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
    ubic.gemma.model.expression.arrayDesign.ArrayDesign
    locateArrayDesign(String identifier)
     
    ubic.gemma.model.expression.bioAssay.BioAssay
    locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String sampleId)
     
    ubic.gemma.model.expression.bioAssay.BioAssay
    locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType quantitationType, String sampleId)
     
    ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics
    locateCellLevelCharacteristics(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String clcIdentifier)
     
    ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
    locateCellTypeAssignment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String cta)
     
    ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
    locateDiffExAnalysis(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String analysisIdentifier)
     
    ubic.gemma.model.expression.experiment.ExperimentalFactor
    locateExperimentalFactor(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, String ctfName)
     
    ubic.gemma.model.expression.experiment.ExpressionExperiment
    locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)
     
    ubic.gemma.model.common.protocol.Protocol
    locateProtocol(String protocolName)
     
    <T extends ubic.gemma.model.expression.bioAssayData.DataVector>
    ubic.gemma.model.common.quantitationtype.QuantitationType
    locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
     
    <T extends ubic.gemma.model.expression.bioAssayData.DataVector>
    Map.Entry<Class<? extends T>,ubic.gemma.model.common.quantitationtype.QuantitationType>
    locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)
     
    ubic.gemma.model.genome.Taxon
    locateTaxon(String identifier)
     

  • Method Details

    • locateTaxon

      ubic.gemma.model.genome.Taxon locateTaxon(String identifier)

    • locateArrayDesign

      ubic.gemma.model.expression.arrayDesign.ArrayDesign locateArrayDesign(String identifier)

    • locateExpressionExperiment

      ubic.gemma.model.expression.experiment.ExpressionExperiment locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)

    • locateProtocol

      ubic.gemma.model.common.protocol.Protocol locateProtocol(String protocolName)

    • locateQuantitationType

      <T extends ubic.gemma.model.expression.bioAssayData.DataVector> ubic.gemma.model.common.quantitationtype.QuantitationType locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Class<? extends T> vectorType)

    • locateQuantitationType

      <T extends ubic.gemma.model.expression.bioAssayData.DataVector> Map.Entry<Class<? extends T>,ubic.gemma.model.common.quantitationtype.QuantitationType> locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)

    • locateCellTypeAssignment

      ubic.gemma.model.expression.bioAssayData.CellTypeAssignment locateCellTypeAssignment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String cta)

    • locateCellLevelCharacteristics

      ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics locateCellLevelCharacteristics(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String clcIdentifier)

    • locateExperimentalFactor

      ubic.gemma.model.expression.experiment.ExperimentalFactor locateExperimentalFactor(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, String ctfName)

    • locateBioAssay

      ubic.gemma.model.expression.bioAssay.BioAssay locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String sampleId)

    • locateBioAssay

      ubic.gemma.model.expression.bioAssay.BioAssay locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType quantitationType, String sampleId)

    • locateDiffExAnalysis

      ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis locateDiffExAnalysis(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String analysisIdentifier)