Interface PrincipalComponentAnalysisService

All Superinterfaces:

BaseImmutableService<PrincipalComponentAnalysis>, BaseReadOnlyService<PrincipalComponentAnalysis>

All Known Implementing Classes:

PrincipalComponentAnalysisServiceImpl

public interface PrincipalComponentAnalysisService
extends BaseImmutableService<PrincipalComponentAnalysis>

Author:

paul

Method Summary

Modifier and Type	Method	Description
PrincipalComponentAnalysis	create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
boolean	existsByExperiment(ExpressionExperiment ee)
List<ProbeLoading>	getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
PrincipalComponentAnalysis	loadForExperiment(ExpressionExperiment ee)
void	removeForExperiment(ExpressionExperiment ee)
PrincipalComponentAnalysis	replaceForExperiment(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)	Remove the experiment's PCA and store the given one, in a single transaction.

Methods inherited from interface BaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Method Details

create

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
PrincipalComponentAnalysis create(ExpressionExperiment ee,
 DoubleMatrix<CompositeSequence, Integer> u,
 double[] eigenvalues,
 DoubleMatrix<Integer, BioMaterial> v,
 BioAssayDimension bad,
 int numComponentsToStore,
 int numLoadingsToStore)

getTopLoadedProbes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<ProbeLoading> getTopLoadedProbes(ExpressionExperiment ee,
 int component,
 int count)

removeForExperiment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeForExperiment(ExpressionExperiment ee)

replaceForExperiment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
PrincipalComponentAnalysis replaceForExperiment(ExpressionExperiment ee,
 DoubleMatrix<CompositeSequence, Integer> u,
 double[] eigenvalues,
 DoubleMatrix<Integer, BioMaterial> v,
 BioAssayDimension bad,
 int numComponentsToStore,
 int numLoadingsToStore)

Remove the experiment's PCA and store the given one, in a single transaction.

🛑 The two halves must not be separate transactions. SVDServiceImpl.svd is Propagation.NEVER — the decomposition between its read and its write takes long enough that a transaction must not be open across it — so calling removeForExperiment(ExpressionExperiment) and create(ExpressionExperiment, DoubleMatrix, double[], DoubleMatrix, BioAssayDimension, int, int) from there would commit the removal, then fail, and leave the experiment with no PCA at all. Same shape as replaceProcessedDataVectors.

loadForExperiment

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
PrincipalComponentAnalysis loadForExperiment(ExpressionExperiment ee)

existsByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
boolean existsByExperiment(ExpressionExperiment ee)