Package ubic.gemma.web.controller.expression.arrayDesign

Class ArrayDesignControllerImpl

java.lang.Object

ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl

All Implemented Interfaces:

ArrayDesignController

@Controller
@RequestMapping("/arrays")
public class ArrayDesignControllerImpl
extends Object
implements ArrayDesignController

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

Constructor Summary

Constructors

Constructor	Description
ArrayDesignControllerImpl()

Method Summary

Modifier and Type	Method	Description
String	addAlternateName(Long arrayDesignId, String alternateName)
JsonReaderResponse<ArrayDesignValueObject>	browse(ListBatchCommand batch, Long[] ids, boolean showMerged, boolean showOrphans)	AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level? Is there security for ArrayDesigns? ids can be null
ModelAndView	delete(Long id)	Delete an arrayDesign.
void	downloadAnnotationFile(Long arrayDesignId, String fileType, javax.servlet.http.HttpServletResponse response)
ModelAndView	filter(String filter)	Show array designs that match search criteria.
ModelAndView	generateSummary(Long id)	Build summary report for an array design
Collection<ArrayDesignValueObject>	getArrayDesigns(Long[] arrayDesignIds, boolean showMergees, boolean showOrphans)
Collection<CompositeSequenceMapValueObject>	getCsSummaries(EntityDelegator<ArrayDesign> ed)	Exposed for AJAX calls.
Collection<CompositeSequenceMapValueObject>	getDesignSummaries(ArrayDesign arrayDesign)
ArrayDesignValueObjectExt	getDetails(Long id)
Map<String,String>	getReportHtml(EntityDelegator<ArrayDesign> ed)
String	getSummaryForArrayDesign(Long id)
Collection<ArrayDesignValueObject>	loadArrayDesignsForShowAll(Long[] arrayDesignIds)
ArrayDesignValueObject	loadArrayDesignsSummary()
String	remove(EntityDelegator<ArrayDesign> ed)
ModelAndView	showAllArrayDesigns()	Show all array designs, or according to a list of IDs passed in.
ModelAndView	showArrayDesign(Long id)
ModelAndView	showArrayDesignByName(String name)
ModelAndView	showCompositeSequences(Long id)	Show (some of) the probes from an array.
ModelAndView	showExpressionExperiments(Long id)	shows a list of BioAssays for an expression experiment subset
String	updateReport(EntityDelegator<ArrayDesign> ed)
String	updateReportById(Long id)

Methods inherited from class java.lang.Object

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

Constructor Detail

ArrayDesignControllerImpl

public ArrayDesignControllerImpl()

Method Detail

addAlternateName

public String addAlternateName(Long arrayDesignId,
                               String alternateName)

Specified by:

addAlternateName in interface ArrayDesignController

browse

public JsonReaderResponse<ArrayDesignValueObject> browse(ListBatchCommand batch,
                                                         Long[] ids,
                                                         boolean showMerged,
                                                         boolean showOrphans)

Description copied from interface: ArrayDesignController

AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level? Is there security for ArrayDesigns? ids can be null

Specified by:

browse in interface ArrayDesignController

delete

@RequestMapping("/deleteArrayDesign.html")
public ModelAndView delete(@RequestParam("id")
                           Long id)

Description copied from interface: ArrayDesignController

Delete an arrayDesign.

Specified by:

delete in interface ArrayDesignController

downloadAnnotationFile

@RequestMapping(value="/downloadAnnotationFile.html",
                produces="application/octet-stream")
public void downloadAnnotationFile(@RequestParam("id")
                                   Long arrayDesignId,
                                   @RequestParam(value="fileType",required=false)
                                   String fileType,
                                   javax.servlet.http.HttpServletResponse response)
                            throws IOException

Specified by:

downloadAnnotationFile in interface ArrayDesignController

Throws:

IOException

filter

@RequestMapping("/filterArrayDesigns.html")
public ModelAndView filter(@RequestParam("filter")
                           String filter)

Description copied from interface: ArrayDesignController

Show array designs that match search criteria.

Specified by:

filter in interface ArrayDesignController

generateSummary

@RequestMapping("/generateArrayDesignSummary.html")
public ModelAndView generateSummary(@RequestParam(value="id",required=false)
                                    Long id)

Description copied from interface: ArrayDesignController

Build summary report for an array design

Specified by:

generateSummary in interface ArrayDesignController

getArrayDesigns

public Collection<ArrayDesignValueObject> getArrayDesigns(Long[] arrayDesignIds,
                                                          boolean showMergees,
                                                          boolean showOrphans)

Specified by:

getArrayDesigns in interface ArrayDesignController

getCsSummaries

public Collection<CompositeSequenceMapValueObject> getCsSummaries(EntityDelegator<ArrayDesign> ed)

Description copied from interface: ArrayDesignController

Exposed for AJAX calls.

Specified by:

getCsSummaries in interface ArrayDesignController

getDesignSummaries

public Collection<CompositeSequenceMapValueObject> getDesignSummaries(ArrayDesign arrayDesign)

Specified by:

getDesignSummaries in interface ArrayDesignController

getDetails

public ArrayDesignValueObjectExt getDetails(Long id)

Specified by:

getDetails in interface ArrayDesignController

getReportHtml

public Map<String,String> getReportHtml(EntityDelegator<ArrayDesign> ed)

Specified by:

getReportHtml in interface ArrayDesignController

Returns:

the HTML to display.

getSummaryForArrayDesign

public String getSummaryForArrayDesign(Long id)

Specified by:

getSummaryForArrayDesign in interface ArrayDesignController

loadArrayDesignsForShowAll

public Collection<ArrayDesignValueObject> loadArrayDesignsForShowAll(Long[] arrayDesignIds)

Specified by:

loadArrayDesignsForShowAll in interface ArrayDesignController

loadArrayDesignsSummary

public ArrayDesignValueObject loadArrayDesignsSummary()

Specified by:

loadArrayDesignsSummary in interface ArrayDesignController

remove

public String remove(EntityDelegator<ArrayDesign> ed)

Specified by:

remove in interface ArrayDesignController

showAllArrayDesigns

@RequestMapping("/showAllArrayDesigns.html")
public ModelAndView showAllArrayDesigns()

Description copied from interface: ArrayDesignController

Show all array designs, or according to a list of IDs passed in.

Specified by:

showAllArrayDesigns in interface ArrayDesignController

showArrayDesign

@RequestMapping(value={"/showArrayDesign.html","/"},
                params="id")
public ModelAndView showArrayDesign(@RequestParam("id")
                                    Long id)

Specified by:

showArrayDesign in interface ArrayDesignController

showArrayDesignByName

@RequestMapping(value={"/showArrayDesign.html","/"},
                params="name")
public ModelAndView showArrayDesignByName(@RequestParam("name")
                                          String name)

Specified by:

showArrayDesignByName in interface ArrayDesignController

showCompositeSequences

@RequestMapping("/showCompositeSequenceSummary.html")
public ModelAndView showCompositeSequences(@RequestParam("id")
                                           Long id)

Description copied from interface: ArrayDesignController

Show (some of) the probes from an array.

Specified by:

showCompositeSequences in interface ArrayDesignController

showExpressionExperiments

@RequestMapping("/showExpressionExperiments.html")
public ModelAndView showExpressionExperiments(@RequestParam("id")
                                              Long id)

Description copied from interface: ArrayDesignController

shows a list of BioAssays for an expression experiment subset

Specified by:

showExpressionExperiments in interface ArrayDesignController

Returns:

ModelAndView

updateReport

public String updateReport(EntityDelegator<ArrayDesign> ed)

Specified by:

updateReport in interface ArrayDesignController

updateReportById

public String updateReportById(Long id)

Specified by:

updateReportById in interface ArrayDesignController