ubic.gemma.persistence.service.analysis

Class SingleExperimentAnalysisDaoBase<T extends SingleExperimentAnalysis>

java.lang.Object

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

ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase<T>

All Implemented Interfaces:

AnalysisDao<T>, SingleExperimentAnalysisDao<T>, BaseDao<T>

Direct Known Subclasses:

CoexpressionAnalysisDaoImpl

public abstract class SingleExperimentAnalysisDaoBase<T extends SingleExperimentAnalysis>
extends AbstractDao<T>
implements SingleExperimentAnalysisDao<T>

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type SingleExperimentAnalysis.

The single experiment analysis has a related BioAssaySet which is typically either a ExpressionExperiment or a ExpressionExperimentSubSet.

See Also:

SingleExperimentAnalysis

Field Summary

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

DEFAULT_BATCH_SIZE, elementClass, log

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SingleExperimentAnalysisDaoBase(Class<T> elementClass, SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method and Description
Collection<T>	findByExperiment(BioAssaySet experiment) Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Map<BioAssaySet,Collection<T>>	findByExperiments(Collection<? extends BioAssaySet> experiments) Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
Collection<T>	findByName(String name)
Collection<T>	findByTaxon(Taxon taxon)

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

countAll, create, create, createInBatch, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, flush, getElementClass, getSessionFactory, load, load, loadAll, remove, remove, remove, removeAllInBatch, removeInBatch, save, save, saveInBatch, update, update, updateInBatch

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, create, createInBatch, find, findOrCreate, getElementClass, load, load, loadAll, remove, remove, remove, removeAllInBatch, removeInBatch, save, save, saveInBatch, update, update, updateInBatch

Constructor Detail

SingleExperimentAnalysisDaoBase

protected SingleExperimentAnalysisDaoBase(Class<T> elementClass,
                                          SessionFactory sessionFactory)

Method Detail

findByExperiment

public Collection<T> findByExperiment(BioAssaySet experiment)

Description copied from interface: SingleExperimentAnalysisDao

Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().

Specified by:

findByExperiment in interface SingleExperimentAnalysisDao<T extends SingleExperimentAnalysis>

findByExperiments

public Map<BioAssaySet,Collection<T>> findByExperiments(Collection<? extends BioAssaySet> experiments)

Description copied from interface: SingleExperimentAnalysisDao

Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with

Specified by:

findByExperiments in interface SingleExperimentAnalysisDao<T extends SingleExperimentAnalysis>

Parameters:

experiments - experiments

Returns:

map to analyses

findByTaxon

public Collection<T> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface AnalysisDao<T extends SingleExperimentAnalysis>

findByName

public Collection<T> findByName(String name)

Specified by:

findByName in interface AnalysisDao<T extends SingleExperimentAnalysis>

Parameters:

name - name

Returns:

a collection of analysis that have a name that starts with the given name