source.jalview.org Git - jabaws.git/log

pvtroshin [Tue, 21 Jun 2011 10:27:17 +0000 (10:27 +0000)]

remove mafft extensions - we do not support them

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4287 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 21 Jun 2011 10:02:51 +0000 (10:02 +0000)]

new mafft v 6.857 with extensions

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4286 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 21 Jun 2011 10:01:52 +0000 (10:01 +0000)]

Removing old version of mafft to replace with the new

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4285 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 20 Jun 2011 16:43:34 +0000 (16:43 +0000)]

todo update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4284 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 20 Jun 2011 16:37:41 +0000 (16:37 +0000)]

new version of muscle 3.8.31
binaries for various systems, sources, help file and configuration is updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4283 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 17 Jun 2011 16:17:57 +0000 (16:17 +0000)]

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4282 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 17 Jun 2011 15:45:17 +0000 (15:45 +0000)]

Web services refactoring & bug fixing

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4281 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 17 Jun 2011 14:06:30 +0000 (14:06 +0000)]

Refactoring of all SequenceAnnotation web services
New version of Metro
Definition for IUPred exec
Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 16:48:52 +0000 (16:48 +0000)]

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4279 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 16:46:41 +0000 (16:46 +0000)]

Binaries relocation

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4278 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 16:18:33 +0000 (16:18 +0000)]

IUPred for windows

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4277 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 14:40:43 +0000 (14:40 +0000)]

Integrating IUPredWS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4276 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 14:30:04 +0000 (14:30 +0000)]

A few more tests for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4275 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 14:22:06 +0000 (14:22 +0000)]

IUPred final touches. All test cases pass

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 13:35:08 +0000 (13:35 +0000)]

Improvements to the code

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4273 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 13:13:19 +0000 (13:13 +0000)]

IUpred integration

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4272 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 16 Jun 2011 13:10:17 +0000 (13:10 +0000)]

Modified IUPred to read multiple fasta as input

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4271 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 14 Jun 2011 17:26:54 +0000 (17:26 +0000)]

Adding XML executable description for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4266 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 14 Jun 2011 17:12:12 +0000 (17:12 +0000)]

IUPred wrapper, tester and new binary for X64 linux systems

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4265 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 14 Jun 2011 15:39:19 +0000 (15:39 +0000)]

IUPred result readers. IUpred binaries compilation scripts. IUpred executable description. IUPred output files for testing

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4263 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 13 Jun 2011 15:50:35 +0000 (15:50 +0000)]

Adding IUPred executables for the new web service

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4262 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 13 Jun 2011 15:01:09 +0000 (15:01 +0000)]

Command line options are described and added to the client. Registry is modified to perform test after 24 hours from last test

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4261 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 8 Jun 2011 17:42:15 +0000 (17:42 +0000)]

JWS2 client

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4238 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 8 Jun 2011 17:36:31 +0000 (17:36 +0000)]

JWS2 client

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4237 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 8 Jun 2011 16:03:25 +0000 (16:03 +0000)]

More work to disorder prediction client & services.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4236 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 8 Jun 2011 12:49:27 +0000 (12:49 +0000)]

Web service stubs are regenerated to incorporate new the methods. Excveption handling improved for tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4231 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 8 Jun 2011 10:09:43 +0000 (10:09 +0000)]

WStester & registry are completed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4230 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 7 Jun 2011 16:47:05 +0000 (16:47 +0000)]

further work on registry & WSTester nearly there

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4229 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 6 Jun 2011 18:16:36 +0000 (18:16 +0000)]

Adding registry web service and changes to WStester and JWS2Client code. Bugs in input/ouput setup for a few web services fixed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4223 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 3 Jun 2011 12:59:24 +0000 (12:59 +0000)]

exclude cancelled jobs from incomplete

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4214 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 1 Jun 2011 13:19:37 +0000 (13:19 +0000)]

Changes to return type of Executable.getType() method to make it compile with Oracle javac.
A few modifications to statistics package.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4201 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 31 May 2011 16:54:27 +0000 (16:54 +0000)]

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4200 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 31 May 2011 16:53:34 +0000 (16:53 +0000)]

A bug fix, help text for stat jsp pages and style improvements

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4199 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 31 May 2011 14:26:36 +0000 (14:26 +0000)]

Latest web site update from JABA_r1 r. 4152

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4196 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 31 May 2011 12:27:37 +0000 (12:27 +0000)]

Stat collection and display done

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4195 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 30 May 2011 17:23:42 +0000 (17:23 +0000)]

TODO

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4194 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 30 May 2011 17:17:34 +0000 (17:17 +0000)]

Further work to enable stat collection and display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4193 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 30 May 2011 17:16:32 +0000 (17:16 +0000)]

New properties to work with work directories

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4192 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 30 May 2011 12:15:28 +0000 (12:15 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4190 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 27 May 2011 18:11:30 +0000 (18:11 +0000)]

new properties for stat collector conf

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4185 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 27 May 2011 18:11:08 +0000 (18:11 +0000)]

Further work on statistics display - improvements to stat collector

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4184 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 17:16:01 +0000 (17:16 +0000)]

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4179 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 17:15:53 +0000 (17:15 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4178 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 17:15:41 +0000 (17:15 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4177 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 16:12:19 +0000 (16:12 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4176 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 15:03:35 +0000 (15:03 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4175 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 15:03:23 +0000 (15:03 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4174 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 26 May 2011 15:02:54 +0000 (15:02 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4173 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 25 May 2011 17:43:31 +0000 (17:43 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4166 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 25 May 2011 17:43:20 +0000 (17:43 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4165 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 25 May 2011 17:43:07 +0000 (17:43 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4164 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 25 May 2011 17:42:50 +0000 (17:42 +0000)]

Further work on statistics display

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4163 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 23 May 2011 17:18:47 +0000 (17:18 +0000)]

Adding JABA web services usage statistics web application. Stat database is to follow

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4157 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 23 May 2011 17:17:32 +0000 (17:17 +0000)]

Adding JABA web services usage statistics web application. Stat database is to follow

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4156 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 23 May 2011 17:17:06 +0000 (17:17 +0000)]

Adding JABA web services usage statistics web application. Stat database is to follow

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4155 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 23 May 2011 17:16:50 +0000 (17:16 +0000)]

Adding JABA web services usage statistics web application. Stat database is to follow

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4154 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 23 May 2011 17:16:06 +0000 (17:16 +0000)]

Adding JABA web services usage statistics web application. Stat database is to follow

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4153 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 17 May 2011 10:56:11 +0000 (10:56 +0000)]

New datamodel src v 1.1

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4134 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 28 Apr 2011 15:18:39 +0000 (15:18 +0000)]

revert build file changed excidentally

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4048 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 28 Apr 2011 15:17:21 +0000 (15:17 +0000)]

Add method to SequenceUtil to clean the protein sequence

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4047 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 28 Apr 2011 10:47:29 +0000 (10:47 +0000)]

FastaReader build into the datamodel

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4045 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 27 Apr 2011 23:39:38 +0000 (23:39 +0000)]

A wee improvement

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4044 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 27 Apr 2011 23:23:08 +0000 (23:23 +0000)]

A wee improvement

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4043 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 27 Apr 2011 23:22:08 +0000 (23:22 +0000)]

A wee improvement

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4042 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 27 Apr 2011 23:10:25 +0000 (23:10 +0000)]

New FastaReader implementing iterator & test case for it

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4041 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 18 Apr 2011 15:11:54 +0000 (15:11 +0000)]

Add task to package sources for datamodel

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3968 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 18 Apr 2011 14:59:49 +0000 (14:59 +0000)]

Refactor:
relocate getLimit() method from Util client to Util engine as SkeletalExecutable (part of the engine depends on it)

Update compile ant task to get rid of warnings.
However, ant still does not complile due to cast issue. TODO later
Updating version of utils and datamodel as it includes the utils

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3967 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 8 Apr 2011 12:35:44 +0000 (12:35 +0000)]

Adding new website from r3934 JABA_r1 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3936 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 8 Apr 2011 12:34:01 +0000 (12:34 +0000)]

Remove old web site to replace with the new web site from JABA_r1 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3935 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 24 Mar 2011 16:37:04 +0000 (16:37 +0000)]

Doc update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3855 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 16 Mar 2011 14:17:31 +0000 (14:17 +0000)]

Fix to JABAWS web.xml file to make it work with tomcat 7

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3829 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 10 Mar 2011 14:43:26 +0000 (14:43 +0000)]

statistics processor further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3818 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Mar 2011 18:55:05 +0000 (18:55 +0000)]

Add exec statistics processor & derby database

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3806 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 3 Mar 2011 16:40:30 +0000 (16:40 +0000)]

Centralized statistic collector. All WS are converted to use the same input and output names
nano time changed to milliseconds time. Is not finished yet

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3789 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 14 Feb 2011 18:22:55 +0000 (18:22 +0000)]

Add limits for presets from jws2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3752 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 14 Feb 2011 18:19:14 +0000 (18:19 +0000)]

Change the way to deal with Limits to simplify wrapper writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3751 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 14 Feb 2011 17:44:51 +0000 (17:44 +0000)]

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pvtroshin [Thu, 10 Feb 2011 13:50:10 +0000 (13:50 +0000)]

Finally, the new web services are working

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3738 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 10 Feb 2011 12:05:04 +0000 (12:05 +0000)]

Fixes to test cases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3734 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Thu, 10 Feb 2011 11:36:12 +0000 (11:36 +0000)]

Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to compensate for JAXB inability to serialize Maps. Propagate the changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3733 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Feb 2011 17:17:43 +0000 (17:17 +0000)]

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pvtroshin [Wed, 9 Feb 2011 15:49:35 +0000 (15:49 +0000)]

new services are registered in wsbuild

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3728 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Feb 2011 14:51:20 +0000 (14:51 +0000)]

DisEMBL and GlobProt web services further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3727 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Feb 2011 11:10:23 +0000 (11:10 +0000)]

Fix a test case for jronn parameters

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3724 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Feb 2011 11:04:49 +0000 (11:04 +0000)]

Disable jronn parameter

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3723 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Wed, 9 Feb 2011 10:42:39 +0000 (10:42 +0000)]

GlobPlot and DIsembl execs all test passed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3722 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 8 Feb 2011 17:27:02 +0000 (17:27 +0000)]

Copying Bio-python to globplot to satisfy the dependency

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3719 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Tue, 8 Feb 2011 17:21:44 +0000 (17:21 +0000)]

Further work on GlobPlot

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3718 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 7 Feb 2011 15:10:30 +0000 (15:10 +0000)]

Add globplot and disembl to web services descriptors

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3710 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Mon, 7 Feb 2011 15:06:27 +0000 (15:06 +0000)]

GlobPlot service, runner and result parser
Some rearrangements for disembl to reuse methods

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3709 e3abac25-378b-4346-85de-24260fe3988d

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pvtroshin [Fri, 4 Feb 2011 17:18:08 +0000 (17:18 +0000)]

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3705 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d

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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 e3abac25-378b-4346-85de-24260fe3988d