Interface ExpressionExperimentDataVectorService

All Known Implementing Classes:

ExpressionExperimentDataVectorServiceImpl

public interface ExpressionExperimentDataVectorService

Raw + processed data vector CRUD operations for ExpressionExperiment.

Phase 3 of the ExpressionExperimentService decomposition (strangler fig, slice 3). Houses the raw / processed expression-data-vector cluster previously implemented directly on the ExpressionExperimentServiceImpl facade: the getRawDataVectors family, the addRawDataVectors / replaceRawDataVectors / replaceAllRawDataVectors / removeRawDataVectors family, the corresponding *ProcessedDataVectors methods, and the supporting BioAssayDimension + QuantitationType create-if-needed orchestration shared between raw and processed paths.

Callers should generally keep using ExpressionExperimentService as the facade — the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring construction cycle through the heavier facade.

ACL / @Secured annotations live on ExpressionExperimentService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• ExpressionExperimentService

Method Summary

Modifier and Type	Method	Description
int	addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors for a quantitation type.
int	createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
Map<QuantitationType, Collection<RawExpressionDataVector>>	getMissingValuesVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	removeAllRawDataVectors(ExpressionExperiment ee)
int	removeProcessedDataVectors(ExpressionExperiment ee)
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)	Equivalent to removeRawDataVectors(ee, qt, false).
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.
int	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)

Method Details

getRawDataVectors

Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, QuantitationType)

getRawDataVectors

Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType qt)

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, List, QuantitationType)

getPreferredRawDataVectors

Collection<RawExpressionDataVector> getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)

See Also:

• ExpressionExperimentDao.getPreferredRawDataVectors(ExpressionExperiment)

getMissingValuesVectors

Map<QuantitationType, Collection<RawExpressionDataVector>> getMissingValuesVectors(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.getMissingValuesVectors(ExpressionExperiment)

addRawDataVectors

int addRawDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<RawExpressionDataVector> newVectors)

Add raw data vectors for a quantitation type. The dimension and QT are created on-demand if they are still transient.

replaceRawDataVectors

int replaceRawDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<RawExpressionDataVector> vectors)

See Also:

• ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection)

replaceAllRawDataVectors

int replaceAllRawDataVectors(ExpressionExperiment ee,
 Collection<RawExpressionDataVector> vectors)

Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.

removeAllRawDataVectors

int removeAllRawDataVectors(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.removeAllRawDataVectors(ExpressionExperiment)

removeRawDataVectors

int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Equivalent to removeRawDataVectors(ee, qt, false).

removeRawDataVectors

int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 boolean keepDimension)

See Also:

• ExpressionExperimentDao.removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean)

getProcessedDataVectors

Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment)

getProcessedDataVectors

Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee,
 List<BioAssay> assays)

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment, List)

createProcessedDataVectors

int createProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

See Also:

• ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment, Collection)

removeProcessedDataVectors

int removeProcessedDataVectors(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.removeProcessedDataVectors(ExpressionExperiment)

replaceProcessedDataVectors

int replaceProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

See Also:

• ExpressionExperimentDao.replaceProcessedDataVectors(ExpressionExperiment, Collection)