Package ubic.gemma.persistence.service.analysis.expression.diff

Class ExpressionAnalysisResultSetDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<ExpressionAnalysisResultSet>

ubic.gemma.persistence.service.AbstractVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, AnalysisResultSetDao<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, ExpressionAnalysisResultSetDao, BaseDao<ExpressionAnalysisResultSet>, BaseVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>, FilteringDao<ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

@Repository
public class ExpressionAnalysisResultSetDaoImpl
extends AbstractCriteriaFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>
implements ExpressionAnalysisResultSetDao

Author:

Paul

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
ExpressionAnalysisResultSetDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
protected void	configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>.FilterablePropertiesConfigurer configurer)	Register filterable properties.
long	countResults(ExpressionAnalysisResultSet ears)	Count the number of results in a given result set.
long	countResults(ExpressionAnalysisResultSet ears, double threshold)	Count the number of results in a given result set below a given corrected P-value threshold.
ExpressionAnalysisResultSet	create(ExpressionAnalysisResultSet entity)	Create an object.
protected DifferentialExpressionAnalysisResultSetValueObject	doLoadValueObject(ExpressionAnalysisResultSet entity)	Load a value object for a given entity.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Baseline	getBaseline(ExpressionAnalysisResultSet ears)	Retrieve the baseline for the given result set.
Map<ExpressionAnalysisResultSet,Baseline>	getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)	Retrieve baselines for all the given result sets representing factor interactions.
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> ids, boolean initializeFactorValues)	Retrieve baselines using result set IDs representing factor interactions.
protected Criteria	getFilteringCriteria(Filters filters)	Obtain a Criteria for loading VOs.
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)	Obtain a histogram of the P-value distribution for a given result set.
Map<Long,Set<Gene>>	loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)	Load a DifferentialExpressionAnalysisResult to Gene multi-map.
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet entity, boolean includeFactorValuesInContrasts, boolean queryGenesByResult, boolean includeTaxonInGenes)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, double threshold, int offset, int limit)	Load a slice of an analysis result set with a corrected P-value threshold.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, int offset, int limit)	Load a slice of an analysis result set.
protected void	postProcessValueObjects(List<DifferentialExpressionAnalysisResultSetValueObject> differentialExpressionAnalysisResultSetValueObjects)	Post-process VOs in bulk.
void	remove(ExpressionAnalysisResultSet entity)	Remove a persistent instance
void	thaw(ExpressionAnalysisResultSet ears)	Initialize the analysis and subset factor vale.

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

afterPropertiesSet, count, getFilterablePropertyMeta, load, load, loadIds, loadValueObjects, loadValueObjects

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

getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyType, getSort

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

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

countAll, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

ExpressionAnalysisResultSetDaoImpl

@Autowired
public ExpressionAnalysisResultSetDaoImpl(SessionFactory sessionFactory)

Method Details

create

public ExpressionAnalysisResultSet create(ExpressionAnalysisResultSet entity)

Description copied from interface: BaseDao

Create an object. If the entity type is immutable, this may also remove any existing entities identified by an appropriate 'find' method.

Specified by:

create in interface BaseDao<ExpressionAnalysisResultSet>

Overrides:

create in class AbstractDao<ExpressionAnalysisResultSet>

Parameters:

entity - the entity to create

Returns:

the persistent version of the entity

remove

public void remove(ExpressionAnalysisResultSet entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<ExpressionAnalysisResultSet>

Overrides:

remove in class AbstractDao<ExpressionAnalysisResultSet>

Parameters:

entity - the entity to be removed

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id)

Description copied from interface: ExpressionAnalysisResultSetDao

Load an analysis result set with its all of its associated results.

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

id - the ID of the analysis result set

Returns:

the analysis result set with its associated results, or null if not found

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 int offset,
 int limit)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a slice of an analysis result set.

Results are sorted by ascending correct P-value.

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

offset - an offset of results to load

limit - a limit of results to load, or -1 to load all results starting at offset

See Also:

• ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long)

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 double threshold,
 int offset,
 int limit)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a slice of an analysis result set with a corrected P-value threshold.

Important note: when using a threshold, results with null P-values will not be included, thus setting the threshold to 1.0 is not equivalent to ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int).

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

threshold - corrected P-value maximum threshold (inclusive)

canDelete

public boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

canDelete in interface ExpressionAnalysisResultSetDao

findByBioAssaySetInAndDatabaseEntryInLimit

public Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
 Collection<BioAssaySet> bioAssaySets,
 @Nullable
 Collection<DatabaseEntry> databaseEntries,
 @Nullable
 Filters filters,
 int offset,
 int limit,
 @Nullable
 Sort sort)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve result sets associated to a set of BioAssaySet and external database entries.

Specified by:

findByBioAssaySetInAndDatabaseEntryInLimit in interface ExpressionAnalysisResultSetDao

Parameters:

bioAssaySets - related BioAssaySet, or any if null

databaseEntries - related external identifier associated to the BioAssaySet, or any if null

filters - filters for restricting results

limit - maximum number of results to return

sort - field and direction by which the collection is ordered

postProcessValueObjects

protected void postProcessValueObjects(List<DifferentialExpressionAnalysisResultSetValueObject> differentialExpressionAnalysisResultSetValueObjects)

Description copied from class: AbstractVoEnabledDao

Post-process VOs in bulk.

Use this as an opportunity to load extra informations that could not be populated in the initial AbstractVoEnabledDao.doLoadValueObject(Identifiable) or AbstractVoEnabledDao.doLoadValueObjects(Collection)

Overrides:

postProcessValueObjects in class AbstractVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

thaw

public void thaw(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Initialize the analysis and subset factor vale.

Specified by:

thaw in interface ExpressionAnalysisResultSetDao

countResults

public long countResults(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Count the number of results in a given result set.

Specified by:

countResults in interface ExpressionAnalysisResultSetDao

countResults

public long countResults(ExpressionAnalysisResultSet ears,
 double threshold)

Description copied from interface: ExpressionAnalysisResultSetDao

Count the number of results in a given result set below a given corrected P-value threshold.

Specified by:

countResults in interface ExpressionAnalysisResultSetDao

getBaseline

public Baseline getBaseline(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve the baseline for the given result set.

Factor values are always initialized.

Specified by:

getBaseline in interface ExpressionAnalysisResultSetDao

Returns:

a baseline, or null if none could be determined for the given result set

getBaselinesForInteractions

public Map<ExpressionAnalysisResultSet,Baseline> getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets,
 boolean initializeFactorValues)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve baselines for all the given result sets representing factor interactions.

Specified by:

getBaselinesForInteractions in interface ExpressionAnalysisResultSetDao

Parameters:

initializeFactorValues - whether to initialize factor values

getBaselinesForInteractionsByIds

public Map<Long,Baseline> getBaselinesForInteractionsByIds(Collection<Long> ids,
 boolean initializeFactorValues)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve baselines using result set IDs representing factor interactions.

Specified by:

getBaselinesForInteractionsByIds in interface ExpressionAnalysisResultSetDao

Parameters:

initializeFactorValues - whether to initialize factor values

loadPvalueDistribution

public Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)

Description copied from interface: ExpressionAnalysisResultSetDao

Obtain a histogram of the P-value distribution for a given result set.

Specified by:

loadPvalueDistribution in interface ExpressionAnalysisResultSetDao

getFilteringCriteria

protected Criteria getFilteringCriteria(@Nullable
 Filters filters)

Description copied from class: AbstractCriteriaFilteringVoEnabledDao

Obtain a Criteria for loading VOs.

Overrides:

getFilteringCriteria in class AbstractCriteriaFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

See Also:

• to obtain a org.hibernate.criterion.DetachedCriteria from a set of filter clauses.

configureFilterableProperties

protected void configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>.FilterablePropertiesConfigurer configurer)

Description copied from class: AbstractFilteringVoEnabledDao

Register filterable properties.

Overrides:

configureFilterableProperties in class AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

doLoadValueObject

protected DifferentialExpressionAnalysisResultSetValueObject doLoadValueObject(ExpressionAnalysisResultSet entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

loadValueObjectWithResults

public DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet entity,
 boolean includeFactorValuesInContrasts,
 boolean queryGenesByResult,
 boolean includeTaxonInGenes)

Description copied from interface: ExpressionAnalysisResultSetDao

Load an analysis result set with its all of its associated results.

Specified by:

loadValueObjectWithResults in interface ExpressionAnalysisResultSetDao

Parameters:

includeFactorValuesInContrasts - include complete FV in the contrasts, only IDs are displayed if false

queryGenesByResult - query genes by results instead of result set, this is considerably faster if the results are sliced (i.e. from ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int))

includeTaxonInGenes - include complete taxon in the contrasts, only the ID is displayed if false

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)
• ExpressionAnalysisResultSetDao.loadResultToGenesMap(ExpressionAnalysisResultSet, boolean)

loadResultToGenesMap

public Map<Long,Set<Gene>> loadResultToGenesMap(ExpressionAnalysisResultSet resultSet,
 boolean queryByResult)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a DifferentialExpressionAnalysisResult to Gene multi-map.

This is much faster than navigating through the probe's alignments, transcripts and then genes as it uses the internal GENE2CS table described in TableMaintenanceUtil.updateGene2CsEntries().

Note: Not all probes have associated genes, so you should use Map.getOrDefault(Object, Object) with an empty collection to handle this case.

Specified by:

loadResultToGenesMap in interface ExpressionAnalysisResultSetDao

Parameters:

queryByResult - query by results instead of result set, this is considerably faster if the results are sliced (i.e. from ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int))