Opened 16 years ago

Closed 16 years ago

Last modified 13 years ago

#163 closed (fixed)

Implement combined hits report

Reported by: Fredrik Levander Owned by: Fredrik Levander
Milestone: 2.0 beta 1 Keywords:
Cc:

Description

The hits report could be used as a basis for a report where scores from multiple search engines are used to filter the list as in Proteios1. Ideally this would yield a new hits report with other columns. Initially it could be saved to a file, but ideally it should be viewable, clickable and exportable.

Change History (24)

comment:1 Changed 16 years ago by Gregory Vincic

Milestone: Alpha 2Beta 1

comment:2 Changed 16 years ago by Gregory Vincic

Owner: changed from Gregory Vincic to Fredrik Levander

comment:3 Changed 16 years ago by Fredrik Levander

Status: newassigned

comment:4 Changed 16 years ago by Fredrik Levander

(In [1451]) Refs #163. Added GUI functionality and dummy plugin for generation of combined hits report with export to file.

comment:5 Changed 16 years ago by Fredrik Levander

(In [1466]) Refs #163. Combined hits report added. Supports any number of score types, but at the moment only protein scores of type Mascot and Tandem are used.

comment:6 Changed 16 years ago by Fredrik Levander

(In [1468]) Refs #163. Got rid of warnings from type safety.

comment:7 Changed 16 years ago by Fredrik Levander

(In [1471]) Refs #163. Allowing for comparisons on the peptide level as well. GUI support for this to be added.

comment:8 Changed 16 years ago by Fredrik Levander

(In [1473]) Refs #163. Now possible to select between peptide or protein combination

comment:9 Changed 16 years ago by Fredrik Levander

In [1475] Default is now peptide filtering

comment:10 Changed 16 years ago by Fredrik Levander

In [1475]. No,no,no... Default is protein comparisons

comment:11 Changed 16 years ago by Fredrik Levander

Resolution: fixed
Status: assignedclosed

(In [1623]) Fixes #163. 1) Plugin lookup for non-root users corrected. 2) Query for hits updated to not query for hits with no external id set.

comment:12 Changed 15 years ago by Fredrik Levander

(In [1925]) Fixes #243. Refs #163. Updated combined hits report to write to project directory. Added select box for gel external id.

comment:13 Changed 14 years ago by Fredrik Levander

(In [2852]) Refs #163. Tidying up combined hits report forms. Preparing for querying for unique score types.

comment:14 Changed 14 years ago by Fredrik Levander

(In [2853]) Refs #163. Added instructions to combined hits report.

comment:15 Changed 14 years ago by Fredrik Levander

(In [2854]) Refs #163. Selection of peptides/proteins check box fixed.

comment:16 Changed 14 years ago by Fredrik Levander

(In [2864]) Refs #163. Corrected peptide comparison so that sequences matching both revere and forward databases are considered correct

comment:17 Changed 14 years ago by Fredrik Levander

(In [2883]) Refs #163. Reformatting output from peptide combination

comment:18 Changed 14 years ago by Fredrik Levander

(In [2972]) Refs #163. Added OMSSA score type to combined hits report

comment:19 Changed 14 years ago by olle

(In [3046]) Refs #500. Refs #163. Refs #287. First support of allowing selection of score types to combine in combined hits report:

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getCombineHitsForm(Project project) by use of three field sets instead of one, where the second one contains new score type select boxes for each available score type, with alternatives "Not used", "E-value", and "Score". The score types and their settings are transferred via VString valid parameters to class/file action/hit/CombineHits.java in client/servlet/.

  1. Class/file action/hit/CombineHits.java in client/servlet/

updated in protected method void runMe() by obtaining the lists of score type names and score type settings from values of the VString valid parameters. New String lists are created that only contain the entries for the score types that were selected to be used. The new lists are transferred as StringParameterType parameter values to the job created.

  1. Class/file plugins/CombinedHitsReport.java in plugin/ updated

in public method void run(Request request, Response response, ProgressReporter? progress) by obtaining the string lists of score types and their settings from job parameters, and creating String and boolean arrays score_types and compareE, respectively, with values corresponding to the obtained list data.

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

comment:20 Changed 14 years ago by olle

(In [3048]) Refs #500. Refs #163. Support of allowing selection of score types to combine in combined hits report is updated by not including score type "Proteios Protein" as a score type alternative, since this score type indicates protein hits generated by "Protein Assembly", and these hits are therefore already combined:

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getCombineHitsForm(Project project) by filtering out score type "Proteios Protein" as an available score type alternative.

comment:21 Changed 14 years ago by Fredrik Levander

(In [3050]) Refs #500. Refs #163. Clearing hit fdr info before generating a new report, in case the report has been run before.

comment:22 Changed 14 years ago by Fredrik Levander

(In [3306]) Refs #163. Added more peptide info to combined hits report

comment:23 Changed 13 years ago by Fredrik Levander

(In [3509]) Refs #163. Added possibility to combine hits for all samples in a project at once.

comment:24 Changed 13 years ago by Fredrik Levander

(In [3523]) Refs #163. Made select all option for local sample ids available only to hits combination.

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