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pvtroshin [Fri, 4 Feb 2011 17:15:33 +0000 (17:15 +0000)]
Disembl and Jronn web services work. Modified to produce raw scores Globplot script is added into binaries. Annotation IF renamed to SequenceAnnotation and getAnnotation() method returns Map<String, Set<Score>> result instead of Set<Score> to unify. Changes cause by this is propagated.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3704
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pvtroshin [Thu, 3 Feb 2011 17:17:42 +0000 (17:17 +0000)]
Parser for DisEMBL results and finished runner, few test cases. DisemblTester has all tests "green"
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3695
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pvtroshin [Thu, 3 Feb 2011 17:06:01 +0000 (17:06 +0000)]
Add py script to executable too
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3694
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pvtroshin [Thu, 3 Feb 2011 16:59:07 +0000 (16:59 +0000)]
got rid of all disembl parameters as they were pointless to change dues to the fact that underlaying executable refuses to accept values or they have no impact
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3693
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pvtroshin [Thu, 3 Feb 2011 14:09:00 +0000 (14:09 +0000)]
add disembl limits
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3688
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pvtroshin [Thu, 3 Feb 2011 14:08:42 +0000 (14:08 +0000)]
Change disembl paths to project internal
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3687
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pvtroshin [Thu, 3 Feb 2011 14:07:26 +0000 (14:07 +0000)]
add disembl source compilation
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3686
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pvtroshin [Thu, 3 Feb 2011 13:16:41 +0000 (13:16 +0000)]
Adding DisEMBL dependency Tisean executable
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3667
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pvtroshin [Thu, 3 Feb 2011 12:19:53 +0000 (12:19 +0000)]
Disembl binaries and its dependancies e.g. minimized BioPython distribution and sovgol executable
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3666
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pvtroshin [Thu, 3 Feb 2011 10:13:15 +0000 (10:13 +0000)]
Disembl further implementation
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3663
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pvtroshin [Wed, 2 Feb 2011 16:53:10 +0000 (16:53 +0000)]
Adding Jronn WS to conf files
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3661
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pvtroshin [Wed, 2 Feb 2011 16:30:22 +0000 (16:30 +0000)]
Remove Annotated and MuptiAnnotated Sequence use Score instead
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3660
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pvtroshin [Wed, 26 Jan 2011 13:17:56 +0000 (13:17 +0000)]
Replacing web site content with fresh version from JWS2 (JABAWS production ) branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3640
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pvtroshin [Wed, 26 Jan 2011 13:14:19 +0000 (13:14 +0000)]
Remove web site to encorporate JWS2 changes
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3639
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pvtroshin [Fri, 7 Jan 2011 14:14:40 +0000 (14:14 +0000)]
Make muscle executable compilation not static to fix problem on Macs
Remove one more digit from the head of non repeatable number to prevent it going beyond long on Mac VMs
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3585
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pvtroshin [Thu, 23 Dec 2010 16:31:53 +0000 (16:31 +0000)]
Style issues are resolved - the copy from JABA production release
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3576
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pvtroshin [Thu, 23 Dec 2010 16:22:56 +0000 (16:22 +0000)]
rename aacon task and resulting file
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3574
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pvtroshin [Thu, 23 Dec 2010 14:29:57 +0000 (14:29 +0000)]
Moving a method from AACon to SequenceUtil
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3567
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pvtroshin [Thu, 23 Dec 2010 12:28:47 +0000 (12:28 +0000)]
AAConWS separate client to be removed later
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3565
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pvtroshin [Tue, 21 Dec 2010 18:34:21 +0000 (18:34 +0000)]
Adding updated javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3556
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pvtroshin [Tue, 21 Dec 2010 18:28:57 +0000 (18:28 +0000)]
Write javadoc for new datamodel classes , remove some incomplete staff
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3555
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pvtroshin [Tue, 21 Dec 2010 18:13:36 +0000 (18:13 +0000)]
remove javadoc to update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3554
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pvtroshin [Tue, 21 Dec 2010 15:02:12 +0000 (15:02 +0000)]
AAConWS further work
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3550
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pvtroshin [Mon, 20 Dec 2010 13:56:37 +0000 (13:56 +0000)]
Further work on AAConWS
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3534
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pvtroshin [Thu, 16 Dec 2010 11:30:06 +0000 (11:30 +0000)]
Gramma improved
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3501
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pvtroshin [Thu, 9 Dec 2010 12:02:15 +0000 (12:02 +0000)]
More javadocs
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3458
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pvtroshin [Thu, 9 Dec 2010 11:42:55 +0000 (11:42 +0000)]
remove old javadoc to replace with new
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3457
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pvtroshin [Fri, 3 Dec 2010 19:03:59 +0000 (19:03 +0000)]
Refactored client class to accomodate new WS interface and reduce the complexity
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3428
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pvtroshin [Fri, 3 Dec 2010 16:19:10 +0000 (16:19 +0000)]
Preset limits for AACon
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3425
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pvtroshin [Fri, 3 Dec 2010 16:12:13 +0000 (16:12 +0000)]
AAConWS further work and test cases
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3424
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pvtroshin [Thu, 2 Dec 2010 18:16:47 +0000 (18:16 +0000)]
Better name for AACon WS test
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3417
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pvtroshin [Thu, 2 Dec 2010 16:56:31 +0000 (16:56 +0000)]
AAConWS is working
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3416
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pvtroshin [Mon, 29 Nov 2010 22:06:31 +0000 (22:06 +0000)]
AAConWS further work
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3407
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pvtroshin [Mon, 29 Nov 2010 22:05:57 +0000 (22:05 +0000)]
AAConWS further work
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3406
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pvtroshin [Wed, 24 Nov 2010 15:08:11 +0000 (15:08 +0000)]
Get rid of unnecessary duplication of config files.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3392
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pvtroshin [Wed, 24 Nov 2010 14:27:11 +0000 (14:27 +0000)]
Changes from JWS2 branch concerning local execution and logging
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3389
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pvtroshin [Wed, 24 Nov 2010 14:25:26 +0000 (14:25 +0000)]
Add LoadBalancer and Limit testers from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3388
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pvtroshin [Wed, 24 Nov 2010 14:24:04 +0000 (14:24 +0000)]
Tests for AACon loader
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3387
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pvtroshin [Wed, 24 Nov 2010 13:13:11 +0000 (13:13 +0000)]
Dundee specific settings from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3385
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pvtroshin [Wed, 24 Nov 2010 13:12:35 +0000 (13:12 +0000)]
Dundee specific settings from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3384
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pvtroshin [Wed, 24 Nov 2010 13:07:42 +0000 (13:07 +0000)]
More work on AAConWS not finished yet!
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3383
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pvtroshin [Wed, 24 Nov 2010 13:04:56 +0000 (13:04 +0000)]
update from JWS2
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3382
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pvtroshin [Wed, 24 Nov 2010 13:03:38 +0000 (13:03 +0000)]
add images from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3381
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pvtroshin [Wed, 24 Nov 2010 13:02:54 +0000 (13:02 +0000)]
remove old images
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3380
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pvtroshin [Wed, 24 Nov 2010 13:00:10 +0000 (13:00 +0000)]
Add updated javadoc from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3379
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pvtroshin [Wed, 24 Nov 2010 12:59:05 +0000 (12:59 +0000)]
remove old javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3378
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pvtroshin [Wed, 24 Nov 2010 12:48:49 +0000 (12:48 +0000)]
Adding changes from JWS2 branch. Fixes for Limit in particular
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3377
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pvtroshin [Wed, 24 Nov 2010 12:43:52 +0000 (12:43 +0000)]
More work on AAConWS not finished yet!
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3376
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pvtroshin [Mon, 22 Nov 2010 15:38:01 +0000 (15:38 +0000)]
Java doc and package infos from JWS" branch. Also rethink of MSAWS interface in light of new web services e.g. AACon web service.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3345
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pvtroshin [Mon, 22 Nov 2010 15:29:47 +0000 (15:29 +0000)]
Changes from JWS2 branch merged, mostly javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3344
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pvtroshin [Mon, 22 Nov 2010 15:09:13 +0000 (15:09 +0000)]
Adding AAConWS
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3343
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pvtroshin [Fri, 19 Nov 2010 16:02:09 +0000 (16:02 +0000)]
Add updated web site from JWS2 branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3338
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pvtroshin [Fri, 19 Nov 2010 15:50:01 +0000 (15:50 +0000)]
Remove old versions of web site
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3337
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pvtroshin [Thu, 19 Aug 2010 14:52:02 +0000 (14:52 +0000)]
updates to jaba2 from jaba release branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2922
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pvtroshin [Thu, 19 Aug 2010 14:43:32 +0000 (14:43 +0000)]
updates to jaba2 from jaba release branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2921
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pvtroshin [Thu, 19 Aug 2010 14:36:46 +0000 (14:36 +0000)]
updates to jaba2 from jaba release branch
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2919
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pvtroshin [Thu, 19 Aug 2010 10:25:41 +0000 (10:25 +0000)]
Fixed version of Preset class from JABA_r1 branch (see bug JWS-19)
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2907
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pvtroshin [Mon, 26 Jul 2010 18:23:44 +0000 (18:23 +0000)]
Adding disembl wrapper
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2685
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pvtroshin [Fri, 23 Jul 2010 13:15:01 +0000 (13:15 +0000)]
Jronn multi core support
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2666
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pvtroshin [Thu, 22 Jul 2010 13:17:08 +0000 (13:17 +0000)]
Set number of thread for execution
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2652
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pvtroshin [Thu, 22 Jul 2010 12:59:22 +0000 (12:59 +0000)]
Some refactoring
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2651
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pvtroshin [Thu, 22 Jul 2010 12:22:47 +0000 (12:22 +0000)]
getStatistics test method fixed
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2650
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pvtroshin [Thu, 22 Jul 2010 11:13:08 +0000 (11:13 +0000)]
Jronn tester
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2648
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pvtroshin [Wed, 21 Jul 2010 16:56:53 +0000 (16:56 +0000)]
Add local engine properties back to version control
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2646
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pvtroshin [Wed, 21 Jul 2010 16:27:56 +0000 (16:27 +0000)]
Add JRonn runner, tester, methods to parse jronn output files.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2638
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pvtroshin [Tue, 20 Jul 2010 12:51:03 +0000 (12:51 +0000)]
Fix copyright header
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2612
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pvtroshin [Tue, 20 Jul 2010 12:48:05 +0000 (12:48 +0000)]
Changes from JWS3 is merged
From now on JWS3 project should not contain any new data. To be deleted later
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2611
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pvtroshin [Tue, 20 Jul 2010 11:44:34 +0000 (11:44 +0000)]
Next version of JABA
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2610
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git://source.jalview.org / jabaws.git / log