypeArgService |
|
| QuantitationTypeByIdArg |
|
| QuantitationTypeByNameArg |
|
| QuantitationTypeConversionException |
|
| QuantitationTypeDao |
|
| QuantitationTypeDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
QuantitationType. |
| QuantitationTypeParameterGuesser |
Has the unpleasant task of figuring out what the quantitation type should look like, given a description and name
string.
|
| QuantitationTypePropertyEditor |
|
| QuantitationTypeService |
|
| QuantitationTypeServiceImpl |
|
| QuantitationTypeValueObject |
|
| QueriedAndFilteredAndPaginatedResponseDataObject<T> |
|
| QueriedAndFilteredResponseDataObject<T> |
|
| QueuingParser<T> |
Defines a class that produces object that can be consumed by other classes.
|
| RankComputationEvent |
For backwards compatibility only.
|
| RatCoexpressionSupportDetailsImpl |
|
| RatExperimentCoexpressionLinkImpl |
|
| RatGeneCoExpression |
|
| RatGeneCoExpression.Factory |
|
| RatGeneCoExpressionImpl |
|
| RawAndProcessedExpressionDataVectorDao |
|
| RawAndProcessedExpressionDataVectorDaoImpl |
|
| RawAndProcessedExpressionDataVectorService |
|
| RawAndProcessedExpressionDataVectorServiceImpl |
|
| RawDataFetcher |
Retrieve and unpack the raw data files for GEO series.
|
| RawExpressionDataVector |
Data for one design element, across one or more bioassays, for a single quantitation type.
|
| RawExpressionDataVector.Factory |
|
| RawExpressionDataVectorDao |
|
| RawExpressionDataVectorDaoImpl |
|
| RawExpressionDataVectorService |
|
| RawExpressionDataVectorServiceImpl |
Provides methods that can be applied to both RawExpressionDataVector and ProcessedExpressionDataVector
|
| ReCaptcha |
|
| ReCaptchaException |
|
| ReCaptchaResponse |
|
| RecordParser<T> |
Abstract record-based parser.
|
| ReferenceAssociation |
An association between a BioSequence and a GeneProduct based on external database identifiers.
|
| ReferenceAssociation.Factory |
|
| ReferenceAssociationDao |
|
| ReferenceAssociationDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ReferenceAssociation.
|
| RelationshipPersister |
Persist objects like Gene2GOAssociation.
|
| ReleaseDetailsUpdateEvent |
Event triggered when the release details of a Versioned entity are
updated. |
| RepeatScan |
Scan sequences for repeats
|
| ReplaceDataCli |
Replace data in an existing data set.
|
| Reporter |
A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and
reporters, and all analysis would take place at the level of CompositeSequences.
|
| Reporter.Factory |
|
| RequestAttributesBasedClientIdRetrievalStrategy |
|
| RequestExceptionEventListener |
Listen and dispatch ApplicationEvent.
|
| RequestExceptionLogger |
Log request exceptions.
|
| RequestHeaderBasedClientIdRetrievalStrategy |
Strategy that retrieves the client ID in a request header.
|
| RequestUtil |
RequestUtil utility class
|
| ResetSuitabilityForDifferentialExpressionAnalysisEvent |
Used to indicate that the suitability status of an experiment is the default.
|
| Responder |
Handles setting of the response status code and composing a proper payload structure.
|
| Responder.FilterMethod<T> |
A functional interface matching the signature of a paginating service method.
|
| ResponseDataObject<T> |
|
| ResponseErrorObject |
|
| RestapidocsIndexRewriteFilter |
Rewrites the path to the index file.
|
| RestAuthEntryPoint |
Implementation of AuthenticationEntryPoint for the RESTful API to handle authentication.
|
| Retryable |
Indicate that the method should be retried on failure.
|
| RetryLogger |
Provide logging when an operation has failed and is being retried.
|
| RgdDatabaseImporterCli |
Deprecated. |
| RNASeqBatchInfoCli |
Deprecated.
|
| RNASeqDataAddCli |
Designed to add count and/or RPKM data to a data set that has only meta-data.
|
| RootWebService |
Handles calls to the root API url and user info api
|
| RootWebService.ApiInfoValueObject |
|
| RootWebService.UserValueObject |
|
| RowLevelFilter |
|
| RowLevelFilter.Method |
|
| RowMissingValueFilter |
Filter out rows that have "too many" missing values.
|
| RowsWithSequencesFilter |
Remove rows that have no BioSequence associated with the row.
|
| RssFeedController |
|
| SampleCoexpressionAnalysis |
The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator
of all the sample coexpression matrices.
|
| SampleCoexpressionAnalysisService |
|
| SampleCoexpressionAnalysisServiceImpl |
Manage the "sample correlation/coexpression" matrices.
|
| SampleCoexpressionMatrix |
Holds the data of the sample coexpression matrix
|
| SampleCoexpressionRelatedPreprocessingException |
Exception raised in preprocessing when there is a problem with sample coexpression analysis.
|
| SampleCorrelationAnalysisEvent |
|
| SampleRemovalEvent |
Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).
|
| SampleRemovalReversionEvent |
Indicates that samples that were previously removed have been "put back", e.g.
|
| ScaleType |
|
| ScaleTypeConverter |
|
| ScanDateExtractor |
Generic interface for classes that extract scan dates from raw data files.
|
| ScoreValueObject |
|
| SDRFFetcher |
Fetch the SRDF file
|
| SearchException |
Exception raised by the SearchService when the search could not be performed. |
| SearchResult<T extends Identifiable> |
|
| SearchResultDisplayObject |
Object to store search results of different classes in a similar way for displaying to user (ex: enables genes and
gene sets to be entries in the same combo box) object types handled are: Gene, GeneSet, GeneSetValueObject,
ExpressionExperiment and ExpressionExperimentSet SearchObject is also handled if the object it holds is of any of
those types for a gene or experiment, the memberIds field is a collection just containing the object's id.
|
| SearchResultSet<T extends Identifiable> |
This is a special kind of set designed for holding SearchResult. |
| SearchService |
|
| SearchService.SearchResultMap |
|
| SearchServiceImpl |
This service is used for performing searches using free text or exact matches to items in the database.
|
| SearchSettings |
Configuration options for searching.
|
| SearchSettings.SearchMode |
|
| SearchSettingsValueObject |
author: anton date: 18/03/13
|
| SearchSource |
Search source that provides SearchResult from a search engine. |
| SearchWebService |
Provides search capabilities to the RESTful API.
|
| SearchWebService.SearchResultsResponseDataObject |
|
| SearchWebService.SearchResultValueObject<T extends IdentifiableValueObject<?>> |
|
| SecureMethodInvokingJobDetailFactoryBean |
Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
|
| 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.
|
| SecurityControllerImpl |
Manages data-level security (ie.
|
| SecurityInfoValueObject |
Carries extensive security information about an entity.
|
| SequenceBinUtils |
Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a
GoldenPath database.
|
| SequenceManipulation |
Convenient methods for manipulating BioSequences and PhysicalLocations
|
| SequenceSimilaritySearchResult |
|
| SequenceType |
|
| SequenceTypePropertyEditor |
|
| SequenceTypeValueObject |
|
| SequenceWriter |
Tools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.
|
| SeriesFetcher |
|
| ServiceBasedEntityConverter<O extends Identifiable> |
|
| ServiceBasedValueObjectConverter<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Perform conversion to value object by entity, ID and collections of entities and IDs and also to entity by ID and
collection of IDs.
|
| ServletMetricsFilter |
Metrics for servlet requests.
|
| ServletUtils |
|
| SessionBoundExpressionExperimentSetValueObject |
|
| SessionBoundGeneSetValueObject |
|
| SessionListManager |
|
| SessionListManagerImpl |
|
| Settings |
Deprecated.
|
| SettingsConfig |
Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
|
| SfariDatabaseImporterCli |
Deprecated. |
| SFARIIntermediateFileParser |
Deprecated. |
| SFARILineInfo |
Deprecated. |
| ShellDelegatingBlat |
Class to manage the gfServer and run BLAT searches.
|
| ShellDelegatingBlat.BlattableGenome |
|
| ShortBibliographicReferenceTag |
|
| SidValueObject |
|
| SignupController |
Controller to signup new users.
|
| SimpleExpressionDataLoaderService |
Load experiment from a flat file.
|
| SimpleExpressionDataLoaderServiceImpl |
Convert a simple matrix and some meta-data into an ExpressionExperiment.
|
| SimpleExpressionExperimentCommandValidation |
Stores information about the validation status of an attempted expression experiment load.
|
| SimpleExpressionExperimentLoadTaskCommand |
Extends a SimpleExpressionExperimentMetaData with information about the file
|
| SimpleExpressionExperimentMetaData |
Represents the basic data to enter about an expression experiment when starting from a delimited file of data
|
| SimpleFastaCmd |
Simple implementation of methods for fetching sequences from blast-formatted databases, using blastdbcmd (aka
fastacmd)
|
| SimpleHTMLFormatter |
A safer substitute for SimpleHTMLFormatter that escape existing HTML tags
and use lowercase <b> tags.
|
| SimpleHttp |
|
| SimpleMarkdownFormatter |
|
| SimplePageContext |
Deprecated. |
| SimpleTreeValueObject |
|
| SingleBatchDeterminationEvent |
Indicates that we got batch information, but there was (as far as we can tell) just one batch.
|
| SingleExperimentAnalysis |
|
| SingleExperimentAnalysisDao<T extends SingleExperimentAnalysis> |
|
| SingleExperimentAnalysisDaoBase<T extends SingleExperimentAnalysis> |
|
| SingleExperimentAnalysisService<T extends SingleExperimentAnalysis> |
Interface for analysis service manipulating single experiments.
|
| SingletonBatchesException |
Indicates that batches with only a single sample were found, which means we don't form batches at all.
|
| SingletonBatchInvalidEvent |
Indiates that there was at least one batch with only one sample.
|
| SlackAppender |
|
| Slice<O> |
Represents a slice of List. |
| Sort |
Represents a directed sort by a property.
|
| Sort.Direction |
Direction of the sort.
|
| SortArg<O extends Identifiable> |
Class representing an API argument that should be an integer.
|
| SortArg.Sort |
|
| SortArg.Sort.Direction |
|
| SortValueObject |
|
| SourceDomainObjectGenerator |
|
| SpearmanMetrics |
Subclass that computes correlations using ranks.
|
| SplitExperimentCli |
Split an experiment into parts based on an experimental factor
|
| SplitExperimentService |
TODO Document Me
|
| SplitExperimentServiceImpl |
Split an experiment into multiple experiments.
|
| SpringContextUtil |
Methods to create Spring contexts for Gemma manually.
|
| SpringProfiles |
Constants used for various Spring profiles.
|
| StandardQuantitationType |
|
| StandardQuantitationTypeConverter |
|
| 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.
|
| StopWatchUtils |
Utilities for working with StopWatch.
|
| StopWatchUtils.StopWatchRegion |
|
| StringArrayArg |
Class representing an API argument that should be an array of Strings.
|
| StringPoint |
|
| SubmittedTask |
Obtained from the TaskRunningService, can be used to monitor status.
|
| SubmittedTask.Status |
|
| SubmittedTaskAbstract |
Shared code between SubmittedTaskLocal and SubmittedTaskProxy.
|
| SubmittedTaskLocal |
SubmittedTask implementation representing the task running on local TaskRunningService.
|
| SubmittedTasksMaintenance |
|
| SubmittedTaskValueObject |
|
| Subquery |
Represents a subquery right-hand side of a Filter. |
| Subquery.Alias |
|
| SubqueryUtils |
|
| SupportDetails |
Represents the datasets in which a link was found in ("supported").
|
| SuspiciousValuesForQuantitationException |
|
| SuspiciousValuesForQuantitationException.SuspiciousValueResult |
|
| SVDCli |
|
| SvdController |
Run SVD on a data set.
|
| SVDException |
Exception raised when the SVD of a given expression data matrix cannot be computed.
|
| SVDRelatedPreprocessingException |
Exception raised if a SVD cannot be computed.
|
| SVDService |
|
| SVDServiceHelper |
Performs Singular value decomposition on experiment data to get eigengenes, and does comparison of those PCs to
factors recorded in the experimental design.
|
| SVDServiceHelperImpl |
Perform SVD on expression data and store the results.
|
| SVDServiceImpl |
Perform SVD on expression data and store the results.
|
| SvdTask |
|
| SvdTaskCommand |
|
| SvdTaskImpl |
|
| SVDValueObject |
Store information about SVD of expression data and comparisons to factors/batch information.
|
| SwissProtParser |
This does a very minimal parse of Swissprot records, just to get mRNAs associated with a single protein.
|
| SystemMonitorController |
Provide statistics about the system: hibernate, caches etc.
|
| SystemStatsController |
System statistics
|
| TableMaintenanceUtil |
|
| TableMaintenanceUtilImpl |
Functions for maintaining the database.
|
| Task<C extends TaskCommand> |
|
| TaskCancelledException |
author: anton
date: 27/03/13
|
| TaskCommand |
This command class is used to allow communication of parameters for a task between a client and task running service,
which might be on a different computer.
|
| TaskCommandToTaskMatcher |
|
| TaskCommandToTaskMatcherImpl |
|
| TaskCompletionController |
Exposes progress status service check result to the front end.
|
| TaskPostProcessing |
author: anton
date: 10/02/13
|
| TaskPostProcessingImpl |
author: anton date: 10/02/13
|
| TaskResult |
This class describes the result of long-running task.
|
| TaskRunningService |
|
| TaskRunningServiceImpl |
Handles the execution of tasks in threads that can be checked by clients later.
|
| TaxaWebService |
RESTful interface for taxa.
|
| Taxon |
|
| Taxon.Factory |
|
| TaxonArg<T> |
Mutable argument type base class for Taxon API
|
| TaxonArgService |
|
| TaxonArrayArg |
|
| TaxonDao |
|
| TaxonDaoImpl |
|
| TaxonFetcher |
Taxon information from NCBI comes as a tar.gz archive; only the names.dmp file is of interest.
|
| TaxonIdArg |
Long argument type for taxon API, referencing the Taxon ID.
|
| TaxonLoader |
Load taxa into the system.
|
| TaxonLoaderCli |
|
| TaxonNameArg |
String argument type for taxon API, referencing the Taxon scientific name or common name.
|
| TaxonNcbiIdArg |
Long argument type for taxon API, referencing the Taxon ID.
|
| TaxonParser |
Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
|
| TaxonPropertyEditor |
Used to convert Taxon from and into strings for display in forms.
|
| TaxonService |
|
| TaxonServiceImpl |
|
| TaxonUtility |
A utility class for taxon.
|
| TaxonValueObject |
|
| TechnologyType |
|
| TestComponent |
This will exclude the component or configuration from component scanning.
|
| TextView |
Simply prints text to the client.
|
| ThreePrimeDistanceMethod |
|
| TimeUtil |
|
| TooSmallDatasetLinkAnalysisEvent |
Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skipped
|
| Treatment |
|
| Treatment.Factory |
|
| TreeCharacteristicValueObject |
|
| TroubledStatusFlagEvent |
Sets the trouble flag of curation details of any Curatable object.
|
| TsvFileService<T> |
Interface for services that produce TSV serialization.
|
| TwoChannelMissingValueController |
Run misssing value computation via web request.
|
| TwoChannelMissingValueHelperService |
|
| TwoChannelMissingValues |
|
| TwoChannelMissingValuesImpl |
Computes a missing value matrix for ratiometric data sets.
|
| TwoChannelMissingValueTaskCommand |
|
| TwoChannelMissingValueTaskImpl |
Space task for computing two channel missing values.
|
| TypedResultTransformer<T> |
|
| UnhandledExceptionMapper |
Render unhandled exceptions.
|
| UninformativeFASTQHeadersForBatchingEvent |
Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of
invalid formatting or lack of information.
|
| Unit |
|
| Unit.Factory |
|
| UnitDao |
|
| UnitDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.measurement.Unit.
|
| UnsuitableForAnalysisException |
*
|
| UnsuitableForDifferentialExpressionAnalysisEvent |
Indicates that the associated Experiment is NOT suitable for differential expression analysis.
|
| UnsupportedQuantitationScaleConversionException |
Exception raised when data from a given scale cannot be converted to another scale.
|
| UnsupportedRawdataFileFormatException |
Used to indicate failure was due to the format being unusable, but the files are available.
|
| UpdateEEDetailsCommand |
|
| UpdatePubMedCli |
Identify experiments in Gemma that have no publication
Fetch their GEO records and check for pubmed IDs
Add the publications where we find them.
|
| UpdatePubMedCommand |
|
| UploadInfo |
|
| UploadListener |
This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
|
| User |
A user of the software system, who is authenticated.
|
| User.Factory |
|
| UserCounterListener |
Count active sessions
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| UserDao |
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| UserDaoImpl |
DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.auditAndSecurity.User.
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| UserFormMultiActionController |
Controller to edit profile of users.
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| UserGroup |
An organized group of researchers with an identifiable leader and group members.
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| UserGroup.Factory |
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| UserGroupDao |
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| UserGroupDaoImpl |
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| UserGroupValueObject |
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| UserIdRetrievalStrategy |
Strategy for retrieving a user ID.
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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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| UserManager |
Overrides gsec's UserManager to provide Gemma-specific types.
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| UserManagerImpl |
Implementation for Spring Security, plus some other handy methods.
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| UserQuery |
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| UserQuery.Factory |
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| UserService |
Override a few definition from gsec so that we can use Gemma-specific implementations safely.
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| UserServiceImpl |
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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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| ValidateEvidenceValueObject |
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| ValueObject |
Annotate class representing value objects.
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| ValueObjectConfig |
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| VectorMergingCli |
For experiments that used multiple array designs, merge the expression profiles
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| VectorMergingService |
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| VectorMergingServiceImpl |
Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
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| Versioned |
Interface implemented by entities that are externally versioned.
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| VersionedEvent |
Base class for events relating to a Versioned entity. |
| VisualizationValueObject |
Stores expression profile data from one expression experiment for plotting.
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| WebApplicationExceptionMapper |
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| WebConstants |
Constant values used throughout the web portion of Gemma.
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| WellComposedErrorBody |
Object acting as a payload for the ResponseErrorObject.
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| WhatsNew |
A value object to hold onto the 'new' objects.
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| WhatsNewController |
Controller to provide information on "what's new" in the system
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| WhatsNewService |
Creates reports that can be shown on the web pages or in social media feeds.
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| WhatsNewServiceImpl |
Service to collect data on object that are new in the system.
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| XMLUtils |
Handy methods for dealing with XML.
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| XmlView |
Model should contain a single value matching XML_PARAM
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