All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
Class |
Description |
AbaGene |
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ABALinkOutValueObject |
Value Object for transporting details needed from other websites to provide convenient links to them in gemma
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AbstractAnalyzer |
Analyzer base class.
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AbstractAsyncFactoryBean<T> |
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AbstractAuditable |
An entity which can have an audit trail attached to it.
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AbstractCriteriaFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
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AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> |
Created by tesarst on 07/03/17.
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AbstractCuratableValueObject<C extends Curatable> |
Created by tesarst on 07/03/17.
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AbstractDao<T extends Identifiable> |
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
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AbstractDescribable |
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AbstractDesignElementDataVectorDao<T extends DesignElementDataVector> |
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AbstractDesignElementDataVectorService<T extends DesignElementDataVector> |
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AbstractDifferentialExpressionAnalyzer |
An abstract differential expression analyzer to be extended
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AbstractFetcher |
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AbstractFileService<T> |
Provide base implementation for all sorts of file services that serialize data in tabular format.
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AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
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AbstractFilteringVoEnabledDao.FilterablePropertyMeta |
Meta-information for a filterable property.
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AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
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AbstractGeoService |
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AbstractMatrixRowPairAnalysis |
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AbstractMeterRegistryConfigurer |
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AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
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AbstractOntologyResourceSimple |
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AbstractPersister |
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AbstractPersister.Caches |
Various caches to refer back to not-yet persisted entities (and thus not easily obtainable from the persistence
context).
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AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
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AbstractService<O extends Identifiable> |
Base for all services handling DAO access.
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AbstractTask<C extends TaskCommand> |
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AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
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AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
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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.
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AclAfterCollectionDataVectorByExpressionExperimentFilter |
Filter collections of DesignElementDataVectors or DataVectorValueObjects based on the permissions of the associated
ExpressionExperiment(s).
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AclAfterCompSeqByArrayDesignFilter |
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AclCriteriaUtils |
Utilities for integrating ACLs with Hibernate Criteria API.
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AclQueryUtils |
Utilities for integrating ACL into Query .
|
AffyChipTypeExtractor |
Extract the chip type from Affymetrix CEL files.
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AffyPowerToolsProbesetSummarize |
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AffyProbeNameFilter |
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AffyProbeNameFilter.Pattern |
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AffyProbeReader |
Reads Affymetrix Probe files, including exon arrays.
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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.
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AlignmentBasedGeneMappingEvent |
Signifies a mapping based on sequence alignment performed by the system.
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AllenBrainAtlasService |
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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).
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AlreadyExistsInSystemException |
Can be thrown when an attempt is made to load data into the system that already exists.
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AlternateName |
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AlternateName.Factory |
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Analysis |
An analysis of one or more Investigations.
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AnalysisDao<T extends SingleExperimentAnalysis> |
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AnalysisResult |
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AnalysisResultSet<R extends AnalysisResult> |
An abstract class representing a related set of generic analysis results, part of an analysis.
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AnalysisResultSetDao<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
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AnalysisResultSetService<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
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AnalysisResultSetValueObject<K extends AnalysisResult,R extends AnalysisResultSet<K>> |
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AnalysisResultValueObject<A extends AnalysisResult> |
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AnalysisSelectionAndExecutionService |
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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.
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AnalysisService<T extends Analysis> |
Provides basic services for dealing with analyses
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AnalysisSuitabilityEvent |
Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
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AnalysisUtilService |
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AnalysisUtilServiceImpl |
Utility methods for dealing with analyses.
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AnalysisValueObject<T extends Analysis> |
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AnnotationAssociation |
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather
than our own sequence analysis.
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AnnotationAssociation.Factory |
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AnnotationAssociationDao |
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AnnotationAssociationDaoImpl |
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AnnotationAssociationService |
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AnnotationAssociationServiceImpl |
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AnnotationBasedGeneMappingEvent |
To signify the array design was mapped from an external source, not by our own sequence analysis.
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AnnotationEvent |
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AnnotationValueObject |
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ArchiveFetcher |
Interface defining a class that downloads archives and unpacks them.
|
ArrayDesign |
Represents an assembly of design elements that are assayed all at once.
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ArrayDesign.Factory |
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ArrayDesignAnalysisEvent |
An event involving the analysis of an ArrayDesign
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ArrayDesignAnnotationService |
Methods to generate annotations for array designs, based on information already in the database.
|
ArrayDesignAnnotationService.OutputType |
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ArrayDesignAnnotationServiceImpl |
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ArrayDesignDao |
Created by tesarst on 13/03/17.
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ArrayDesignDaoImpl |
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ArrayDesignGeneMappingEvent |
The mapping of probes to genes for an ArrayDesign
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ArrayDesignMapResultService |
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ArrayDesignMapResultServiceImpl |
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
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ArrayDesignMergeEvent |
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ArrayDesignMergeHelperService |
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ArrayDesignMergeHelperServiceImpl |
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ArrayDesignMergeService |
Make new array design based on others
Keep map of relation between new design elements and old ones
Store relationship with mergees
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ArrayDesignMergeServiceImpl |
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ArrayDesignParser |
Deprecated. |
ArrayDesignPersister |
This class handles persisting array designs.
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ArrayDesignProbeMapperService |
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ArrayDesignProbeMapperServiceImpl |
For an array design, generate gene product mappings for the sequences.
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ArrayDesignProbeMapperTaskImpl |
A probe mapper spaces task .
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ArrayDesignProbeMapTaskCommand |
A command object to be used by spaces.
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ArrayDesignProbeRenamingEvent |
Signifies that the probes were renamed from their original values.
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ArrayDesignRepeatAnalysisEvent |
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ArrayDesignReportService |
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ArrayDesignReportServiceImpl |
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ArrayDesignSequenceAlignmentService |
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ArrayDesignSequenceAlignmentServiceImpl |
Aligns sequences from array designs to the genome, using blat, and persists the blat results.
|
ArrayDesignSequenceAnalysisEvent |
The sequence alignment analysis of an ArrayDesign
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ArrayDesignSequenceProcessingService |
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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.
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ArrayDesignSequenceUpdateEvent |
The updating of the sequences associated with an ArrayDesign
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ArrayDesignService |
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ArrayDesignServiceImpl |
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ArrayDesignsForExperimentCache |
Used to hold information for matching to a new experiment, during persisting.
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ArrayDesignSubsumeCheckEvent |
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ArrayDesignValueObject |
Value object for quickly displaying varied information about Array Designs.
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ArrayExpressUtil |
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AsyncFactoryBean<T> |
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AsyncFactoryBeanUtils |
Utilities for manipulating async factory beans.
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Auditable |
Created by tesarst on 07/03/17.
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AuditableObject |
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AuditAction |
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AuditAdvice |
Manage audit trails on objects.
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AuditEvent |
An event in the life of an object.
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AuditEvent.Factory |
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AuditEventDao |
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AuditEventDaoImpl |
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AuditEventService |
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AuditEventServiceImpl |
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AuditEventType |
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AuditEventValueObject |
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AuditTrail |
The trail of events (create or update) that occurred in an objects lifetime.
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AuditTrail.Factory |
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AuditTrailDao |
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AuditTrailDaoImpl |
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AuditTrailService |
Create and manipulate audit trails.
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AuditTrailServiceImpl |
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AutomatedAnnotationEvent |
Deprecated.
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BaseCodeConfigurer |
Configure the baseCode library from a given property sources.
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BaseCodeOntologySearchException |
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BaseDao<T> |
Interface that supports basic CRUD operations.
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BaseExpressionDataMatrix<T> |
Base class for ExpressionDataMatrix implementations.
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BaseImmutableService<O extends Identifiable> |
Base service class for an immutable entity.
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BaselineSelection |
Utilities for deciding if a factor value is a baseline condition.
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BaseReadOnlyService<O extends Identifiable> |
Interface for read-only services.
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BaseScanDateExtractor |
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BaseService<O extends Identifiable> |
Interface that supports basic CRUD operations.
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BaseValueObject |
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BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
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BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
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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.
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BatchConfound |
Represents a summary of a batch effect confound.
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BatchConfoundUtils |
Test if an experimental design is confounded with batches.
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BatchCorrectionEvent |
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BatchEffectDetails |
provide some basic information about the properties and strength of a batch effect, if any.
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BatchEffectType |
Represents a batch effect.
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BatchEffectType |
Workaround to handle existing batch effect value in the database.
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BatchInfoFetchTask |
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BatchInfoFetchTaskCommand |
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BatchInfoFetchTaskImpl |
Task to try to get 'batch' information about an experiment.
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BatchInfoParser |
Parse information on batch from raw data files.
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BatchInfoPopulationException |
Used to indicate a problem with the population of batch information for a given
ExpressionExperiment .
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BatchInfoPopulationHelperService |
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BatchInfoPopulationHelperServiceImpl |
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BatchInfoPopulationService |
Retrieve batch information from the data source, if possible, and populate it into experiments.
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BatchInfoPopulationServiceImpl |
Retrieve batch information from the data source, if possible, and populate it into experiments.
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BatchInformationEvent |
Abstract class for events related to batch information.
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BatchInformationFetchingEvent |
Indicates that batch information was successfully obtained.
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BatchInformationMissingEvent |
Indicate that batch information has been looked for and was missing.
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BatchProblemsUpdateEvent |
Event that tracks when batch effects or problems are detected.
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BeanFactoryUtils |
Utilities for working with bean factories.
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BeanInitializationTimeMonitor |
Hook into the bean post-processing lifecycle and record bean initialization time.
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BeanNameGenerator |
Our \@Service etc.
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BibliographicPhenotypesValueObject |
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BibliographicReference |
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BibliographicReference.Factory |
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BibliographicReferenceDao |
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BibliographicReferenceDaoImpl |
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BibliographicReferenceService |
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BibliographicReferenceServiceImpl |
Implementation of BibliographicReferenceService.
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BibliographicReferenceValueObject |
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists
in web
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BibRefAnnotation |
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BioAssay |
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
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BioAssay.Factory |
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BioAssayDao |
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BioAssayDaoImpl |
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BioAssayDimension |
Stores the order of BioAssays referred to in DataVectors.
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BioAssayDimension.Factory |
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BioAssayDimensionDao |
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BioAssayDimensionDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.bioAssayData.BioAssayDimension .
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BioAssayDimensionService |
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BioAssayDimensionServiceImpl |
Spring Service base class for BioAssayDimensionService , provides access to all services and entities
referenced by this service.
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BioAssayDimensionValueObject |
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BioAssayOutlierProcessingTask |
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BioAssayOutlierProcessingTaskCommand |
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BioAssayOutlierProcessingTaskImpl |
Handle 'flagging' a sample as an outlier.
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BioAssayService |
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BioAssayServiceImpl |
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BioAssaySet |
Represents a set of BioAssays.
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BioAssaySetService |
Generic service for dealing with all subclasses of BioAssaySet .
|
BioAssaySetServiceImpl |
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BioAssayValueObject |
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BiomartEnsembleNcbiParser |
Parser for BioMart file.
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BiomartEnsemblNcbiFetcher |
BioMart is a query-oriented data management system.
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BiomartEnsemblNcbiObjectGenerator |
Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble
protein id.
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BioMaterial |
In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA,
proteins, etc...
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BioMaterial.Factory |
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BioMaterialDao |
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BioMaterialDaoImpl |
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BioMaterialMappingUpdate |
To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.
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BioMaterialService |
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BioMaterialServiceImpl |
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BioMaterialValueObject |
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BioSequence |
The sequence of a biological polymer such as a protein or DNA.
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BioSequence.Factory |
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BioSequence2GeneProduct |
An association between a BioSequence and a Gene Product.
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BioSequenceDao |
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BioSequenceDaoImpl |
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BioSequenceService |
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BioSequenceServiceImpl |
Spring Service base class for BioSequenceService , provides access to
all services and entities referenced by this service.
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BioSequenceValueObject |
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BlacklistedEntity |
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BlacklistedEntityDao |
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BlacklistedEntityDaoImpl |
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BlacklistedEntityService |
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BlacklistedEntityServiceImpl |
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BlacklistedExperiment |
TODO Document Me
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BlacklistedPlatform |
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BlacklistedValueObject |
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Blat |
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BlatAssociation |
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BlatAssociation.Factory |
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BlatAssociationDao |
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BlatAssociationDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
BlatAssociation .
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BlatAssociationScorer |
Given a set of BlatAssociations that might be redundant, clean them up and score them.
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BlatAssociationService |
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BlatAssociationServiceImpl |
Spring Service base class for BlatAssociationService , provides access to all services and entities
referenced by this service.
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BlatResult |
Represents the result of a BLAT search.
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BlatResult.Factory |
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BlatResult2Psl |
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
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BlatResultDao |
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BlatResultDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.sequenceAnalysis.BlatResult .
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BlatResultParser |
Loader to handle results generated by Jim Kent's Blat.
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BlatResultService |
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BlatResultServiceImpl |
Spring Service base class for BlatResultService , provides access to all services and entities referenced
by this service.
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BlatResultValueObject |
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BooleanVectorValueObject |
This is used to represent missing value data.
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BrowsingDao<T> |
Support for paging through the data.
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BuildInfo |
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BusinessKey |
Methods to test business-key-related issues on objects.
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CachedFilteringDao<O extends Identifiable> |
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CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
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CacheKeyLock |
Represents a lock over a cache key.
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CacheKeyLock.LockAcquisition |
Represents an acquired lock on a cache key.
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CacheUtils |
Created by tesarst on 04/04/17.
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ChannelUtils |
Determine if a quantitation type (by name) represents background or signal.
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Characteristic |
Instances of this are used to describe other entities.
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Characteristic.Factory |
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CharacteristicDao |
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CharacteristicDao.CharacteristicUsageFrequency |
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CharacteristicDaoImpl |
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CharacteristicService |
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CharacteristicServiceImpl |
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CharacteristicUpdateCommand |
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CharacteristicUpdateTask |
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CharacteristicUpdateTaskImpl |
This handles characteristic updates from the client: experiment tags, characteristic browser
|
CharacteristicUtils |
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CharacteristicValueObject |
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Chromosome |
Immutable representation of a chromosome
|
ChromosomeDao |
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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
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ChromosomeLocation |
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ChromosomeService |
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ChromosomeServiceImpl |
Spring Service base class for ChromosomeService , provides access to all services
and entities referenced by this service.
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ChromosomeUtils |
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CitationValueObject |
Represents a BibliographicReference as a citation string (which is really super light value object).
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CoexpCorrelationDistribution |
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CoexpCorrelationDistribution.Factory |
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CoexpressionAnalysis |
A coexpression analysis of one experiment.
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CoexpressionAnalysis.Factory |
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CoexpressionAnalysisDao |
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CoexpressionAnalysisDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis .
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CoexpressionAnalysisService |
Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
|
CoexpressionAnalysisServiceImpl |
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CoexpressionCache |
Cache for coexpression results.
|
CoexpressionCacheImpl |
Configures the cache for gene2gene coexpression.
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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 |
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CoexpressionDaoImpl |
Manages and queries coexpression 'links' between genes.
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CoexpressionMetaValueObject |
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CoexpressionNodeDegreeDao |
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CoexpressionNodeDegreeDaoImpl |
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CoexpressionSearchCommand |
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CoexpressionService |
A key service for working with coexpression at a fairly low level.
|
CoexpressionServiceImpl |
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CoexpressionSummaryValueObject |
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CoexpressionValueObject |
Lightweight/convenient object for manipulating coexpression for a pair of genes.
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CoexpressionValueObjectExt |
A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
|
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.
|
CompositeSearchSource |
A search source constituted of multiple other sources.
|
CompositeSequence |
A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
|
CompositeSequence.Factory |
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CompositeSequenceDao |
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CompositeSequenceDaoImpl |
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CompositeSequenceGeneMapperService |
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CompositeSequenceMapSummary |
This is a convenience object to hold the results of CompositeSequence mapping results.
|
CompositeSequenceMapValueObject |
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CompositeSequenceParser |
Parse the "old" array description format.
|
CompositeSequenceService |
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CompositeSequenceServiceImpl |
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CompositeSequenceValueObject |
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Compound |
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Compound.Factory |
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CompoundDao |
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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.
|
Contact |
Representing a person or organization that can be contacted about, or is the source of, data in the system.
|
Contact.Factory |
|
ContactDao |
|
ContactDaoImpl |
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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.
|
Converter<S,T> |
Defines a class that can convert objects from one type to another.
|
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.
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CurationDetailsEvent |
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CurationNoteUpdateEvent |
Indicates that previous validation is being invalidated
|
DataAddedEvent |
Indicates that a data type (for a specific QuantitationType, possibly new) was added.
|
DataAnalysisEvidence |
Deprecated. |
DatabaseBackedGeneSetValueObject |
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DatabaseEntry |
A reference to a record in a database.
|
DatabaseEntry.Factory |
|
DatabaseEntryDao |
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DatabaseEntryDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
DatabaseEntry .
|
DatabaseEntryService |
|
DatabaseEntryServiceImpl |
Spring Service base class for DatabaseEntryService , provides access to all services and entities
referenced by this service.
|
DatabaseEntryValueObject |
ValueObject for database entry
|
DatabaseSearchSource |
Search source for direct database results.
|
DatabaseType |
|
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.
|
DataRemovedEvent |
Indicates that a data type (for a specific QuantitationType, possibly new) was removed.
|
DataReplacedEvent |
Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the
system.
|
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.
|
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 |
|
DefaultHighlighter |
|
Describable |
|
DescribableComparator |
|
DesignElementDataVector |
|
DesignElementDataVectorDao<T extends DesignElementDataVector> |
|
DifferentialExpressionAnalysis |
An analysis of changes in expression levels across experimental conditions
|
DifferentialExpressionAnalysis.Factory |
|
DifferentialExpressionAnalysisConfig |
Holds the settings used for differential expression analysis, and defines some defaults.
|
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
|
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.
|
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 |
|
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 |
|
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 |
|
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.
|
DoesNotNeedAttentionEvent |
An event that occurs when a curator has validated the entity and indicated that it is "approved".
|
DoubleVectorValueObject |
Simple wrapper for a double[] that is derived from a DesignElementDataVector.
|
DummyMailSender |
Mock mail sender for testing.
|
DumpsValueObject |
|
EE2CAclQueryUtils |
This class provides a fast-path to AclQueryUtils that uses the denormalized mask for anonymous users.
|
EhCache24Metrics |
Metrics for Ehcache 2.4 series.
|
EhcacheConfig |
|
EhcacheKeyLock |
|
Eigenvalue |
|
Eigenvalue.Factory |
|
Eigenvector |
A right singular vector (a.k.a.
|
Eigenvector.Factory |
|
EmailNotificationContext |
author: anton date: 10/02/13
|
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.
|
EntityNotFoundException |
Deprecated. |
EntityUtils |
|
EnvironmentProfiles |
Environment profiles used in the Spring context.
|
ESearchException |
|
ESearchXMLParser |
|
EutilFetch |
|
EutilFetch.Mode |
|
EvidenceFilter |
Used to filter values received depending on taxon and privacy chosen
|
EvidenceSecurityValueObject |
|
EvidenceSourceValueObject |
|
EvidenceValueObject<E extends PhenotypeAssociation> |
Parent class of all evidence value objects
|
ExperimentalDesign |
|
ExperimentalDesign.Factory |
|
ExperimentalDesignDao |
|
ExperimentalDesignDaoImpl |
|
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 |
|
ExperimentalDesignVisualizationService |
|
ExperimentalDesignVisualizationServiceImpl |
Tools for visualizing experimental designs.
|
ExperimentalDesignWriter |
|
ExperimentalEvidence |
Deprecated. |
ExperimentalEvidence.Factory |
|
ExperimentalEvidenceDao |
|
ExperimentalEvidenceDaoImpl |
|
ExperimentalEvidenceValueObject |
Deprecated. |
ExperimentalFactor |
ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
|
ExperimentalFactor.Factory |
|
ExperimentalFactorDao |
|
ExperimentalFactorDaoImpl |
|
ExperimentalFactorService |
|
ExperimentalFactorServiceImpl |
|
ExperimentalFactorValueObject |
|
ExperimentCoexpressionLink |
Represents coexpression at the level of experiment, referinng to links stored as Gene2GeneCoexpression.
|
ExperimentExpressionLevelsValueObject |
|
ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject |
|
ExperimentExpressionLevelsValueObject.VectorElementValueObject |
|
ExperimentPlatformSwitchHelperService |
Use to finish final transactional step in updating platform
|
ExpressionAnalysis |
An analysis of one or more ExpressionExperiments
|
ExpressionAnalysisResultSet |
A group of results for an ExpressionExperiment.
|
ExpressionAnalysisResultSet.Factory |
|
ExpressionAnalysisResultSetDao |
|
ExpressionAnalysisResultSetDaoImpl |
|
ExpressionAnalysisResultSetFileService |
|
ExpressionAnalysisResultSetFileServiceImpl |
|
ExpressionAnalysisResultSetService |
|
ExpressionAnalysisResultSetServiceImpl |
|
ExpressionDataBooleanMatrix |
Matrix of booleans mapped from an ExpressionExperiment.
|
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.
|
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.
|
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 |
|
ExpressionExperimentDao |
Created by tesarst on 13/03/17.
|
ExpressionExperimentDaoImpl |
|
ExpressionExperimentDetailsValueObject |
|
ExpressionExperimentFilter |
Methods to handle filtering expression experiments for analysis.
|
ExpressionExperimentLoadTask |
|
ExpressionExperimentLoadTaskCommand |
|
ExpressionExperimentLoadTaskImpl |
|
ExpressionExperimentMetaFileType |
|
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.
|
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 |
|
ExpressionExperimentSetDao |
|
ExpressionExperimentSetDaoImpl |
|
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 |
|
ExpressionExperimentUpdateFromGEOEvent |
Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.
|
ExpressionExperimentValueObject |
|
ExpressionExperimentVectorManipulatingService |
|
ExpressionExperimentVectorMergeEvent |
Indicates that the "Vector merging" has been done on the associated experiment.
|
ExpressionPersister |
|
ExternalDatabase |
|
ExternalDatabase.Factory |
|
ExternalDatabaseDao |
|
ExternalDatabaseDaoImpl |
|
ExternalDatabases |
|
ExternalDatabaseService |
|
ExternalDatabaseServiceImpl |
|
ExternalDatabaseStatisticsValueObject |
|
ExternalDatabaseUtils |
Provides convenience methods to provide ExternalDatabases and DatabaseEntries for common cases, such as Genbank.
|
ExternalDatabaseValueObject |
|
ExternalFileGeneLoaderService |
|
ExternalFileGeneLoaderServiceImpl |
Class to provide functionality to load genes from a tab delimited file.
|
FactorAssociatedAnalysisResultSet<R extends AnalysisResult> |
|
FactorType |
|
FactorValue |
The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
|
FactorValue.Factory |
|
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.
|
FactorValueMigratorService |
|
FactorValueMigratorService.Migration |
|
FactorValueMigratorService.MigrationFailedException |
Keep track of the first failed migration when multiple migrations are performed in a single transaction.
|
FactorValueMigratorService.MigrationResult |
|
FactorValueMigratorServiceImpl |
Deprecated. |
FactorValueNeedsAttentionEvent |
Indicates that a factor value needs attention.
|
FactorValueOntologyService |
Ontology service for factor values and their annotations.
|
FactorValueOntologyService.OntologyStatement |
Represents an ontology statement.
|
FactorValueOntologyServiceImpl |
|
FactorValueOntologyUtils |
|
FactorValueOntologyUtils.Annotation |
|
FactorValueOntologyUtils.AnnotationIds |
|
FactorValueOntologyUtils.StatementVisitor<U,E extends Throwable> |
|
FactorValueService |
|
FactorValueServiceImpl |
Spring Service base class for FactorValueService , provides access
to all services and entities referenced by this service.
|
FactorValueUtils |
|
FactorValueValueObject |
Deprecated.
|
FactorValueVector |
|
FailedBatchInformationFetchingEvent |
Indicates that the attempt to get batch information failed due to an error.
|
FailedBatchInformationMissingEvent |
Deprecated.
|
FailedDataReplacedEvent |
Represents a failed data replace.
|
FailedDifferentialExpressionAnalysisEvent |
|
FailedLinkAnalysisEvent |
|
FailedMeanVarianceUpdateEvent |
|
FailedMissingValueAnalysisEvent |
|
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.
|
Fetcher |
Interface for classes that can fetch files from a remote location and copy them to a specified location.
|
FieldAwareSearchSource |
Search source that can retrieve results matching specific fields.
|
FileFormatException |
Use to indicate a file format error.
|
FileService<T> |
Interface for a service that serialize entities.
|
Filter |
Holds the necessary information to filter an entity with a property, operator and right-hand side value.
|
Filter.Operator |
|
FilterConfig |
Holds settings for filtering.
|
FilterCriteriaUtils |
|
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.
|
GeeqDao |
|
GeeqDaoImpl |
|
GeeqEvent |
|
GeeqService |
|
GeeqService.ScoreMode |
Modes for filling GEEQ scores.
|
GeeqServiceImpl |
|
GeeqValueObject |
Represents publicly available geeq information
|
GemmaOntologyService |
Ontology created for Gemma.
|
GemmaRestApiClient |
A minimalist client for accessing Gemma's RESTful API.
|
GemmaRestApiClient.DataResponse |
|
GemmaRestApiClient.EmptyResponse |
For endpoints that return no data (i.e.
|
GemmaRestApiClient.ErrorResponse |
|
GemmaRestApiClient.ErrorResponse.Error |
|
GemmaRestApiClient.Redirection |
For endpoint that return a redirection.
|
GemmaRestApiClient.Response |
|
GemmaRestApiClientException |
|
GemmaRestApiClientImpl |
|
GemmaRestOnly |
Indicate that a property or type is only visible not visible outside of Gemma REST.
|
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 |
|
Gene2OntologyEntryAssociation |
|
Gene2OntologyEntryAssociationImpl |
|
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 .
|
GeneCoexpressedGenes |
Important: this is slightly misnamed, since it potentially includes links that have support of zero.
|
GeneCoexpressionNodeDegree |
Represents the coexpression node degree for a gene summarized across experiments, at each level of support.
|
GeneCoexpressionNodeDegree.Factory |
|
GeneCoexpressionNodeDegreeValueObject |
Represents a GeneCoexpressionNodeDegree
|
GeneCoexpressionSearchService |
Provides access to Gene2Gene links.
|
GeneCoexpressionSearchServiceImpl |
|
GeneCoexpressionTestedIn |
Tracks the datasets in which coexpression for a gene has been tested.
|
GeneCoreService |
core service for Gene
|
GeneDao |
|
GeneDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Gene .
|
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 |
|
GeneEvidenceValueObject |
Deprecated. |
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.
|
GeneOntologyService |
|
GeneOntologyServiceImpl |
|
GeneOntologyServiceImpl.GOAspect |
|
GeneOntologyTermValueObject |
|
GeneProduct |
|
GeneProduct.Factory |
|
GeneProductDao |
|
GeneProductDaoImpl |
|
GeneProductService |
|
GeneProductServiceImpl |
|
GeneProductValueObject |
|
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 |
|
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
|
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 |
|
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 .
|
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.
|
GeneTestedInCache |
Cache of the 'tested-in' information for genes.
|
GeneTestedInCacheImpl |
|
GeneValueObject |
|
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.
|
GeoFamilyParser |
Class for parsing GSE and GDS files from NCBI GEO.
|
GeoFetcher |
|
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.
|
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.
|
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 |
|
GroupAuthority |
Authority for groups (kind of like a "user role", but for group-based authorization)
|
GroupAuthority.Factory |
|
GroupAuthorityImpl |
|
H2Dialect |
|
Hibernate4Metrics |
Metrics for Hibernate 4.
|
Hibernate4QueryMetrics |
Query metrics for Hibernate 4.
|
HibernateSearchException |
|
HibernateSearchSource |
Search source based on Hibernate Search.
|
HibernateUtils |
|
Highlighter |
Custom highlighter for search results.
|
HikariCPMetrics |
|
HitListSize |
The number of probes meeting a given q-value threshold in the result set.
|
HitListSize.Factory |
|
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 |
|
IndexerService |
Indexer service.
|
IndexerServiceImpl |
|
IndexerTask |
Created with IntelliJ IDEA.
|
IndexerTaskCommand |
|
IndexerTaskImpl |
|
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
|
IOExceptionWithRetry |
|
JobInfo |
|
JobInfo.Factory |
|
JsonFileService<T> |
Interface for service that provides JSON serialization.
|
Keyword |
|
Keyword.Factory |
|
LazyInitByDefaultPostProcessor |
Mark beans as lazy-init by default.
|
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.
|
LinkAnalysisConfig |
Holds parameters needed for LinkAnalysis.
|
LinkAnalysisConfig.NormalizationMethod |
|
LinkAnalysisConfig.SingularThreshold |
Configures whether only one of the two thresholds should be used.
|
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.
|
ListUtils |
Utilities and algorithms for List .
|
LiteratureEvidence |
Deprecated. |
LiteratureEvidence.Factory |
|
LiteratureEvidenceDao |
|
LiteratureEvidenceDaoImpl |
|
LiteratureEvidenceValueObject |
|
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).
|
LuceneHighlighter |
Highlighter with additional capabilities for Lucene.
|
LuceneParseSearchException |
|
LuceneQueryUtils |
Utilities for parsing search queries using Lucene.
|
MailEngine |
|
MailEngineImpl |
|
MakePrivateEvent |
|
MakePublicEvent |
|
ManualAnnotationEvent |
|
ManualAuthenticationServiceBasedSecurityContextFactory |
Creates a security context using manual authentication.
|
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 |
|
MedicalSubjectHeading |
|
MedicalSubjectHeading.Factory |
|
MeterRegistryEhcacheConfigurer |
Add metrics from each available Ehcache in the given CacheManager to the supplied meter registry.
|
MissingResult |
Represents a gene that was not tested.
|
MissingValueAnalysisEvent |
Computing missing values for an expression experiment
|
MondoOntologyService |
|
MouseCoexpressionSupportDetailsImpl |
|
MouseExperimentCoexpressionLinkImpl |
|
MouseGeneCoExpression |
|
MouseGeneCoExpression.Factory |
|
MouseGeneCoExpressionImpl |
|
Multifunctionality |
|
Multifunctionality.Factory |
|
MySQL57InnoDBDialect |
|
NCBIGene2Accession |
See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
|
NcbiGene2AccessionParser |
Class to parse the NCBI gene2accession files.
|
NCBIGene2GOAssociationLoader |
|
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.
|
NCBIUtil |
|
NeedsAttentionEvent |
Indicates that previous validation is being invalidated
|
NetDatasourceUtil |
Helper methods to get FTP connection.
|
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.
|
NotTroubledStatusFlagEvent |
This event type resets the trouble flag of curation details of a curatable object.
|
OntologyHighlighter |
Highlighter specialized for ontology terms.
|
OntologyIndividualSimple |
|
OntologyPropertySimple |
|
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.
|
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 |
|
Parser<T> |
Interface for classes that allow parsing of files and streams.
|
ParserAndLoaderTools |
Utilities to be used by parsers and loaders.
|
ParseSearchException |
An exception that indicate that the search query could not be parsed.
|
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 |
|
PhenotypeGroupValueObject |
|
PhenotypeMappingType |
Deprecated. |
PhenotypeValueObject |
|
PhysicalLocation |
|
PhysicalLocation.Factory |
|
PhysicalLocationValueObject |
A very simple value object to represent a physical location
|
PlatformFetcher |
Fetch GEO "GPLXXX_family.soft.gz" files
|
Pointcuts |
General-purpose pointcuts to recognize CRUD operations etc.
|
PolymerType |
|
PreparedCoexMatrices |
Helper class for sample coexpression analysis.
|
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 |
Primitive storage types for data vectors.
|
PrincipalComponentAnalysis |
|
PrincipalComponentAnalysis.Factory |
|
PrincipalComponentAnalysisDao |
|
PrincipalComponentAnalysisDaoImpl |
|
PrincipalComponentAnalysisService |
|
PrincipalComponentAnalysisServiceImpl |
|
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.
|
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
|
ProfilingConfig |
|
ProgressData |
|
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 |
|
PropertySourcesConfiguration |
Deprecated.
|
Protocol |
|
Protocol.Factory |
|
ProtocolDao |
|
ProtocolDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Protocol .
|
ProtocolService |
|
ProtocolServiceImpl |
|
PubMedSearch |
Search PubMed for terms, retrieve document records.
|
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 |
|
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.
|
QuantitationTypeService |
|
QuantitationTypeServiceImpl |
|
QuantitationTypeValueObject |
|
QueryUtils |
|
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
|
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
|
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 |
|
ResetSuitabilityForDifferentialExpressionAnalysisEvent |
Used to indicate that the suitability status of an experiment is the default.
|
Retryable |
Indicate that the method should be retried on failure.
|
RetryLogger |
Provide logging when an operation has failed and is being retried.
|
RowLevelFilter |
|
RowLevelFilter.Method |
|
RowMissingValueFilter |
Filter out rows that have "too many" missing values.
|
RowsWithSequencesFilter |
Remove rows that have no BioSequence associated with the row.
|
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 |
|
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> |
Represents an individual search result.
|
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.
|
SearchTimeoutException |
|
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 |
|
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.
|
SessionBoundExpressionExperimentSetValueObject |
|
SessionBoundGeneSetValueObject |
|
Settings |
Deprecated.
|
SettingsConfig |
Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
|
SFARIIntermediateFileParser |
Deprecated. |
SFARILineInfo |
Deprecated. |
ShellDelegatingBlat |
Class to manage the gfServer and run BLAT searches.
|
ShellDelegatingBlat.BlattableGenome |
|
SimpleExpressionDataLoaderService |
Load experiment from a flat file.
|
SimpleExpressionDataLoaderServiceImpl |
Convert a simple matrix and some meta-data into an ExpressionExperiment.
|
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.
|
SimpleMarkdownFormatter |
|
SimpleThreadFactory |
A simple thread factory based on a preferably unique thread name prefix.
|
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.
|
Slice<O> |
Represents a slice of List .
|
SlicedDoubleVectorValueObject |
|
Sort |
Represents a directed sort by a property.
|
Sort.Direction |
Direction of the sort.
|
SourceDomainObjectGenerator |
|
SpearmanMetrics |
Subclass that computes correlations using ranks.
|
SplitExperimentService |
TODO Document Me
|
SplitExperimentServiceImpl |
Split an experiment into multiple experiments.
|
SpringContextUtils |
Methods to create Spring contexts for Gemma manually.
|
StandardQuantitationType |
|
Statement |
A special kind of characteristic that act as a statement.
|
Statement.Factory |
|
StatementDao |
|
StatementDaoImpl |
|
StatementValueObject |
|
StaticCacheKeyLock |
Implementation of the CacheKeyLock interface that uses a static week map to store locks by key.
|
StopWatchUtils |
Utilities for working with StopWatch .
|
StopWatchUtils.StopWatchRegion |
|
SubmittedTask |
Obtained from the TaskRunningService, can be used to monitor status.
|
SubmittedTask.Status |
|
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 |
|
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.
|
TableMaintenanceUtil |
|
TableMaintenanceUtilImpl |
Functions for maintaining the database.
|
Task<C extends TaskCommand> |
|
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.
|
TaskMailUtils |
|
TaskMailUtilsImpl |
|
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.
|
Taxon |
|
Taxon.Factory |
|
TaxonDao |
|
TaxonDaoImpl |
|
TaxonFetcher |
Taxon information from NCBI comes as a tar.gz archive; only the names.dmp file is of interest.
|
TaxonLoader |
Load taxa into the system.
|
TaxonParser |
Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
|
TaxonService |
|
TaxonServiceImpl |
|
TaxonUtils |
A utility class for taxon.
|
TaxonValueObject |
|
TechnologyType |
|
TestComponent |
This will exclude the component or configuration from component scanning.
|
TextResourceToSetOfLinesFactoryBean |
Converts a text resource into a set of lines.
|
TGFVO |
Vocabulary for The Gemma Factor Value Ontology (TGFVO).
|
ThreadPoolExecutorMetrics |
|
ThreadPoolTaskExecutorMetrics |
|
ThreePrimeDistanceMethod |
|
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.
|
TwoChannelMissingValueHelperService |
|
TwoChannelMissingValues |
|
TwoChannelMissingValuesImpl |
Computes a missing value matrix for ratiometric data sets.
|
TwoChannelMissingValueTaskCommand |
|
TwoChannelMissingValueTaskImpl |
Space task for computing two channel missing values.
|
TypedResultTransformer<T> |
|
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 |
|
UpdatePubMedCommand |
|
User |
A user of the software system, who is authenticated.
|
User.Factory |
|
UserDao |
|
UserDaoImpl |
DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.auditAndSecurity.User .
|
UserGroup |
An organized group of researchers with an identifiable leader and group members.
|
UserGroup.Factory |
|
UserGroupDao |
|
UserGroupDaoImpl |
|
UserManager |
Overrides gsec's UserManager to provide Gemma-specific types.
|
UserManagerImpl |
Implementation for Spring Security, plus some other handy methods.
|
UserQuery |
|
UserQuery.Factory |
|
UserService |
Override a few definition from gsec so that we can use Gemma-specific implementations safely.
|
UserServiceImpl |
|
ValidateEvidenceValueObject |
|
ValueObject |
Annotate class representing value objects.
|
ValueObjectConfig |
|
VectorMergingService |
|
VectorMergingServiceImpl |
Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
|
Versioned |
Interface implemented by entities that are externally versioned.
|
VersionedEvent |
Base class for events relating to a Versioned entity.
|
WhatsNew |
A value object to hold onto the 'new' objects.
|
WhatsNewService |
Creates reports that can be shown on the web pages or in social media feeds.
|
WhatsNewServiceImpl |
Service to collect data on object that are new in the system.
|
XMLUtils |
Handy methods for dealing with XML.
|