Timeline



Jul 20, 2009:

8:34 AM Changeset [3378] by Gregory Vincic
Refactoring variable definition to beginning of method runMe
8:33 AM Ticket #601 (Error message missleading when creating new project with duplicate name) created by Gregory Vincic
The error message says "Duplicate created", but no project is actually …
8:26 AM Changeset [3377] by Gregory Vincic
fixing column problem

Jul 17, 2009:

2:53 PM Ticket #599 (Restoring some spectrum id view action features) closed by olle
fixed: Ticket closed as the requested functionality has been added.
2:51 PM Ticket #600 (Alternative 3D server URL when downloading protein 3D structure data) closed by olle
fixed: Ticket closed as the desired functionality has been added.
2:48 PM Changeset [3376] by olle
Refs #600. Refs #541. Class/file action/hit/ShowPDBFileStructure.java …
1:36 PM Changeset [3375] by olle
Refs #600. Refs #541. Class/file action/hit/ViewActiveHitPDBFile.java …
1:29 PM Changeset [3374] by olle
Refs #600. Refs #541. Class/file action/hit/ShowPDBFileStructure.java …
1:16 PM Ticket #600 (Alternative 3D server URL when downloading protein 3D structure data) created by olle
When web pages are parsed to find a web link to downloadable PDB …
12:40 PM Changeset [3373] by olle
Refs #599. Refs #552. Refs #507. Class/file …
12:34 PM Changeset [3372] by olle
Refs #599. Refs #552. Class/file action/ActionFactory.java in …
12:24 PM Changeset [3371] by olle
Refs #599. Refs #552. Class/file action/hit/ViewActiveHitSpectrum.java …
12:01 PM Ticket #599 (Restoring some spectrum id view action features) created by olle
When the view action for spectrum id in the Hits table was updated to …

Jul 16, 2009:

12:38 PM Changeset [3370] by olle
Refs #592. First version of support for zoom functionality when …
11:19 AM Changeset [3369] by olle
Refs #592. Class/file …
11:12 AM Changeset [3368] by olle
Refs #592. Class/file action/hit/ViewActiveHitSpectrum.java in …

Jul 15, 2009:

1:30 PM Changeset [3367] by olle
Refs #592. Refs #540. Refs #287. First version of support for zoom …
12:36 PM Changeset [3366] by olle
Refs #425. Refs #592. Class/file …
12:31 PM Changeset [3365] by olle
Refs #537. Refs #592. Class/file io/SpectrumImpl.java in api/core/ …

Jul 13, 2009:

9:57 AM Ticket #595 (Pre-release version) closed by olle
fixed: Ticket closed as the desired functionality has been added.
9:44 AM ReleaseProcedure edited by olle
Updated section "Create Package" with new sub-section "Set version … (diff)
9:17 AM Changeset [3364] by olle
Refs #595. Class Application updated with new public static …

Jul 10, 2009:

4:54 PM Changeset [3363] by olle
Refs #595. Class/file core/Application.java in api/core/ updated by …
4:52 PM Changeset [3362] by olle
Refs #595. Changes committed in changeset …
4:40 PM Changeset [3361] by olle
Refs #595. Class/file core/Application.java in api/core/ updated by …
4:32 PM Changeset [3360] by olle
Refs #595. Proteios SE version specification extended with an optional …
3:58 PM Changeset [3359] by Gregory Vincic
Bumping minor revision to 9
3:11 PM ServerAdministration edited by Fredrik Levander
(diff)
3:11 PM ServerAdministration edited by Fredrik Levander
(diff)
2:58 PM Changeset [3358] by Gregory Vincic
Fixing rounding problem in db2html.pl
2:38 PM Changeset [3357] by Gregory Vincic
Updateing generated_schema after 2.8.0 release
2:32 PM Milestone Proteios SE 2.8 completed
* Protein and peptide identification comparisons. * More search …
1:55 PM Changeset [3356] by Gregory Vincic
Tagging 2.8.0 release
1:38 PM Changeset [3355] by olle
Refs #463. Refs #565. Classes/files core/Project.java and …
12:40 PM Ticket #598 (Deletion of items such as a gel) created by Jari Häkkinen
I have many gels named test, test2, testwhatever and I'd like to …
9:02 AM Ticket #535 (Comparison of Hits reports) closed by olle
fixed: Ticket closed as the the core features of hits comparison have been …
8:47 AM Ticket #565 (Possible to generate search parameters in read-only project) closed by olle
fixed: Ticket closed as package private method `void initPermissions(int …

Jul 8, 2009:

3:28 PM Changeset [3354] by olle
Refs #535. Class/file plugins/HitsComparisonReportPlugin.java in …
1:35 PM Ticket #597 (Directory and files inaccesible) created by Fredrik Levander
User A creates project P1 and adds user B to the project with full …
1:24 PM Ticket #584 (Improved parsing of fraction id in non-gel import) closed by Fredrik Levander
fixed: Worked fine in tests
11:48 AM Changeset [3353] by Fredrik Levander
Refs #555. Added local sample id to default non-gel hits view.

Jul 7, 2009:

2:57 PM Changeset [3352] by olle
Refs #535. Class/file gui/form/FormFactory.java in client/servlet/ …
2:09 PM Ticket #596 (Allow admin to list active users) created by Fredrik Levander
Administrators should be able to view which users are currently logged in.
12:44 PM Changeset [3351] by olle
Refs #535. Refs #287. Support for hits comparison updated with protein …
8:43 AM Changeset [3350] by olle
Refs #535. Class/file plugins/HitsComparisonReportPlugin.java in …

Jul 6, 2009:

1:44 PM Changeset [3349] by olle
Refs #535. Refs #287. Support for hits comparison updated: 1. …
1:31 PM Changeset [3348] by olle
Refs #535. Class/file action/hit/HitsComparisonReportStep1.java in …

Jul 3, 2009:

3:11 PM Changeset [3347] by Fredrik Levander
Refs #552. Avoiding null pointer exception in case spectrum id is null
2:41 PM Changeset [3346] by Fredrik Levander
Fixes #552. Spectrum string id is now shown in hits properties with …
2:41 PM Ticket #552 (Preferential use of spectrum ids as string) closed by Fredrik Levander
fixed: (In [3346]) Fixes #552. Spectrum string id is now shown in hits …
2:04 PM Ticket #595 (Pre-release version) created by Fredrik Levander
It would be good if the trunk version could have a version indicating …
2:03 PM Ticket #590 (Directories inaccessible) closed by Fredrik Levander
fixed: More tests also successful
2:01 PM Ticket #534 (Mascot GUI) closed by Fredrik Levander
fixed
2:00 PM Ticket #550 (Propagation of random hits) closed by Fredrik Levander
fixed: Random hits are now also updated in the hits list to get combined FDR. …
1:51 PM Changeset [3345] by Fredrik Levander
Refs #552. Updates to GUI for spectrum string id.
1:50 PM Changeset [3344] by Fredrik Levander
Refs #550. Added keep random to dictionary
1:10 PM Changeset [3343] by olle
Refs #535. Refs #287. Support for comparison of hits report updated by …
12:38 PM Changeset [3342] by olle
Refs #535. Refs #287. Support for comparison of hits report updated by …
12:07 PM Changeset [3341] by olle
Refs #535. Refs #287. Support for comparison of hits report updated by …
10:42 AM Ticket #594 (Update hibernate lib) created by Gregory Vincic
10:29 AM Ticket #571 (Automatic sharing to projects does not work) closed by Gregory Vincic
worksforme
9:26 AM Ticket #593 (batch sample import) created by Fredrik Levander
It should be possible to import samples / extracts, and annotations …
9:26 AM Changeset [3340] by Gregory Vincic
Fixed login link on proteios.org
9:18 AM Ticket #592 (zoom in spectra) created by Fredrik Levander
It would be nice if it was possible to zoom in spectra. A possiblity …
9:00 AM Ticket #555 (Alternate default columns in Hits report) closed by Fredrik Levander
fixed: (In [3339]) Fixes #555. Filtering is working properly. Also added …
9:00 AM Changeset [3339] by Fredrik Levander
Fixes #555. Filtering is working properly. Also added protein/peptide …
8:54 AM Ticket #591 (Workflow for using mzData files with OMSSA) created by Fredrik Levander
OMSSA does not support mzData files for searching. To enable usage of …

Jul 2, 2009:

10:51 AM Changeset [3338] by olle
Refs #590. Refs #241. Class/file …

Jul 1, 2009:

4:20 PM Changeset [3337] by olle
Refs #565. Class/file core/Directory.java in api/core/ updated with …
3:33 PM Ticket #545 (Allow mzML as source files in Hits report) closed by Fredrik Levander
fixed: Working with limited testing, since only X!Tandem available for testing.
2:38 PM Changeset [3336] by Fredrik Levander
Refs #535. Changed initial query to find selectable projects so that …
12:08 PM Changeset [3335] by Fredrik Levander
Fixes #589. Fixes #551. Added possibility to limit protein assembly by …
12:08 PM Tickets #551,​589 batch updated by Fredrik Levander
fixed: (In [3335]) Fixes #589. Fixes #551. Added possibility to limit protein …
10:47 AM Changeset [3334] by Fredrik Levander
Refs #589. Further refactoring to avoid problems with too long …
9:08 AM Changeset [3333] by Fredrik Levander
Refs #589. Refactoring of Protein Assembly. Solving duplication …
9:06 AM Ticket #586 (Protein grouping repeats the same protein) closed by Fredrik Levander
duplicate: See #589

Jun 30, 2009:

1:20 PM Ticket #526 (Not all OMSSA modifications shown) closed by olle
fixed: Ticket closed as a solution has been implemented for default OMSSA …
12:47 PM Changeset [3332] by olle
Refs #526. Refs #471. Class/file gui/form/FormFactory.java in …
12:27 PM Changeset [3331] by olle
Refs #584. Refs #392. Non-gel import updated to make parsing of …
9:57 AM Ticket #590 (Directories inaccessible) created by Fredrik Levander
When there is more than 20 subdirectories, those after 20 are not …
8:53 AM Ticket #589 (Protein assembly sometimes repeats the same protein) created by Fredrik Levander
When running Protein Assembly (#495 , #484) there is sometimes a …

Jun 29, 2009:

4:46 PM Changeset [3330] by Fredrik Levander
Refs #129. Modified accession number parsing to split at pipe
1:38 PM FAQ edited by Fredrik Levander
(diff)
1:34 PM KnownIssuesProteios edited by Fredrik Levander
(diff)
1:33 PM KnownIssuesProteios edited by Fredrik Levander
(diff)
1:30 PM FAQ edited by Fredrik Levander
(diff)
1:20 PM Changeset [3329] by olle
Refs #565. Class/file core/Directory.java in api/core/ updated for a …
12:26 PM Changeset [3328] by Fredrik Levander
Refs #587. Making query a bit more robust in case database column …

Jun 26, 2009:

4:41 PM Ticket #580 (Clear hits removes more than hits ... all my spots where removed!) closed by olle
fixed: Ticket closed as the desired changes in button label and warning text …
4:37 PM Changeset [3327] by olle
Refs #580. Refs #187. Refs #287. Text of button to clear the Hits …
9:44 AM Changeset [3326] by olle
Refs #463. Refs #565. Classes/files core/Project.java and …

Jun 24, 2009:

12:39 PM Changeset [3325] by olle
Refs #584. Refs #287. Non-gel import updated to check length of …
11:07 AM Changeset [3324] by olle
Refs #584. Class/file core/Hit.java and related data class/file …

Jun 23, 2009:

9:47 AM Changeset [3323] by olle
Refs #535. Class/file plugins/HitsComparisonReportPlugin.java in …

Jun 22, 2009:

4:26 PM Changeset [3322] by olle
Refs #471. Refs #526. Class/file io/OMSSAParameterFileUtil.java in …
2:35 PM Changeset [3321] by olle
Refs #535. Refs #287. Refs #290. First revision of support for …
1:49 PM Changeset [3320] by olle
Refs #535. Api/core updated to simplify database query for unique …
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