ubic.gemma.web.controller.expression.arrayDesign

Interface ArrayDesignController

All Known Implementing Classes:

ArrayDesignControllerImpl

@RequestMapping(value="/arrays")
public interface 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:

paul

Method Summary

Modifier and Type	Method and 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(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Delete an arrayDesign.
void	downloadAnnotationFile(Long arrayDesignId, String fileType, javax.servlet.http.HttpServletResponse httpServletResponse)
ModelAndView	filter(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Show array designs that match search criteria.
ModelAndView	generateSummary(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Build summary report for an array design
Collection<ArrayDesignValueObject>	getArrayDesigns(Long[] arrayDesignIds, boolean showMergees, boolean showOrphans)
Collection<CompositeSequenceMapValueObject>	getCsSummaries(EntityDelegator ed) Exposed for AJAX calls.
Collection<CompositeSequenceMapValueObject>	getDesignSummaries(ArrayDesign arrayDesign)
ArrayDesignValueObject	getDetails(Long id)
Map<String,String>	getReportHtml(EntityDelegator ed)
String	getSummaryForArrayDesign(Long id)
Collection<ArrayDesignValueObject>	loadArrayDesignsForShowAll(Long[] arrayDesignIds)
ArrayDesignValueObject	loadArrayDesignsSummary()
String	remove(EntityDelegator ed)
ModelAndView	showAllArrayDesigns(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Show all array designs, or according to a list of IDs passed in.
ModelAndView	showArrayDesign(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
ModelAndView	showCompositeSequences(javax.servlet.http.HttpServletRequest request) Show (some of) the probes from an array.
ModelAndView	showExpressionExperiments(javax.servlet.http.HttpServletRequest request) shows a list of BioAssays for an expression experiment subset
String	updateReport(EntityDelegator ed)
String	updateReportById(Long id)

Method Detail

addAlternateName

String addAlternateName(Long arrayDesignId,
                        String alternateName)

browse

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

delete

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

Delete an arrayDesign.

downloadAnnotationFile

@RequestMapping(value="/downloadAnnotationFile.html")
void downloadAnnotationFile(@RequestParam(value="id")
                                                                                  Long arrayDesignId,
                                                                                  @RequestParam(value="fileType",required=false)
                                                                                  String fileType,
                                                                                  javax.servlet.http.HttpServletResponse httpServletResponse)
                                                                           throws IOException

Throws:

IOException

filter

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

Show array designs that match search criteria.

generateSummary

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

Build summary report for an array design

getArrayDesigns

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

getCsSummaries

Collection<CompositeSequenceMapValueObject> getCsSummaries(EntityDelegator ed)

Exposed for AJAX calls.

getDesignSummaries

Collection<CompositeSequenceMapValueObject> getDesignSummaries(ArrayDesign arrayDesign)

getReportHtml

Map<String,String> getReportHtml(EntityDelegator ed)

Returns:

the HTML to display.

getSummaryForArrayDesign

String getSummaryForArrayDesign(Long id)

loadArrayDesignsForShowAll

Collection<ArrayDesignValueObject> loadArrayDesignsForShowAll(Long[] arrayDesignIds)

loadArrayDesignsSummary

ArrayDesignValueObject loadArrayDesignsSummary()

remove

String remove(EntityDelegator ed)

showAllArrayDesigns

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

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

showArrayDesign

@RequestMapping(value={"/showArrayDesign.html","/"})
ModelAndView showArrayDesign(javax.servlet.http.HttpServletRequest request,
                                                                                  javax.servlet.http.HttpServletResponse response)

showCompositeSequences

@RequestMapping(value="/showCompositeSequenceSummary.html")
ModelAndView showCompositeSequences(javax.servlet.http.HttpServletRequest request)

Show (some of) the probes from an array.

showExpressionExperiments

@RequestMapping(value="/showExpressionExperiments.html")
ModelAndView showExpressionExperiments(javax.servlet.http.HttpServletRequest request)

shows a list of BioAssays for an expression experiment subset

Returns:

ModelAndView

updateReport

String updateReport(EntityDelegator ed)

updateReportById

String updateReportById(Long id)

getDetails

ArrayDesignValueObject getDetails(Long id)