All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
| Class |
Description |
| AbaGene |
|
| ABALinkOutValueObject |
Value Object for transporting details needed from other websites to provide convenient links to them in gemma
|
| AbstractAnalyzer |
Analyzer base class.
|
| AbstractAsyncFactoryBean<T> |
|
| AbstractAuditable |
An entity which can have an audit trail attached to it.
|
| AbstractCriteriaFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> |
Created by tesarst on 07/03/17.
|
| AbstractCuratableValueObject<C extends Curatable> |
Created by tesarst on 07/03/17.
|
| AbstractDao<T extends Identifiable> |
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
|
| AbstractDescribable |
|
| AbstractDesignElementDataVectorDao<T extends DesignElementDataVector> |
|
| AbstractDesignElementDataVectorService<T extends DesignElementDataVector> |
|
| AbstractDifferentialExpressionAnalyzer |
An abstract differential expression analyzer to be extended
|
| AbstractFactorValueValueObject |
The bare minimum to represent a factor value.
|
| AbstractFetcher |
|
| AbstractFileService<T> |
Provide base implementation for all sorts of file services that serialize data in tabular format.
|
| AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractFilteringVoEnabledDao.FilterablePropertyMeta |
Meta-information for a filterable property.
|
| AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractGeoService |
|
| AbstractMatrixRowPairAnalysis |
|
| AbstractMeterRegistryConfigurer |
|
| AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
|
| AbstractOntologyResourceSimple |
|
| AbstractPersister |
|
| AbstractPersister.Caches |
Various caches to refer back to not-yet persisted entities (and thus not easily obtainable from the persistence
context).
|
| AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| AbstractService<O extends Identifiable> |
Base for all services handling DAO access.
|
| AbstractTask<C extends TaskCommand> |
|
| AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| AclAdvice |
For permissions modification to be triggered, the method name must match certain patterns, which include "create", or
"remove".
|
| AclAfterCollectionCompSeqByArrayDesignFilter |
For this particular AfterInvocationProvider, composite sequence authorization is determined based on the secured
array design acl.
|
| AclAfterCollectionDataVectorByExpressionExperimentFilter |
Filter collections of DesignElementDataVectors or DataVectorValueObjects based on the permissions of the associated
ExpressionExperiment(s).
|
| AclAfterCompSeqByArrayDesignFilter |
|
| AclCriteriaUtils |
Utilities for integrating ACLs with Hibernate Criteria API. |
| AclQueryUtils |
Utilities for integrating ACL into Query. |
| AffyChipTypeExtractor |
Extract the chip type from Affymetrix CEL files.
|
| AffyPowerToolsProbesetSummarize |
|
| AffyProbeNameFilter |
|
| AffyProbeNameFilter.Pattern |
|
| AffyProbeReader |
Reads Affymetrix Probe files, including exon arrays.
|
| AffyScanDateExtractor |
Extract the scan date from Affymetrix CEL files.
|
| AgilentScanDateExtractor |
Because agilent makes slides that work with any scanner, the formats are not that predictable.
|
| AlignmentBasedGeneMappingEvent |
Signifies a mapping based on sequence alignment performed by the system.
|
| AllenBrainAtlasService |
|
| AllenBrainAtlasServiceImpl |
Acts as a convenient front end to the Allen Brain Atlas REST (web) services Used the ABAApi.java as the original
template for this Service (found in ABA demo code).
|
| AlreadyExistsInSystemException |
Can be thrown when an attempt is made to load data into the system that already exists.
|
| AlternateName |
|
| AlternateName.Factory |
|
| Analysis |
An analysis of one or more Investigations.
|
| AnalysisDao<T extends SingleExperimentAnalysis> |
|
| AnalysisResult |
|
| AnalysisResultSet<R extends AnalysisResult> |
An abstract class representing a related set of generic analysis results, part of an analysis.
|
| AnalysisResultSetDao<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
|
| AnalysisResultSetService<K extends AnalysisResult,O extends AnalysisResultSet<K>> |
|
| AnalysisResultSetValueObject<K extends AnalysisResult,R extends AnalysisResultSet<K>> |
|
| AnalysisResultValueObject<A extends AnalysisResult> |
|
| AnalysisSelectionAndExecutionService |
|
| AnalysisSelectionAndExecutionServiceImpl |
A differential expression analysis tool that executes the appropriate analysis based on the number of experimental
factors and factor values, as well as the block design.
|
| AnalysisService<T extends Analysis> |
Provides basic services for dealing with analyses
|
| AnalysisSuitabilityEvent |
Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
|
| AnalysisUtilService |
|
| AnalysisUtilServiceImpl |
Utility methods for dealing with analyses.
|
| AnalysisValueObject<T extends Analysis> |
|
| AnnotationAssociation |
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather
than our own sequence analysis.
|
| AnnotationAssociation.Factory |
|
| AnnotationAssociationDao |
|
| AnnotationAssociationDaoImpl |
|
| AnnotationAssociationService |
|
| AnnotationAssociationServiceImpl |
|
| AnnotationBasedGeneMappingEvent |
To signify the array design was mapped from an external source, not by our own sequence analysis.
|
| AnnotationEvent |
|
| AnnotationValueObject |
|
| ArchiveFetcher |
Interface defining a class that downloads archives and unpacks them.
|
| ArrayDesign |
Represents an assembly of design elements that are assayed all at once.
|
| ArrayDesign.Factory |
|
| ArrayDesignAnalysisEvent |
An event involving the analysis of an ArrayDesign
|
| ArrayDesignAnnotationService |
Methods to generate annotations for array designs, based on information already in the database.
|
| ArrayDesignAnnotationService.OutputType |
|
| ArrayDesignAnnotationServiceImpl |
|
| ArrayDesignDao |
Created by tesarst on 13/03/17.
|
| ArrayDesignDaoImpl |
|
| ArrayDesignGeneMappingEvent |
The mapping of probes to genes for an ArrayDesign
|
| ArrayDesignMapResultService |
|
| ArrayDesignMapResultServiceImpl |
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
|
| ArrayDesignMergeEvent |
|
| ArrayDesignMergeHelperService |
|
| ArrayDesignMergeHelperServiceImpl |
|
| ArrayDesignMergeService |
Make new array design based on others
Keep map of relation between new design elements and old ones
Store relationship with mergees
|
| ArrayDesignMergeServiceImpl |
|
| ArrayDesignParser |
Deprecated. |
| ArrayDesignPersister |
This class handles persisting array designs.
|
| ArrayDesignProbeMapperService |
|
| ArrayDesignProbeMapperServiceImpl |
For an array design, generate gene product mappings for the sequences.
|
| ArrayDesignProbeMapperTaskImpl |
A probe mapper spaces task .
|
| ArrayDesignProbeMapTaskCommand |
A command object to be used by spaces.
|
| ArrayDesignProbeRenamingEvent |
Signifies that the probes were renamed from their original values.
|
| ArrayDesignRepeatAnalysisEvent |
|
| ArrayDesignReportService |
|
| ArrayDesignReportServiceImpl |
|
| ArrayDesignSequenceAlignmentService |
|
| ArrayDesignSequenceAlignmentServiceImpl |
Aligns sequences from array designs to the genome, using blat, and persists the blat results.
|
| ArrayDesignSequenceAnalysisEvent |
The sequence alignment analysis of an ArrayDesign
|
| ArrayDesignSequenceProcessingService |
|
| ArrayDesignSequenceProcessingServiceImpl |
Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
|
| ArrayDesignSequenceRemoveEvent |
Used to indicate that all associations that this array design has with BioSequences have been removed.
|
| ArrayDesignSequenceUpdateEvent |
The updating of the sequences associated with an ArrayDesign
|
| ArrayDesignService |
|
| ArrayDesignServiceImpl |
|
| ArrayDesignsForExperimentCache |
Used to hold information for matching to a new experiment, during persisting.
|
| ArrayDesignSubsumeCheckEvent |
|
| ArrayDesignValueObject |
Value object for quickly displaying varied information about Array Designs.
|
| ArrayExpressUtil |
|
| AsyncFactoryBean<T> |
|
| AsyncFactoryBeanUtils |
Utilities for manipulating async factory beans.
|
| Auditable |
Created by tesarst on 07/03/17.
|
| AuditableObject |
|
| AuditAction |
|
| AuditAdvice |
Manage audit trails on objects.
|
| AuditEvent |
An event in the life of an object.
|
| AuditEvent.Factory |
|
| AuditEventDao |
|
| AuditEventDaoImpl |
|
| AuditEventService |
|
| AuditEventServiceImpl |
|
| AuditEventType |
|
| AuditEventValueObject |
|
| AuditTrail |
The trail of events (create or update) that occurred in an objects lifetime.
|
| AuditTrail.Factory |
|
| AuditTrailDao |
|
| AuditTrailDaoImpl |
|
| AuditTrailService |
Create and manipulate audit trails.
|
| AuditTrailServiceImpl |
|
| AutomatedAnnotationEvent |
Deprecated.
|
| BaseCodeConfigurer |
Configure the baseCode library from a given property sources.
|
| BaseCodeOntologySearchException |
|
| BaseDao<T> |
Interface that supports basic CRUD operations.
|
| BaseExpressionDataMatrix<T> |
Base class for ExpressionDataMatrix implementations.
|
| BaseImmutableService<O extends Identifiable> |
Base service class for an immutable entity.
|
| Baseline |
Represents a baseline for a single factor or an interaction of factors.
|
| BaselineSelection |
Utilities for deciding if a factor value is a baseline condition.
|
| BaseReadOnlyService<O extends Identifiable> |
Interface for read-only services.
|
| BaseScanDateExtractor |
|
| BaseService<O extends Identifiable> |
Interface that supports basic CRUD operations.
|
| BaseValueObject |
|
| BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
Created by tesarst on 01/06/17.
|
| BasicLineMapParser<K,T> |
A line parser that produces a Map instead of a Collection.
|
| BasicLineParser<T> |
A simple LineParser implementation that doesn't do anything.
|
| BatchConfound |
Represents a summary of a batch effect confound.
|
| BatchConfoundUtils |
Test if an experimental design is confounded with batches.
|
| BatchCorrectionEvent |
|
| BatchEffectDetails |
provide some basic information about the properties and strength of a batch effect, if any.
|
| BatchEffectType |
Represents a batch effect.
|
| BatchInfoFetchTask |
|
| BatchInfoFetchTaskCommand |
|
| BatchInfoFetchTaskImpl |
Task to try to get 'batch' information about an experiment.
|
| BatchInfoMissingException |
Indicate that batch information is missing.
|
| BatchInfoParser |
Parse information on batch from raw data files.
|
| BatchInfoPopulationException |
Used to indicate a problem with the population of batch information for a given
ExpressionExperiment. |
| BatchInfoPopulationHelperService |
|
| BatchInfoPopulationHelperServiceImpl |
|
| BatchInfoPopulationService |
Retrieve batch information from the data source, if possible, and populate it into experiments.
|
| BatchInfoPopulationServiceImpl |
Retrieve batch information from the data source, if possible, and populate it into experiments.
|
| BatchInformationEvent |
Abstract class for events related to batch information.
|
| BatchInformationFetchingEvent |
Indicates that batch information was successfully obtained.
|
| BatchInformationMissingEvent |
Indicate that batch information has been looked for and was missing.
|
| BatchProblemsUpdateEvent |
Event that tracks when batch effects or problems are detected.
|
| BeanFactoryUtils |
Utilities for working with bean factories.
|
| BeanInitializationTimeMonitor |
Hook into the bean post-processing lifecycle and record bean initialization time.
|
| BeanNameGenerator |
Our \@Service etc.
|
| BibliographicPhenotypesValueObject |
|
| BibliographicReference |
|
| BibliographicReference.Factory |
|
| BibliographicReferenceDao |
|
| BibliographicReferenceDaoImpl |
|
| BibliographicReferenceService |
|
| BibliographicReferenceServiceImpl |
Implementation of BibliographicReferenceService.
|
| BibliographicReferenceValueObject |
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists
in web
|
| BibRefAnnotation |
|
| BioAssay |
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
|
| BioAssay.Factory |
|
| BioAssayDao |
|
| BioAssayDaoImpl |
|
| BioAssayDimension |
Stores the order of BioAssays referred to in DataVectors.
|
| BioAssayDimension.Factory |
|
| BioAssayDimensionDao |
|
| BioAssayDimensionDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
|
| BioAssayDimensionService |
|
| BioAssayDimensionServiceImpl |
Spring Service base class for BioAssayDimensionService, provides access to all services and entities
referenced by this service.
|
| BioAssayDimensionValueObject |
|
| BioAssayOutlierProcessingTask |
|
| BioAssayOutlierProcessingTaskCommand |
|
| BioAssayOutlierProcessingTaskImpl |
Handle 'flagging' a sample as an outlier.
|
| BioAssayService |
|
| BioAssayServiceImpl |
|
| BioAssaySet |
Represents a set of BioAssays.
|
| BioAssaySetService |
Generic service for dealing with all subclasses of BioAssaySet. |
| BioAssaySetServiceImpl |
|
| BioAssayValueObject |
|
| BiomartEnsembleNcbiParser |
Parser for BioMart file.
|
| BiomartEnsemblNcbiFetcher |
BioMart is a query-oriented data management system.
|
| BiomartEnsemblNcbiObjectGenerator |
Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble
protein id.
|
| BioMaterial |
In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA,
proteins, etc...
|
| BioMaterial.Factory |
|
| BioMaterialDao |
|
| BioMaterialDaoImpl |
|
| BioMaterialMappingUpdate |
To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.
|
| BioMaterialService |
|
| BioMaterialServiceImpl |
|
| BioMaterialValueObject |
|
| BioSequence |
The sequence of a biological polymer such as a protein or DNA.
|
| BioSequence.Factory |
|
| BioSequence2GeneProduct |
An association between a BioSequence and a Gene Product.
|
| BioSequenceDao |
|
| BioSequenceDaoImpl |
|
| BioSequenceService |
|
| BioSequenceServiceImpl |
Spring Service base class for BioSequenceService, provides access to
all services and entities referenced by this service.
|
| BioSequenceValueObject |
|
| BlacklistedEntity |
|
| BlacklistedEntityDao |
|
| BlacklistedEntityDaoImpl |
|
| BlacklistedEntityService |
|
| BlacklistedEntityServiceImpl |
|
| BlacklistedExperiment |
TODO Document Me
|
| BlacklistedPlatform |
|
| BlacklistedValueObject |
|
| Blat |
|
| BlatAssociation |
|
| BlatAssociation.Factory |
|
| BlatAssociationDao |
|
| BlatAssociationDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
BlatAssociation.
|
| BlatAssociationScorer |
Given a set of BlatAssociations that might be redundant, clean them up and score them.
|
| BlatAssociationService |
|
| BlatAssociationServiceImpl |
Spring Service base class for BlatAssociationService, provides access to all services and entities
referenced by this service.
|
| BlatResult |
Represents the result of a BLAT search.
|
| BlatResult.Factory |
|
| BlatResult2Psl |
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
|
| BlatResultDao |
|
| BlatResultDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.sequenceAnalysis.BlatResult.
|
| BlatResultParser |
Loader to handle results generated by Jim Kent's Blat.
|
| BlatResultService |
|
| BlatResultServiceImpl |
Spring Service base class for BlatResultService, provides access to all services and entities referenced
by this service.
|
| BlatResultValueObject |
|
| BooleanVectorValueObject |
This is used to represent missing value data.
|
| BootstrappedDataSourceFactory |
A bootstrapped data source that strips the database from the JDBC URL.
|
| BrowsingDao<T> |
Support for paging through the data.
|
| BuildInfo |
|
| BusinessKey |
Methods to test business-key-related issues on objects.
|
| CachedFilteringDao<O extends Identifiable> |
|
| CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> |
|
| CachedProcessedExpressionDataVectorService |
|
| CachedProcessedExpressionDataVectorServiceImpl |
|
| CacheKeyLock |
Represents a lock over a cache key.
|
| CacheKeyLock.LockAcquisition |
Represents an acquired lock on a cache key.
|
| CacheUtils |
Created by tesarst on 04/04/17.
|
| ChannelUtils |
Determine if a quantitation type (by name) represents background or signal.
|
| Characteristic |
Instances of this are used to describe other entities.
|
| Characteristic.Factory |
|
| CharacteristicDao |
|
| CharacteristicDao.CharacteristicUsageFrequency |
|
| CharacteristicDaoImpl |
|
| CharacteristicService |
|
| CharacteristicServiceImpl |
|
| CharacteristicUpdateCommand |
|
| CharacteristicUpdateTask |
|
| CharacteristicUpdateTaskImpl |
This handles characteristic updates from the client: experiment tags, characteristic browser
|
| CharacteristicUtils |
|
| CharacteristicValueObject |
|
| Chromosome |
Immutable representation of a chromosome
|
| ChromosomeDao |
|
| ChromosomeDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.Chromosome.
|
| ChromosomeFeature |
Some part of a chromosome
|
| ChromosomeLocation |
|
| ChromosomeService |
|
| ChromosomeServiceImpl |
Spring Service base class for ChromosomeService, provides access to all services
and entities referenced by this service.
|
| ChromosomeUtils |
|
| CitationValueObject |
Represents a BibliographicReference as a citation string (which is really super light value object).
|
| CoexpCorrelationDistribution |
|
| CoexpCorrelationDistribution.Factory |
|
| CoexpressionAnalysis |
A coexpression analysis of one experiment.
|
| CoexpressionAnalysis.Factory |
|
| CoexpressionAnalysisDao |
|
| CoexpressionAnalysisDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.
|
| CoexpressionAnalysisService |
Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
|
| CoexpressionAnalysisServiceImpl |
|
| CoexpressionCache |
Cache for coexpression results.
|
| CoexpressionCacheImpl |
Configures the cache for gene2gene coexpression.
|
| CoexpressionCacheValueObject |
Used to cache results; these objects are unmodifiable, and contains the coexpression data for one query gene and one
result gene, in all experiments.
|
| CoexpressionDao |
|
| CoexpressionDaoImpl |
Manages and queries coexpression 'links' between genes.
|
| CoexpressionMetaValueObject |
|
| CoexpressionNodeDegreeDao |
|
| CoexpressionNodeDegreeDaoImpl |
|
| CoexpressionSearchCommand |
|
| CoexpressionService |
A key service for working with coexpression at a fairly low level.
|
| CoexpressionServiceImpl |
|
| CoexpressionSummaryValueObject |
|
| CoexpressionValueObject |
Lightweight/convenient object for manipulating coexpression for a pair of genes.
|
| CoexpressionValueObjectExt |
A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
|
| 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 |
|
| CompositeSequenceDao |
|
| CompositeSequenceDaoImpl |
|
| CompositeSequenceGeneMapperService |
|
| CompositeSequenceMapSummary |
This is a convenience object to hold the results of CompositeSequence mapping results.
|
| CompositeSequenceMapValueObject |
|
| CompositeSequenceParser |
Parse the "old" array description format.
|
| CompositeSequenceService |
|
| CompositeSequenceServiceImpl |
|
| CompositeSequenceValueObject |
|
| Compound |
|
| Compound.Factory |
|
| CompoundDao |
|
| CompoundDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.biomaterial.Compound.
|
| CompoundService |
|
| CompoundServiceImpl |
Spring Service base class for CompoundService, provides access to all services and entities referenced
by this service.
|
| Contact |
Representing a person or organization that can be contacted about, or is the source of, data in the system.
|
| Contact.Factory |
|
| ContactDao |
|
| ContactDaoImpl |
|
| ContactService |
|
| ContactServiceImpl |
|
| Contrast |
Represents a contrast.
|
| 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.
|
| CreateDatabasePopulator |
Create a new database and drop an existing one if desired.
|
| Curatable |
Created by tesarst on 06/03/17.
|
| CuratableDao<C extends Curatable> |
Created by tesarst on 13/03/17.
|
| CurationDetails |
Class encapsulating all the curation information for Curatable objects.
|
| CurationDetailsEvent |
|
| 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 |
|
| DatabaseEntry |
A reference to a record in a database.
|
| DatabaseEntry.Factory |
|
| DatabaseEntryDao |
|
| 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
|
| DatabaseSchemaPopulator |
Populates the database schema.
|
| 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 |
|
| DifferentialExpressionAnalysisResultListFileService |
|
| DifferentialExpressionAnalysisResultListFileServiceImpl |
|
| 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.
|
| ExpressionExperimentBatchInformationService |
Provides status of batch information for datasets.
|
| ExpressionExperimentBatchInformationServiceImpl |
|
| 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 |
For endpoints that may return an error.
|
| GemmaRestApiClient.ErrorResponse.Error |
|
| 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 |
|
| 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.
|
| GeneOntologySearchSource |
GO-based search source.
|
| GeneOntologyService |
|
| GeneOntologyServiceImpl |
|
| GeneOntologyServiceImpl.GOAspect |
|
| GeneOntologyTermValueObject |
|
| GeneOntologyUtils |
|
| 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.
|
| IdentifiableUtils |
|
| 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. |
| InitialDataPopulator |
Populate some initial data for tests.
|
| 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).
|
| LocalSessionFactoryBean |
|
| 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 |
|
| NcbiEntityResolver |
Resolve a bunch of NCBI DTDs in the classpath.
|
| 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.
|
| NonUniqueQuantitationTypeByNameException |
Exception raised when retrieving a non-unique QT by name.
|
| 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 |
|
| SearchSettingsUtils |
|
| SearchSettingsValueObject |
author: anton date: 18/03/13
|
| SearchSource |
Search source that provides SearchResult from a search engine. |
| SearchTimeoutException |
|
| Securable |
|
| SecurableBaseImmutableService<C extends Securable> |
|
| SecurableBaseReadOnlyService<C extends Securable> |
|
| SecurableBaseService<C extends Securable> |
A base service for securable entities.
|
| SecurableBaseVoEnabledService<C extends Securable,VO extends IdentifiableValueObject<C>> |
|
| SecurableFilteringVoEnabledService<C extends Securable,VO extends IdentifiableValueObject<C>> |
A base service for securable entities with filtering and VO capabilities.
|
| SecuredChild |
|
| SecuredNotChild |
|
| 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 |
|
| SubqueryMode |
Mode to use when filtering with a subquery.
|
| 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 |
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| TwoChannelMissingValuesImpl |
Computes a missing value matrix for ratiometric data sets.
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| TwoChannelMissingValueTaskCommand |
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| TwoChannelMissingValueTaskImpl |
Space task for computing two channel missing values.
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| TypedResultTransformer<T> |
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| UninformativeFASTQHeadersForBatchingEvent |
Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of
invalid formatting or lack of information.
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| Unit |
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| Unit.Factory |
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| UnitDao |
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| UnitDaoImpl |
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.measurement.Unit.
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| UnsuitableForAnalysisException |
*
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| UnsuitableForDifferentialExpressionAnalysisEvent |
Indicates that the associated Experiment is NOT suitable for differential expression analysis.
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| UnsupportedQuantitationScaleConversionException |
Exception raised when data from a given scale cannot be converted to another scale.
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| UnsupportedRawdataFileFormatException |
Used to indicate failure was due to the format being unusable, but the files are available.
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| UpdateEEDetailsCommand |
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| UpdatePubMedCommand |
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| User |
A user of the software system, who is authenticated.
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| User.Factory |
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| UserDao |
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| UserDaoImpl |
DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.auditAndSecurity.User.
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| UserGroup |
An organized group of researchers with an identifiable leader and group members.
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| UserGroup.Factory |
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| UserGroupDao |
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| UserGroupDaoImpl |
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| UserManager |
Overrides gsec's UserManager to provide Gemma-specific types.
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| UserManagerImpl |
Implementation for Spring Security, plus some other handy methods.
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| UserQuery |
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| UserQuery.Factory |
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| UserService |
Override a few definition from gsec so that we can use Gemma-specific implementations safely.
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| UserServiceImpl |
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| ValidateEvidenceValueObject |
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| ValueObject |
Annotate class representing value objects.
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| ValueObjectConfig |
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| VectorMergingService |
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| VectorMergingServiceImpl |
Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
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| Versioned |
Interface implemented by entities that are externally versioned.
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| VersionedEvent |
Base class for events relating to a Versioned entity. |
| WhatsNew |
A value object to hold onto the 'new' objects.
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| WhatsNewService |
Creates reports that can be shown on the web pages or in social media feeds.
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| WhatsNewServiceImpl |
Service to collect data on object that are new in the system.
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| XMLUtils |
Handy methods for dealing with XML.
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| XSDEntityResolver |
Resolves Hibernate XSD schemas from the classpath.
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