Sasha [Fri, 26 Apr 2013 17:19:05 +0000 (18:19 +0100)]
Re-formatting files
Sasha [Wed, 24 Apr 2013 16:37:43 +0000 (17:37 +0100)]
New build of JABAWS
Sasha [Wed, 24 Apr 2013 16:35:39 +0000 (17:35 +0100)]
debug version of /log4j.properties
Sasha [Wed, 24 Apr 2013 16:35:11 +0000 (17:35 +0100)]
delete wronigly located log4j.properties
Sasha [Wed, 24 Apr 2013 16:09:22 +0000 (17:09 +0100)]
cleat stats array and simplify internal structure
Sasha [Wed, 24 Apr 2013 16:05:00 +0000 (17:05 +0100)]
better way to set stat collection time, but should be moved to Engine.*.properties
Sasha [Wed, 24 Apr 2013 16:02:44 +0000 (17:02 +0100)]
add Logger to the class
Sasha [Mon, 22 Apr 2013 12:35:25 +0000 (13:35 +0100)]
log4j in no longer needed for minimal client
Sasha [Fri, 19 Apr 2013 15:17:15 +0000 (16:17 +0100)]
Changes in jar files
Sasha [Fri, 19 Apr 2013 15:16:59 +0000 (16:16 +0100)]
IntelliJ profile changes
Sasha [Fri, 19 Apr 2013 15:15:47 +0000 (16:15 +0100)]
formatting text
Sasha [Fri, 19 Apr 2013 15:14:27 +0000 (16:14 +0100)]
correct comment
Sasha [Fri, 19 Apr 2013 15:13:49 +0000 (16:13 +0100)]
Small internal code changes
Sasha [Fri, 19 Apr 2013 15:11:55 +0000 (16:11 +0100)]
simplify loops
Alexander Sherstnev [Fri, 29 Mar 2013 15:47:36 +0000 (15:47 +0000)]
Add intelliJ configuration files
Alexander Sherstnev [Fri, 29 Mar 2013 14:34:19 +0000 (14:34 +0000)]
Website files updated for JABAWS 3.0a
Alexander Sherstnev [Fri, 29 Mar 2013 13:41:30 +0000 (13:41 +0000)]
Restore jobsout/README
Alexander Sherstnev [Fri, 29 Mar 2013 13:34:45 +0000 (13:34 +0000)]
delete jobsout/README
Alexander Sherstnev [Fri, 8 Mar 2013 17:09:06 +0000 (17:09 +0000)]
remove unnecessary import
Alexander Sherstnev [Fri, 8 Mar 2013 17:08:00 +0000 (17:08 +0000)]
JWS-55 temporary fix for wrong security configuration
jprocter [Tue, 23 Oct 2012 16:46:26 +0000 (17:46 +0100)]
Merge branch 'JABAWS_Release_2_0' of https://source.jalview.org/git/jabaws into develop
jprocter [Fri, 3 Aug 2012 11:06:00 +0000 (12:06 +0100)]
JWS-48 patch to ensure JAX-WS 2.1 client code source generation with JAX-WS 2.2 libraries
jprocter [Thu, 2 Aug 2012 14:55:51 +0000 (15:55 +0100)]
JWS-43 development deployment context changed to "jabaws" so TestNG web service client tests can run against the development server
jprocter [Thu, 2 Aug 2012 11:55:05 +0000 (12:55 +0100)]
JWS-47 patch test to default local JABAWS server and source tidy
jprocter [Thu, 2 Aug 2012 11:53:01 +0000 (12:53 +0100)]
JWS-47 override custom/preset analize methods so the input can be validated appropriately for AACons
jprocter [Thu, 2 Aug 2012 11:51:38 +0000 (12:51 +0100)]
JWS-47 AACons validation shouldn't be done for generic analysis services
jprocter [Thu, 2 Aug 2012 11:46:51 +0000 (12:46 +0100)]
JWS-47 new customAnalize test for IUPredWS - with several unaligned sequences of different lengths.
jprocter [Wed, 6 Jun 2012 18:02:52 +0000 (19:02 +0100)]
JWS-44 - attempt to make a file executable if it is supposed to be executable according to jabaws configuration.
jprocter [Wed, 6 Jun 2012 18:00:06 +0000 (19:00 +0100)]
JWS-43 eclipse project metadata for dynamic web project directly deployable on development server
jprocter [Mon, 4 Jun 2012 16:09:07 +0000 (17:09 +0100)]
Merge branch 'JWS-27-jronn' into develop
jprocter [Mon, 4 Jun 2012 16:08:56 +0000 (17:08 +0100)]
Merge branch 'JWS-27-jronn' into JABAWS_Release_2_0
jprocter [Mon, 4 Jun 2012 16:06:13 +0000 (17:06 +0100)]
JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for large sets of sequences in multithreaded mode
jprocter [Fri, 1 Jun 2012 11:56:37 +0000 (12:56 +0100)]
Merge branch 'JWS-29' into develop
jprocter [Fri, 1 Jun 2012 11:56:14 +0000 (12:56 +0100)]
Merge branch 'JWS-29' into JABAWS_Release_2_0
jprocter [Fri, 1 Jun 2012 11:53:39 +0000 (12:53 +0100)]
JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance to end of file rather than start of next FASTA header
jprocter [Fri, 1 Jun 2012 10:17:01 +0000 (11:17 +0100)]
test demonstrating JWS-29 assertion failure
jprocter [Fri, 1 Jun 2012 10:08:28 +0000 (11:08 +0100)]
Merge branch 'JWS-36' into JABAWS_Release_2_0
jprocter [Fri, 1 Jun 2012 10:08:04 +0000 (11:08 +0100)]
Merge branch 'JWS-36' into develop
jprocter [Fri, 1 Jun 2012 09:57:51 +0000 (10:57 +0100)]
JWS-36 patched Scores writer to put spaces between ranges and space separated scores
jprocter [Thu, 31 May 2012 17:27:18 +0000 (18:27 +0100)]
patch fixes JWS-35
jprocter [Thu, 31 May 2012 17:27:02 +0000 (18:27 +0100)]
test for JWS-35 - check that range and first value of prediction for each method matches expected values
jprocter [Thu, 31 May 2012 17:31:28 +0000 (18:31 +0100)]
Merge branch 'JWS-35' into JABAWS_Release_2_0
jprocter [Thu, 31 May 2012 17:27:18 +0000 (18:27 +0100)]
patch fixes JWS-35
jprocter [Thu, 31 May 2012 17:27:02 +0000 (18:27 +0100)]
test for JWS-35 - check that range and first value of prediction for each method matches expected values
pvtroshin [Tue, 20 Dec 2011 12:00:16 +0000 (12:00 +0000)]
File puller tester
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4832
e3abac25-378b-4346-85de-
24260fe3988d
jprocter [Tue, 15 May 2012 15:55:08 +0000 (16:55 +0100)]
remove jabaws 3 development code
jprocter [Tue, 15 May 2012 15:54:20 +0000 (16:54 +0100)]
ensure we never check in autogenerated documentation or build artefacts
jprocter [Tue, 15 May 2012 15:53:15 +0000 (16:53 +0100)]
fix jabaws download link
pvtroshin [Mon, 12 Dec 2011 16:19:50 +0000 (16:19 +0000)]
word order
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4814
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Mon, 12 Dec 2011 14:46:33 +0000 (14:46 +0000)]
load the driver explicitly
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4813
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 9 Dec 2011 17:23:23 +0000 (17:23 +0000)]
AMI ID update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4809
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 9 Dec 2011 15:07:50 +0000 (15:07 +0000)]
web site minor tweaks
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4808
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 9 Dec 2011 13:20:54 +0000 (13:20 +0000)]
web pages url updates
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4805
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Thu, 8 Dec 2011 17:44:10 +0000 (17:44 +0000)]
Bug fix to the stat pages
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4802
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 7 Dec 2011 14:06:53 +0000 (14:06 +0000)]
updated javadoc for the system as well as new redirect address for download app
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4793
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 7 Dec 2011 12:29:20 +0000 (12:29 +0000)]
remove old project javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4790
e3abac25-378b-4346-85de-
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pvtroshin [Wed, 7 Dec 2011 12:04:26 +0000 (12:04 +0000)]
remove old datamodel javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4789
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 7 Dec 2011 11:54:34 +0000 (11:54 +0000)]
web pages updates to point to new download location also the redirect servlet
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4788
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Tue, 8 Nov 2011 16:19:29 +0000 (16:19 +0000)]
Fix for potential NullPointer exception if the results are an empty file
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4721
e3abac25-378b-4346-85de-
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pvtroshin [Thu, 3 Nov 2011 10:15:05 +0000 (10:15 +0000)]
remove a copy of category tester
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4708
e3abac25-378b-4346-85de-
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jprocter [Wed, 2 Nov 2011 17:34:40 +0000 (17:34 +0000)]
test that methods and fields of Category are publicly accessible
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4707
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 2 Nov 2011 11:56:11 +0000 (11:56 +0000)]
A few minor changes to the test
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4706
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 2 Nov 2011 11:44:36 +0000 (11:44 +0000)]
update binaries
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4705
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 2 Nov 2011 11:41:50 +0000 (11:41 +0000)]
Assign a test to an appropriate test category
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4704
e3abac25-378b-4346-85de-
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pvtroshin [Wed, 2 Nov 2011 11:39:06 +0000 (11:39 +0000)]
Fix bug in category class and use Jim's test as a test case
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4703
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 31 Oct 2011 17:48:42 +0000 (17:48 +0000)]
update build artefacts
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4701
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 31 Oct 2011 17:47:35 +0000 (17:47 +0000)]
Move Category into data.msa package from ws.server to get it into min jabaws package.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4700
e3abac25-378b-4346-85de-
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pvtroshin [Thu, 13 Oct 2011 14:47:09 +0000 (14:47 +0000)]
JABAWS web site update - new logo and title page
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4655
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 11 Oct 2011 11:44:28 +0000 (11:44 +0000)]
change tracker code to compbio
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4652
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 11 Oct 2011 11:37:05 +0000 (11:37 +0000)]
Google Analytics statistics is added
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4651
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 11 Oct 2011 11:15:22 +0000 (11:15 +0000)]
ga config file
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4650
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Mon, 10 Oct 2011 17:13:34 +0000 (17:13 +0000)]
Changing of input type
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4648
e3abac25-378b-4346-85de-
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pvtroshin [Wed, 5 Oct 2011 10:52:23 +0000 (10:52 +0000)]
Web site updates
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4643
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Wed, 5 Oct 2011 10:51:38 +0000 (10:51 +0000)]
Remove test jobs from statistics
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4642
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 16 Sep 2011 15:17:24 +0000 (15:17 +0000)]
Service status pages update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4592
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 16 Sep 2011 14:39:42 +0000 (14:39 +0000)]
web site update new pages for awss beanstalk deployment
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4591
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Fri, 16 Sep 2011 14:38:53 +0000 (14:38 +0000)]
allow head method for all jabaws servlets
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4590
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 16 Sep 2011 14:38:31 +0000 (14:38 +0000)]
add response to head method
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4589
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 6 Sep 2011 17:15:55 +0000 (17:15 +0000)]
comment out services checkers from the security constrain
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4574
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 6 Sep 2011 17:15:22 +0000 (17:15 +0000)]
doc update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4573
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 6 Sep 2011 16:12:47 +0000 (16:12 +0000)]
Web services status checking servlets, new clustalo x32 binary from Fabian, other small changes
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4571
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Tue, 6 Sep 2011 12:05:44 +0000 (12:05 +0000)]
Head title change
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4568
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 5 Sep 2011 15:20:11 +0000 (15:20 +0000)]
Update for web services stubs
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4566
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 5 Sep 2011 15:12:40 +0000 (15:12 +0000)]
Binaries for Mac in a war file
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4565
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 5 Sep 2011 15:11:55 +0000 (15:11 +0000)]
updates to web site
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4564
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 5 Sep 2011 15:11:23 +0000 (15:11 +0000)]
Adding listener for setting executable flag on the web application start up
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4563
e3abac25-378b-4346-85de-
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pvtroshin [Mon, 5 Sep 2011 15:09:58 +0000 (15:09 +0000)]
Add an implementation for Services.getServiceInfo method and categorization for services.
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4562
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 2 Sep 2011 17:22:37 +0000 (17:22 +0000)]
web pages updates
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4559
e3abac25-378b-4346-85de-
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pvtroshin [Thu, 25 Aug 2011 15:46:49 +0000 (15:46 +0000)]
An attempt to automatically make binaries executables - not successful but the code is commented out and let in for future use
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4548
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Tue, 16 Aug 2011 13:22:10 +0000 (13:22 +0000)]
Minor changes
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4526
e3abac25-378b-4346-85de-
24260fe3988d
pvtroshin [Tue, 16 Aug 2011 11:38:54 +0000 (11:38 +0000)]
minor change
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4525
e3abac25-378b-4346-85de-
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pvtroshin [Tue, 16 Aug 2011 11:38:38 +0000 (11:38 +0000)]
adding one more window web service into the test case
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4524
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:37:46 +0000 (13:37 +0000)]
rearrangement for mac binaries to link up with a web page
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4509
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:35:18 +0000 (13:35 +0000)]
Javadoc fixes
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4508
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:34:38 +0000 (13:34 +0000)]
adding clustalO documentation
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4507
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:34:07 +0000 (13:34 +0000)]
updated javadoc
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4506
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:29:30 +0000 (13:29 +0000)]
remove dm javadoc to update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4505
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)]
delete old javadoc to update
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4504
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 12:39:57 +0000 (12:39 +0000)]
build client source when build all
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4503
e3abac25-378b-4346-85de-
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pvtroshin [Fri, 12 Aug 2011 12:38:29 +0000 (12:38 +0000)]
Mac binaries
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4502
e3abac25-378b-4346-85de-
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git://source.jalview.org / jabaws.git / log