ubic.gemma.web.controller.expression.experiment

Interface ExperimentalDesignController

All Known Implementing Classes:

ExperimentalDesignControllerImpl

@RequestMapping(value="/experimentalDesign")
public interface ExperimentalDesignController

Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take. See bug 2756. Use arrays instead.

Method Summary

Modifier and Type	Method and Description
void	createDesignFromFile(Long eeid, String filePath)
void	createExperimentalFactor(EntityDelegator e, ExperimentalFactorValueObject efvo) Creates a new ExperimentalFactor and adds it to the ExperimentalDesign specified by the EntityDelegator.
void	createFactorValue(EntityDelegator e) Creates a new FactorValue and adds it to the ExperimentalFactor specified by the EntityDelegator.
void	createFactorValueCharacteristic(EntityDelegator e, Characteristic c) Creates a new Characteristic and adds it to the FactorValue specified by the EntityDelegator.
void	deleteExperimentalFactors(EntityDelegator e, Long[] efIds) Deletes the specified ExperimentalFactors and removes them from the ExperimentalDesign specified by the EntityDelegator.
void	deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos) Deletes the specified Characteristics from their parent FactorValues.
void	deleteFactorValues(EntityDelegator e, Long[] fvIds) Deletes the specified FactorValues and removes them from the ExperimentalFactor specified by the EntityDelegator.
Collection<BioMaterialValueObject>	getBioMaterials(EntityDelegator e) Returns BioMaterialValueObjects for each BioMaterial in the ExpressionExperiment specified by the EntityDelegator.
Collection<ExperimentalFactorValueObject>	getExperimentalFactors(EntityDelegator e) Returns ExperimentalFactorValueObjects for each ExperimentalFactor in the ExperimentalDesign or ExpressionExperiment specified by the EntityDelegator.
Collection<FactorValueValueObject>	getFactorValues(EntityDelegator e) Returns FactorValueValueObjects for each FactorValue in the ExperimentalFactor specified by the EntityDelegator.
Collection<FactorValueValueObject>	getFactorValuesWithCharacteristics(EntityDelegator e) Returns FactorValueValueObjects for each Characteristic belonging to a FactorValue in the ExperimentalFactor specified by the EntityDelegator.
ModelAndView	show(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
void	updateBioMaterials(BioMaterialValueObject[] bmvos) Updates the specified BioMaterials's factor values.
void	updateExperimentalFactors(ExperimentalFactorValueObject[] efvos) Updates the specified ExperimentalFactors.
void	updateFactorValueCharacteristics(FactorValueValueObject[] fvvos) Updates the specified Characteristics.

Method Detail

createDesignFromFile

void createDesignFromFile(Long eeid,
                          String filePath)

createExperimentalFactor

void createExperimentalFactor(EntityDelegator e,
                              ExperimentalFactorValueObject efvo)

Creates a new ExperimentalFactor and adds it to the ExperimentalDesign specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing an ExperimentalDesign

efvo - an ExperimentalFactorValueObject representing the new ExperimentalFactor

createFactorValue

void createFactorValue(EntityDelegator e)

Creates a new FactorValue and adds it to the ExperimentalFactor specified by the EntityDelegator. The new FactorValue may have some initial Characteristics created to match any previously existing FactorValues for the same ExperimentalFactor. Note that this applies only to 'categorical' variables. For continuous variables, you merely set the value.

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

createFactorValueCharacteristic

void createFactorValueCharacteristic(EntityDelegator e,
                                     Characteristic c)

Creates a new Characteristic and adds it to the FactorValue specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing a FactorValue

deleteExperimentalFactors

void deleteExperimentalFactors(EntityDelegator e,
                               Long[] efIds)

Deletes the specified ExperimentalFactors and removes them from the ExperimentalDesign specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing an ExperimentalDesign

efIds - a collection of ExperimentalFactor ids

deleteFactorValueCharacteristics

void deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)

Deletes the specified Characteristics from their parent FactorValues.

Parameters:

fvvos - a collection of FactorValueValueObjects containing the Characteristics to remove

deleteFactorValues

void deleteFactorValues(EntityDelegator e,
                        Long[] fvIds)

Deletes the specified FactorValues and removes them from the ExperimentalFactor specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

fvIds - a collection of FactorValue ids

getBioMaterials

Collection<BioMaterialValueObject> getBioMaterials(EntityDelegator e)

Returns BioMaterialValueObjects for each BioMaterial in the ExpressionExperiment specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing an ExpressionExperiment

Returns:

a collection of BioMaterialValueObjects

getExperimentalFactors

Collection<ExperimentalFactorValueObject> getExperimentalFactors(EntityDelegator e)

Returns ExperimentalFactorValueObjects for each ExperimentalFactor in the ExperimentalDesign or ExpressionExperiment specified by the EntityDelegator.

Parameters:

e - an EntityDelegator representing an ExperimentalDesign OR an ExpressionExperiment

Returns:

a collection of ExperimentalFactorValueObjects

getFactorValues

Collection<FactorValueValueObject> getFactorValues(EntityDelegator e)

Returns FactorValueValueObjects for each FactorValue in the ExperimentalFactor specified by the EntityDelegator. There will be one row per FactorValue

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

Returns:

a collection of FactorValueValueObjects

getFactorValuesWithCharacteristics

Collection<FactorValueValueObject> getFactorValuesWithCharacteristics(EntityDelegator e)

Returns FactorValueValueObjects for each Characteristic belonging to a FactorValue in the ExperimentalFactor specified by the EntityDelegator. There will be one row per Characteristic.

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

Returns:

a collection of FactorValueValueObjects

show

@RequestMapping(value="/showExperimentalDesign.html")
ModelAndView show(javax.servlet.http.HttpServletRequest request,
                                                                        javax.servlet.http.HttpServletResponse response)

Parameters:

request - with either 'eeid' (expression experiment id) or 'edid' (experimental design id)

response - response

Returns:

ModelAndView

updateBioMaterials

void updateBioMaterials(BioMaterialValueObject[] bmvos)

Updates the specified BioMaterials's factor values. This completely removes any pre-existing factor values.

Parameters:

bmvos - a collection of BioMaterialValueObjects containing the updated values

updateExperimentalFactors

void updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)

Updates the specified ExperimentalFactors.

Parameters:

efvos - a collection of ExperimentalFactorValueObjects containing the updated values

updateFactorValueCharacteristics

void updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)

Updates the specified Characteristics.

Parameters:

fvvos - a collection of FactorValueValueObjects containing the updated values