Package ubic.gemma.persistence.service.expression.experiment

Class GeeqServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledService<Geeq,GeeqValueObject>

ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl

All Implemented Interfaces:

BaseImmutableService<Geeq>, BaseReadOnlyService<Geeq>, BaseService<Geeq>, BaseVoEnabledService<Geeq,GeeqValueObject>, GeeqService

@Service
public class GeeqServiceImpl
extends AbstractVoEnabledService<Geeq,GeeqValueObject>
implements GeeqService

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.expression.experiment.GeeqService

GeeqService.ScoreMode

Field Summary

Fields

Modifier and Type	Field	Description
static final double	BATCH_CONF_HAS
static final double	BATCH_CONF_NO_HAS
static final double	BATCH_EFF_NONE
static final double	BATCH_EFF_STRONG
static final double	BATCH_EFF_WEAK

Constructor Summary

Constructors

Constructor

Description

GeeqServiceImpl(GeeqDao geeqDao, ExpressionExperimentService expressionExperimentService, ExpressionExperimentBatchInformationService expressionExperimentBatchInformationService, ArrayDesignService arrayDesignService, ExpressionDataMatrixService expressionDataMatrixService, OutlierDetectionService outlierDetectionService, AuditTrailService auditTrailService, SampleCoexpressionAnalysisService sampleCoexpressionAnalysisService)

Method Summary

Modifier and Type	Method	Description
Geeq	calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode)	Calculates the GEEQ score in the given mode for the experiment with the given id.

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractService

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

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

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Field Details

BATCH_EFF_WEAK

public static final double BATCH_EFF_WEAK

See Also:

• Constant Field Values

BATCH_CONF_NO_HAS

public static final double BATCH_CONF_NO_HAS

See Also:

• Constant Field Values

BATCH_EFF_NONE

public static final double BATCH_EFF_NONE

See Also:

• Constant Field Values

BATCH_CONF_HAS

public static final double BATCH_CONF_HAS

See Also:

• Constant Field Values

BATCH_EFF_STRONG

public static final double BATCH_EFF_STRONG

See Also:

• Constant Field Values

Constructor Details

GeeqServiceImpl

@Autowired
public GeeqServiceImpl(GeeqDao geeqDao,
 ExpressionExperimentService expressionExperimentService,
 ExpressionExperimentBatchInformationService expressionExperimentBatchInformationService,
 ArrayDesignService arrayDesignService,
 ExpressionDataMatrixService expressionDataMatrixService,
 OutlierDetectionService outlierDetectionService,
 AuditTrailService auditTrailService,
 SampleCoexpressionAnalysisService sampleCoexpressionAnalysisService)

Method Details

calculateScore

@Transactional
public Geeq calculateScore(ExpressionExperiment ee,
 GeeqService.ScoreMode mode)

Description copied from interface: GeeqService

Calculates the GEEQ score in the given mode for the experiment with the given id.

Specified by:

calculateScore in interface GeeqService

Parameters:

ee - the id of the experiment to calculate the scores for.

mode - either run all scores, or only re-score batch effect, batch confound or replicates.