Package ubic.gemma.cli.util

Class EntityLocatorImpl

java.lang.Object

ubic.gemma.cli.util.EntityLocatorImpl

All Implemented Interfaces:

EntityLocator

@Component
public class EntityLocatorImpl
extends Object
implements EntityLocator

Constructor Summary

Constructors

Constructor	Description
EntityLocatorImpl()

Method Summary

Modifier and Type	Method	Description
ArrayDesign	locateArrayDesign(String identifier)
BioAssay	locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	locateBioAssay(ExpressionExperiment ee, QuantitationType qt, String sampleId)
CellLevelCharacteristics	locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)
CellTypeAssignment	locateCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String cta)
DifferentialExpressionAnalysis	locateDiffExAnalysis(ExpressionExperiment ee, String analysisIdentifier)
ExperimentalFactor	locateExperimentalFactor(ExpressionExperiment expressionExperiment, String identifier)
ExpressionExperiment	locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)	Attempt to locate an experiment using the given identifier.
Protocol	locateProtocol(String protocolName)
<T extends DataVector> QuantitationType	locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> org.apache.commons.lang3.tuple.Pair<Class<? extends T>,QuantitationType>	locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorTypes)
Taxon	locateTaxon(String identifier)

Methods inherited from class java.lang.Object

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

Constructor Details

EntityLocatorImpl

public EntityLocatorImpl()

Method Details

locateTaxon

public Taxon locateTaxon(String identifier)

Specified by:

locateTaxon in interface EntityLocator

locateArrayDesign

public ArrayDesign locateArrayDesign(String identifier)

Specified by:

locateArrayDesign in interface EntityLocator

locateExpressionExperiment

public ExpressionExperiment locateExpressionExperiment(String identifier,
 boolean useReferencesIfPossible)

Attempt to locate an experiment using the given identifier.

Specified by:

locateExpressionExperiment in interface EntityLocator

locateProtocol

public Protocol locateProtocol(String protocolName)

Specified by:

locateProtocol in interface EntityLocator

locateQuantitationType

public <T extends DataVector> QuantitationType locateQuantitationType(ExpressionExperiment ee,
 String qt,
 Class<? extends T> vectorType)

Specified by:

locateQuantitationType in interface EntityLocator

locateQuantitationType

public <T extends DataVector>
org.apache.commons.lang3.tuple.Pair<Class<? extends T>,QuantitationType> locateQuantitationType(ExpressionExperiment ee,
 String qt,
 Collection<Class<? extends T>> vectorTypes)

Specified by:

locateQuantitationType in interface EntityLocator

locateCellTypeAssignment

public CellTypeAssignment locateCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String cta)

Specified by:

locateCellTypeAssignment in interface EntityLocator

locateCellLevelCharacteristics

public CellLevelCharacteristics locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String clcIdentifier)

Specified by:

locateCellLevelCharacteristics in interface EntityLocator

locateExperimentalFactor

public ExperimentalFactor locateExperimentalFactor(ExpressionExperiment expressionExperiment,
 String identifier)

Specified by:

locateExperimentalFactor in interface EntityLocator

locateBioAssay

public BioAssay locateBioAssay(ExpressionExperiment ee,
 String sampleId)

Specified by:

locateBioAssay in interface EntityLocator

locateBioAssay

public BioAssay locateBioAssay(ExpressionExperiment ee,
 QuantitationType qt,
 String sampleId)

Specified by:

locateBioAssay in interface EntityLocator

locateDiffExAnalysis

public DifferentialExpressionAnalysis locateDiffExAnalysis(ExpressionExperiment ee,
 String analysisIdentifier)

Specified by:

locateDiffExAnalysis in interface EntityLocator