Package ubic.gemma.web.controller.expression.experiment

Class DEDVController

java.lang.Object

ubic.gemma.web.controller.expression.experiment.DEDVController

@Controller
@RequestMapping("/dedv")
public class DEDVController
extends Object

Exposes methods for accessing underlying Design Element Data Vectors. eg: ajax methods for visualization

Author:

kelsey

Constructor Summary

Constructors

Constructor	Description
DEDVController()

Method Summary

Modifier and Type	Method	Description
Map<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject,Map<Long,Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject>>>	getDEDV(Collection<Long> eeIds, Collection<Long> geneIds)	Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes.
VisualizationValueObject[]	getDEDVForCoexpressionVisualization(Collection<Long> eeIds, Long queryGeneId, Long coexpressedGeneId)	AJAX exposed method
VisualizationValueObject[]	getDEDVForDiffExVisualization(Collection<Long> eeIds, Collection<Long> geneIds, Double threshold, Collection<ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand> factorMap)	AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow, DifferentialExpressionAnalysesSummaryTree
VisualizationValueObject[]	getDEDVForDiffExVisualizationByExperiment(Long eeId, Long geneId, Double threshold, Boolean isSubset)	AJAX exposed method Batch factor value analyses are filtered out; for ProbeLevelDiffExGrid:VisualizationDifferentialWindow.
VisualizationValueObject[]	getDEDVForDiffExVisualizationByThreshold(Long resultSetId, Double givenThreshold)	AJAX exposed method
VisualizationValueObject[]	getDEDVForPcaVisualization(Long eeId, int component, int count)	AJAX
VisualizationValueObject[]	getDEDVForVisualization(Collection<Long> eeIds, Collection<Long> geneIds)	AJAX exposed method
VisualizationValueObject[]	getDEDVForVisualizationByProbe(Collection<Long> eeIds, Collection<Long> probeIds)	AJAX exposed method
ModelAndView	handleRequestInternal(javax.servlet.http.HttpServletRequest request)	Handle case of text export of the results.

Methods inherited from class java.lang.Object

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

Constructor Detail

DEDVController

public DEDVController()

Method Detail

getDEDV

public Map<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject,Map<Long,Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject>>> getDEDV(Collection<Long> eeIds,
                                                                                                                                                                                              Collection<Long> geneIds)

Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes. The EE info is in the value object. FIXME handle subsets.

getDEDVForCoexpressionVisualization

public VisualizationValueObject[] getDEDVForCoexpressionVisualization(Collection<Long> eeIds,
                                                                      Long queryGeneId,
                                                                      Long coexpressedGeneId)

AJAX exposed method

getDEDVForDiffExVisualization

public VisualizationValueObject[] getDEDVForDiffExVisualization(Collection<Long> eeIds,
                                                                Collection<Long> geneIds,
                                                                Double threshold,
                                                                Collection<ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand> factorMap)

AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow, DifferentialExpressionAnalysesSummaryTree

Parameters:

eeIds - FIXME accommodate ExpressionExperimentSubSets. Currently we pass in the "source experiment" so we don't get the slice.

geneIds - (could be just one)

threshold - for 'significance'

factorMap - Collection of DiffExpressionSelectedFactorCommand showing which factors to use.

getDEDVForDiffExVisualizationByExperiment

public VisualizationValueObject[] getDEDVForDiffExVisualizationByExperiment(Long eeId,
                                                                            Long geneId,
                                                                            Double threshold,
                                                                            Boolean isSubset)

AJAX exposed method Batch factor value analyses are filtered out; for ProbeLevelDiffExGrid:VisualizationDifferentialWindow.

getDEDVForDiffExVisualizationByThreshold

public VisualizationValueObject[] getDEDVForDiffExVisualizationByThreshold(Long resultSetId,
                                                                           Double givenThreshold)

AJAX exposed method

Parameters:

resultSetId - The resultset we're specifically interested. Note that this is what is used to choose the vectors, since it could be a subset of an experiment.

Returns:

collection of visualization value objects

getDEDVForPcaVisualization

public VisualizationValueObject[] getDEDVForPcaVisualization(Long eeId,
                                                             int component,
                                                             int count)

AJAX

getDEDVForVisualization

public VisualizationValueObject[] getDEDVForVisualization(Collection<Long> eeIds,
                                                          Collection<Long> geneIds)

AJAX exposed method

getDEDVForVisualizationByProbe

public VisualizationValueObject[] getDEDVForVisualizationByProbe(Collection<Long> eeIds,
                                                                 Collection<Long> probeIds)

AJAX exposed method

handleRequestInternal

@RequestMapping("/downloadDEDV.html")
public ModelAndView handleRequestInternal(javax.servlet.http.HttpServletRequest request)

Handle case of text export of the results.