Jim Procter [Thu, 23 May 2013 09:12:17 +0000 (10:12 +0100)]
JAL-1295 JAL-1296 clearer assertion failed message
Jim Procter [Wed, 22 May 2013 17:06:21 +0000 (18:06 +0100)]
JAL-1295 JAL-1297 enhance test to check graph visiblity and graphGroup set equivalence
Jim Procter [Wed, 22 May 2013 16:53:03 +0000 (17:53 +0100)]
fix for JAL-1297: COMBINE output now follows specification and all additional annotation rows included in output (not just the first one which wasn't hidden)
Jim Procter [Wed, 22 May 2013 16:49:09 +0000 (17:49 +0100)]
JAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294
test alignment annotation file IO for example given in documentation and for multiple combine statement
Jim Procter [Wed, 22 May 2013 16:46:25 +0000 (17:46 +0100)]
JAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment+annotation equivalence test to be used in other tests
Jim Procter [Wed, 22 May 2013 16:45:42 +0000 (17:45 +0100)]
javadoc and formatting
Jim Procter [Wed, 22 May 2013 16:45:29 +0000 (17:45 +0100)]
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefit of annotation IO test
Jim Procter [Wed, 22 May 2013 16:43:40 +0000 (17:43 +0100)]
JAL-1297 JAL-1295 JAL-1294 improve test logic for comparing annotation elements
Jim Procter [Tue, 21 May 2013 14:05:47 +0000 (15:05 +0100)]
JAL-1296 reinstated tab characters so example annotation file can be copied and pasted to a file and imported
Jim Procter [Tue, 21 May 2013 13:12:15 +0000 (14:12 +0100)]
JAL-1070 - [ not a real patch ] - include offending line number and content in output when an Alignment annotation file parsing exception stacktraces to stderr
Jim Procter [Tue, 21 May 2013 09:53:37 +0000 (10:53 +0100)]
JAL-966 paintrefresher should be abstract [ Merge branch 'jv3_notes' into JAL-1161_optAnnotPanelRendering ]
Jim Procter [Tue, 21 May 2013 09:52:14 +0000 (10:52 +0100)]
JAL-1161 conditional parameters for controlling clipping
Jim Procter [Tue, 21 May 2013 08:33:56 +0000 (09:33 +0100)]
JAL-1292 avoid exception by using bitset of arbitrary width for remembering which graphgroups have been drawn
Jim Procter [Mon, 20 May 2013 14:35:04 +0000 (15:35 +0100)]
JAL-1161 changed signature to allow clipping bounds for panel to be obtained
Jim Procter [Mon, 20 May 2013 14:33:46 +0000 (15:33 +0100)]
formatting
Jim Procter [Sun, 19 May 2013 18:29:51 +0000 (19:29 +0100)]
JAL-1161 only trigger an annotation repaint in unwrapped view when the horizontal offset changes.
Jim Procter [Sun, 19 May 2013 18:28:25 +0000 (19:28 +0100)]
JAL-1161 enable fastPaint for nudges from scroll bars or trackpad
Jim Procter [Sun, 19 May 2013 18:27:16 +0000 (19:27 +0100)]
JAL-1161 stick to api
Jim Procter [Sun, 19 May 2013 18:26:46 +0000 (19:26 +0100)]
typo
Jim Procter [Tue, 21 May 2013 15:36:03 +0000 (16:36 +0100)]
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
Jim Procter [Fri, 15 Feb 2013 15:43:27 +0000 (15:43 +0000)]
split test for general Stockholm IO consistency (JAL-1199) from test for IO of sequence metadata (JAL-1265)
Jim Procter [Fri, 15 Feb 2013 15:42:21 +0000 (15:42 +0000)]
JAL-1199 JAL-1272 remove main() method from test class
Jim Procter [Fri, 15 Feb 2013 15:40:34 +0000 (15:40 +0000)]
formatting
Jim Procter [Fri, 15 Feb 2013 15:40:12 +0000 (15:40 +0000)]
JAL-1199 JAL-1272 refactored Natasha's test to a generic alignment data consistency test
Jim Procter [Mon, 13 May 2013 13:55:32 +0000 (14:55 +0100)]
Merge branch 'JAL-1289_initCallBack' into Release_2_8_Branch
Jim Procter [Mon, 13 May 2013 13:25:11 +0000 (14:25 +0100)]
JAL-1289 call oninit callback even if no alignment data was loaded
Jim Procter [Fri, 12 Apr 2013 04:39:40 +0000 (14:39 +1000)]
Merge branch 'JAL-1286_gzip' into Release_2_8_Branch
Jim Procter [Fri, 12 Apr 2013 04:37:56 +0000 (14:37 +1000)]
JAL-1286 URL stream reader tries to use a GZIPInputStream if URL ends in .gz
jprocter [Wed, 6 Feb 2013 17:04:23 +0000 (17:04 +0000)]
Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing
jprocter [Wed, 6 Feb 2013 16:49:01 +0000 (16:49 +0000)]
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
jprocter [Wed, 6 Feb 2013 16:43:45 +0000 (16:43 +0000)]
JAL-1265 basic support for parsing database accessions from Stockholm
JAL-851 - guess the primary sequence accession based on RFAM or PFAM alignment accession code
jprocter [Wed, 6 Feb 2013 16:41:01 +0000 (16:41 +0000)]
JAL-1199 added test for Rfam Stockholm file example
jprocter [Wed, 6 Feb 2013 15:43:50 +0000 (15:43 +0000)]
JAL-1199 refactored stockholm test code from main class and added a Pfam Stockholm file for testing purposes (with new PDB dbref test)
jprocter [Tue, 5 Feb 2013 15:18:18 +0000 (15:18 +0000)]
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
jprocter [Tue, 5 Feb 2013 15:17:56 +0000 (15:17 +0000)]
formatting
jprocter [Tue, 5 Feb 2013 15:00:37 +0000 (15:00 +0000)]
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
jprocter [Sun, 20 Jan 2013 14:28:43 +0000 (14:28 +0000)]
Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch
jprocter [Fri, 18 Jan 2013 15:56:36 +0000 (15:56 +0000)]
JAL-1238 test to see if the primary Uniprot source is placed first in list of Uniprot sources
jprocter [Fri, 18 Jan 2013 15:55:58 +0000 (15:55 +0000)]
JAL-1238 order to place primary sources before lower tier sources
jprocter [Fri, 18 Jan 2013 15:55:32 +0000 (15:55 +0000)]
JAL-1238 method to test if DAS source is a primary reference source
jprocter [Fri, 18 Jan 2013 15:52:17 +0000 (15:52 +0000)]
JAL-1238 tier index indicating distance of a source from the primary source for that database - level 0 sources are the only ones that should be used to validate sequences.
jprocter [Fri, 18 Jan 2013 08:09:40 +0000 (08:09 +0000)]
Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch
jprocter [Fri, 18 Jan 2013 08:01:53 +0000 (08:01 +0000)]
JAL-1255 don't show 'Right click to add annotations' message in wrapped mode
jprocter [Fri, 18 Jan 2013 07:51:31 +0000 (07:51 +0000)]
JAL-1254 patch for NPE in annotation renderer when no annotations shown in alignment.
Natasha [Mon, 17 Dec 2012 15:48:23 +0000 (15:48 +0000)]
test for output a file in Stockholm format
Natasha [Wed, 12 Dec 2012 21:02:44 +0000 (21:02 +0000)]
Output accession number for file in stockholm format
jprocter [Tue, 11 Dec 2012 17:27:39 +0000 (17:27 +0000)]
JAL-1217 check and avoid NPE if no datastore object instantiated
jprocter [Tue, 11 Dec 2012 17:27:25 +0000 (17:27 +0000)]
JAL-1217 report exception for service when no datastore can be created
Natasha [Fri, 23 Nov 2012 07:49:49 +0000 (07:49 +0000)]
stockholm file output code developed by Natasha Sherstneva
jprocter [Wed, 21 Nov 2012 15:51:37 +0000 (15:51 +0000)]
valid URLs in website menu frame and fixed GA code
jprocter [Sat, 17 Nov 2012 21:58:30 +0000 (21:58 +0000)]
Merge branch 'master' into Release_2_8_Branch
Paolo Di Tommaso [Thu, 15 Nov 2012 21:43:30 +0000 (22:43 +0100)]
Fixed T-Coffee file scores parser to support extended format including residue numbers
jprocter [Mon, 12 Nov 2012 11:36:47 +0000 (11:36 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:36:16 +0000 (11:36 +0000)]
final tweaks to help landing page
jprocter [Mon, 12 Nov 2012 11:12:49 +0000 (11:12 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:10:12 +0000 (11:10 +0000)]
update footer for static page
jprocter [Mon, 12 Nov 2012 10:00:29 +0000 (10:00 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Sun, 11 Nov 2012 11:23:11 +0000 (11:23 +0000)]
tidy help
jprocter [Fri, 9 Nov 2012 17:00:09 +0000 (17:00 +0000)]
property to configure webstart image
jprocter [Fri, 9 Nov 2012 16:56:10 +0000 (16:56 +0000)]
tweak file association comment and make sure webstart image is published
jprocter [Fri, 9 Nov 2012 16:35:45 +0000 (16:35 +0000)]
push jalview v2.8 release date to monday 12th November
jprocter [Fri, 9 Nov 2012 16:08:50 +0000 (16:08 +0000)]
ga tracking, footers and footer link styles
jprocter [Fri, 9 Nov 2012 15:32:04 +0000 (15:32 +0000)]
more tweaking of static pages and rejigging applet parameter documentation for accessibility
jprocter [Fri, 9 Nov 2012 14:38:11 +0000 (14:38 +0000)]
tweak whats new again
jprocter [Fri, 9 Nov 2012 13:04:39 +0000 (13:04 +0000)]
tweaking welcome message and what's new
jprocter [Fri, 9 Nov 2012 08:02:00 +0000 (08:02 +0000)]
constructor takes settings from any existing feature renderer on alignment panel
jprocter [Thu, 8 Nov 2012 17:45:43 +0000 (17:45 +0000)]
JAL-1193 ensure the 'loadedComplete' method gets called for all views
after the views have been opened by using the Swing stack as a queue
cruisecontrol [Thu, 8 Nov 2012 16:49:53 +0000 (16:49 +0000)]
update installAnywhere classpath and libs for jalview 2.8
jprocter [Thu, 8 Nov 2012 16:29:30 +0000 (16:29 +0000)]
update release notes for JAL-1202
cruisecontrol [Thu, 8 Nov 2012 16:21:39 +0000 (16:21 +0000)]
JAL-1202 included examples and also added in jdas jars and the groovy library
jprocter [Thu, 8 Nov 2012 15:41:51 +0000 (15:41 +0000)]
remember to close input file!
jprocter [Thu, 8 Nov 2012 15:41:34 +0000 (15:41 +0000)]
tidy imports
jprocter [Thu, 8 Nov 2012 10:59:13 +0000 (10:59 +0000)]
embed links to major features in main page
jprocter [Thu, 8 Nov 2012 10:58:54 +0000 (10:58 +0000)]
tweak wording
jprocter [Wed, 7 Nov 2012 17:28:32 +0000 (17:28 +0000)]
patch broken link
jprocter [Wed, 7 Nov 2012 17:18:20 +0000 (17:18 +0000)]
and more tweaks.
jprocter [Wed, 7 Nov 2012 17:15:08 +0000 (17:15 +0000)]
JAL-1201 more layout tweaks
jprocter [Wed, 7 Nov 2012 17:07:05 +0000 (17:07 +0000)]
JAL-1201 tweak layout for applet page and allow monospace <pre> tags
jprocter [Wed, 7 Nov 2012 15:59:39 +0000 (15:59 +0000)]
JAL-1201 more tweaks to page layout
jprocter [Wed, 7 Nov 2012 15:42:19 +0000 (15:42 +0000)]
Jalview 2.8 release notes and whats new! text
jprocter [Wed, 7 Nov 2012 15:11:58 +0000 (15:11 +0000)]
updated release notes for Jalview Version 2.8
jprocter [Wed, 7 Nov 2012 15:11:16 +0000 (15:11 +0000)]
JAL-1201 update pages to use new website design
jprocter [Wed, 7 Nov 2012 15:04:25 +0000 (15:04 +0000)]
JAL-957 manual update to applet authorlist - need to use authorprops (JAL-1200)
jprocter [Wed, 31 Oct 2012 17:05:58 +0000 (17:05 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Wed, 31 Oct 2012 17:04:29 +0000 (17:04 +0000)]
JAL-1130 fix gif palette (arggh!)
cruisecontrol [Tue, 30 Oct 2012 18:06:48 +0000 (18:06 +0000)]
JAL-1197 tweak installer more
cruisecontrol [Tue, 30 Oct 2012 17:51:13 +0000 (17:51 +0000)]
JAL-1197 JAL-1198 migrate to IA2012 and new build VM
jprocter [Tue, 30 Oct 2012 17:22:05 +0000 (17:22 +0000)]
JAL-1130 JAL-1197 nice installer splashscreens and fireworks readable pngs for splashscreens
jprocter [Tue, 30 Oct 2012 16:59:19 +0000 (16:59 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Tue, 30 Oct 2012 16:58:32 +0000 (16:58 +0000)]
JAL-1130 fireworks editable huge jalview logo in RGB
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:17:18 +0000 (16:17 +0000)]
JAL-1130 updated installAnywhere program logos
jprocter [Tue, 30 Oct 2012 16:16:11 +0000 (16:16 +0000)]
JAL-1130 preserved old installAnywhere installer logo as logo_v2
jprocter [Mon, 29 Oct 2012 10:42:43 +0000 (10:42 +0000)]
JAL-1130 made background transparent for small logo (used for application and window icon on Windows platform)
jprocter [Wed, 24 Oct 2012 16:04:11 +0000 (17:04 +0100)]
JAL-1193 call setLoadingFromArchiveFinished(true) for any new structure views, but only after all windows have been loaded and gathered
jprocter [Wed, 24 Oct 2012 16:00:59 +0000 (17:00 +0100)]
JAL-1193 patch prevents JalviewJmolBinding from handling colourBySequence events until setLoadingFromArchiveFinished(true) called
jprocter [Thu, 4 Oct 2012 16:43:26 +0000 (17:43 +0100)]
Jalview 2.8 Source Header
jprocter [Thu, 4 Oct 2012 16:05:22 +0000 (17:05 +0100)]
Merge branch 'develop' into Release_2_8_Branch
jprocter [Thu, 4 Oct 2012 15:56:41 +0000 (16:56 +0100)]
JAL-636 switch to simple REST interface to dbfetch (//ebi.ac.uk/Tools/webservices/services/dbfetch_rest)
git://source.jalview.org / jalview.git / log