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)
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> QuantitationType	locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)
Taxon	locateTaxon(String identifier)

Method Detail

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> 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)