ubic.gemma.web.controller.expression.experiment

Class ExperimentalDesignControllerImpl

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl

All Implemented Interfaces:

ExperimentalDesignController

@Controller
 @RequestMapping(value="/experimentalDesign")
public class ExperimentalDesignControllerImpl
extends BaseController
implements ExperimentalDesignController

Main entry point to editing and viewing experimental designs. 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.

Author:

keshav

Field Summary

Fields inherited from class ubic.gemma.web.controller.BaseController

log

Constructor Summary

Constructors

Constructor and Description
ExperimentalDesignControllerImpl()

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.

Methods inherited from class ubic.gemma.web.controller.BaseController

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMailEngine, setMessageSource, setMessageUtil

Methods inherited from class java.lang.Object

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

Constructor Detail

ExperimentalDesignControllerImpl

public ExperimentalDesignControllerImpl()

Method Detail

createDesignFromFile

public void createDesignFromFile(Long eeid,
                                 String filePath)

Specified by:

createDesignFromFile in interface ExperimentalDesignController

createExperimentalFactor

public void createExperimentalFactor(EntityDelegator e,
                                     ExperimentalFactorValueObject efvo)

Description copied from interface: ExperimentalDesignController

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

Specified by:

createExperimentalFactor in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalDesign

efvo - an ExperimentalFactorValueObject representing the new ExperimentalFactor

createFactorValue

public void createFactorValue(EntityDelegator e)

Description copied from interface: ExperimentalDesignController

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.

Specified by:

createFactorValue in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

createFactorValueCharacteristic

public void createFactorValueCharacteristic(EntityDelegator e,
                                            Characteristic c)

Description copied from interface: ExperimentalDesignController

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

Specified by:

createFactorValueCharacteristic in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing a FactorValue

deleteExperimentalFactors

public void deleteExperimentalFactors(EntityDelegator e,
                                      Long[] efIds)

Description copied from interface: ExperimentalDesignController

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

Specified by:

deleteExperimentalFactors in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalDesign

efIds - a collection of ExperimentalFactor ids

deleteFactorValueCharacteristics

public void deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)

Description copied from interface: ExperimentalDesignController

Deletes the specified Characteristics from their parent FactorValues.

Specified by:

deleteFactorValueCharacteristics in interface ExperimentalDesignController

Parameters:

fvvos - a collection of FactorValueValueObjects containing the Characteristics to remove

deleteFactorValues

public void deleteFactorValues(EntityDelegator e,
                               Long[] fvIds)

Description copied from interface: ExperimentalDesignController

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

Specified by:

deleteFactorValues in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

fvIds - a collection of FactorValue ids

getBioMaterials

public Collection<BioMaterialValueObject> getBioMaterials(EntityDelegator e)

Description copied from interface: ExperimentalDesignController

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

Specified by:

getBioMaterials in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExpressionExperiment

Returns:

a collection of BioMaterialValueObjects

getExperimentalFactors

public Collection<ExperimentalFactorValueObject> getExperimentalFactors(EntityDelegator e)

Description copied from interface: ExperimentalDesignController

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

Specified by:

getExperimentalFactors in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalDesign OR an ExpressionExperiment

Returns:

a collection of ExperimentalFactorValueObjects

getFactorValues

public Collection<FactorValueValueObject> getFactorValues(EntityDelegator e)

Description copied from interface: ExperimentalDesignController

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

Specified by:

getFactorValues in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

Returns:

a collection of FactorValueValueObjects

getFactorValuesWithCharacteristics

public Collection<FactorValueValueObject> getFactorValuesWithCharacteristics(EntityDelegator e)

Description copied from interface: ExperimentalDesignController

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

Specified by:

getFactorValuesWithCharacteristics in interface ExperimentalDesignController

Parameters:

e - an EntityDelegator representing an ExperimentalFactor

Returns:

a collection of FactorValueValueObjects

show

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

Specified by:

show in interface ExperimentalDesignController

Parameters:

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

response - response

Returns:

ModelAndView

updateBioMaterials

public void updateBioMaterials(BioMaterialValueObject[] bmvos)

Description copied from interface: ExperimentalDesignController

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

Specified by:

updateBioMaterials in interface ExperimentalDesignController

Parameters:

bmvos - a collection of BioMaterialValueObjects containing the updated values

updateExperimentalFactors

public void updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)

Description copied from interface: ExperimentalDesignController

Updates the specified ExperimentalFactors.

Specified by:

updateExperimentalFactors in interface ExperimentalDesignController

Parameters:

efvos - a collection of ExperimentalFactorValueObjects containing the updated values

updateFactorValueCharacteristics

public void updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)

Description copied from interface: ExperimentalDesignController

Updates the specified Characteristics.

Specified by:

updateFactorValueCharacteristics in interface ExperimentalDesignController

Parameters:

fvvos - a collection of FactorValueValueObjects containing the updated values