Package ubic.gemma.cli.util

Interface EntityLocator

All Known Implementing Classes:

EntityLocatorImpl

public interface EntityLocator

Locate various entities using identifiers supplied by the CLI.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
ArrayDesign	locateArrayDesign(String identifier)
BioAssay	locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	locateBioAssay(ExpressionExperiment ee, QuantitationType quantitationType, 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 ctfName)
ExpressionExperiment	locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)
Protocol	locateProtocol(String protocolName)
<T extends DataVector> QuantitationType	locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> Map.Entry<Class<? extends T>,QuantitationType>	locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)
Taxon	locateTaxon(String identifier)

Method Details

locateTaxon

Taxon locateTaxon(String identifier)

locateArrayDesign

ArrayDesign locateArrayDesign(String identifier)

locateExpressionExperiment

ExpressionExperiment locateExpressionExperiment(String identifier,
 boolean useReferencesIfPossible)

locateProtocol

Protocol locateProtocol(String protocolName)

locateQuantitationType

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

locateQuantitationType

<T extends DataVector>
Map.Entry<Class<? extends T>,QuantitationType> locateQuantitationType(ExpressionExperiment ee,
 String qt,
 Collection<Class<? extends T>> vectorType)

locateCellTypeAssignment

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

locateCellLevelCharacteristics

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

locateExperimentalFactor

ExperimentalFactor locateExperimentalFactor(ExpressionExperiment expressionExperiment,
 String ctfName)

locateBioAssay

BioAssay locateBioAssay(ExpressionExperiment ee,
 String sampleId)

locateBioAssay

BioAssay locateBioAssay(ExpressionExperiment ee,
 QuantitationType quantitationType,
 String sampleId)

locateDiffExAnalysis

DifferentialExpressionAnalysis locateDiffExAnalysis(ExpressionExperiment ee,
 String analysisIdentifier)