Class PrincipalComponentAnalysisServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<PrincipalComponentAnalysis>

ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl

All Implemented Interfaces:

PrincipalComponentAnalysisService, BaseImmutableService<PrincipalComponentAnalysis>, BaseReadOnlyService<PrincipalComponentAnalysis>, BaseService<PrincipalComponentAnalysis>

@Service
public class PrincipalComponentAnalysisServiceImpl
extends AbstractService<PrincipalComponentAnalysis>
implements PrincipalComponentAnalysisService

Author:

paul

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
PrincipalComponentAnalysisServiceImpl(PrincipalComponentAnalysisDao principalComponentAnalysisDao)

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 class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Constructor Details

PrincipalComponentAnalysisServiceImpl

@Autowired
public PrincipalComponentAnalysisServiceImpl(PrincipalComponentAnalysisDao principalComponentAnalysisDao)

Method Details

create

@Transactional
public PrincipalComponentAnalysis create(ExpressionExperiment ee,
 DoubleMatrix<CompositeSequence, Integer> u,
 double[] eigenvalues,
 DoubleMatrix<Integer, BioMaterial> v,
 BioAssayDimension bad,
 int numComponentsToStore,
 int numLoadingsToStore)

Specified by:

create in interface PrincipalComponentAnalysisService

getTopLoadedProbes

public List<ProbeLoading> getTopLoadedProbes(ExpressionExperiment ee,
 int component,
 int count)

Specified by:

getTopLoadedProbes in interface PrincipalComponentAnalysisService

loadForExperiment

public PrincipalComponentAnalysis loadForExperiment(ExpressionExperiment ee)

Specified by:

loadForExperiment in interface PrincipalComponentAnalysisService

existsByExperiment

public boolean existsByExperiment(ExpressionExperiment ee)

Specified by:

existsByExperiment in interface PrincipalComponentAnalysisService

replaceForExperiment

@Transactional
public PrincipalComponentAnalysis replaceForExperiment(ExpressionExperiment ee,
 DoubleMatrix<CompositeSequence, Integer> u,
 double[] eigenvalues,
 DoubleMatrix<Integer, BioMaterial> v,
 BioAssayDimension bad,
 int numComponentsToStore,
 int numLoadingsToStore)

Description copied from interface: PrincipalComponentAnalysisService

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 PrincipalComponentAnalysisService.removeForExperiment(ExpressionExperiment) and PrincipalComponentAnalysisService.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.

Specified by:

replaceForExperiment in interface PrincipalComponentAnalysisService

removeForExperiment

@Transactional
public void removeForExperiment(ExpressionExperiment ee)

Specified by:

removeForExperiment in interface PrincipalComponentAnalysisService