gmungoc [Tue, 20 Jan 2015 09:46:30 +0000 (09:46 +0000)]
JAL-1619 test that reordering cDNA does not change translation results
gmungoc [Tue, 20 Jan 2015 09:11:43 +0000 (09:11 +0000)]
JAL-1619 tweaked for better reusability
gmungoc [Mon, 19 Jan 2015 17:18:20 +0000 (17:18 +0000)]
JAL-1619 refactored cDNA translation; modified codon comparison; tests
gmungoc [Mon, 19 Jan 2015 17:17:07 +0000 (17:17 +0000)]
JAL-1636 typed collections now in ResidueProperties
gmungoc [Mon, 19 Jan 2015 17:16:11 +0000 (17:16 +0000)]
JAL-1636 fix for mouseover of 'X' in translated protein
gmungoc [Sun, 18 Jan 2015 11:58:13 +0000 (11:58 +0000)]
JAL-1619 refactoring wip
gmungoc [Sat, 17 Jan 2015 06:51:37 +0000 (06:51 +0000)]
JAL-1619 further refactoring
gmungoc [Fri, 16 Jan 2015 15:09:06 +0000 (15:09 +0000)]
JAL-1619 refactoring in progress for Dna translation
gmungoc [Wed, 14 Jan 2015 16:36:34 +0000 (16:36 +0000)]
JAL-1619 AlignedCodonFrame in new alignment should references realigned
sequences
gmungoc [Wed, 14 Jan 2015 16:35:41 +0000 (16:35 +0000)]
JAL-1619 modified repaint after 'Align As' action
gmungoc [Wed, 14 Jan 2015 16:33:27 +0000 (16:33 +0000)]
JAL-1619 Javadoc
gmungoc [Mon, 12 Jan 2015 17:13:45 +0000 (17:13 +0000)]
JAL-1619 load/align cDNA for protein (wip)
gmungoc [Wed, 7 Jan 2015 17:23:04 +0000 (17:23 +0000)]
JAL-845 TODO comment added
gmungoc [Sun, 4 Jan 2015 17:33:20 +0000 (17:33 +0000)]
JAL-1619 first draft of 'linked protein and cDNA'
gmungoc [Sun, 28 Dec 2014 09:54:56 +0000 (09:54 +0000)]
JAL-845 first working linked edit protein -> cDNA
gmungoc [Tue, 16 Dec 2014 11:21:54 +0000 (11:21 +0000)]
JAL-1328 System.exit() removed as it aborts an entire JUnit suite
gmungoc [Tue, 16 Dec 2014 10:47:48 +0000 (10:47 +0000)]
JAL-845 first simple unit tests added
gmungoc [Tue, 16 Dec 2014 10:46:46 +0000 (10:46 +0000)]
JAL-845 move main method to 'test' class (needs further work);
formatting
gmungoc [Tue, 16 Dec 2014 10:44:16 +0000 (10:44 +0000)]
JAL-1618 feature parsing bug (and formatting)
gmungoc [Tue, 16 Dec 2014 10:40:59 +0000 (10:40 +0000)]
JAL-1619 refactorings: Map, StringBuilder, Override
gmungoc [Tue, 16 Dec 2014 10:29:08 +0000 (10:29 +0000)]
JAL-845 formatting only (block parentheses)
gmungoc [Tue, 16 Dec 2014 10:27:23 +0000 (10:27 +0000)]
JAL-1619 don't copy hidden or RNA SS annotations to protein translation
gmungoc [Fri, 12 Dec 2014 15:29:11 +0000 (15:29 +0000)]
JAL-845 don't translate hidden annotation (plus formatting)
gmungoc [Tue, 9 Dec 2014 12:21:20 +0000 (12:21 +0000)]
JAL-1616 loading of datasets from XML patched
Charles Ofoegbu [Mon, 8 Dec 2014 11:47:36 +0000 (11:47 +0000)]
JAL-1613 hotfix for duplicated sequence after pairwise alignment
gmungoc [Fri, 5 Dec 2014 10:52:38 +0000 (10:52 +0000)]
JAL-1614 flag 'protein' removed
gmungoc [Wed, 3 Dec 2014 15:05:54 +0000 (15:05 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 12:02:49 +0000 (12:02 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 12:02:18 +0000 (12:02 +0000)]
JAL-1517 update applet authors list
Jim Procter [Wed, 3 Dec 2014 09:21:29 +0000 (09:21 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 09:20:54 +0000 (09:20 +0000)]
JAL-1517 disable desktop 'take snapshot' menu item for release
Jim Procter [Wed, 3 Dec 2014 08:16:21 +0000 (08:16 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 08:16:02 +0000 (08:16 +0000)]
JAL-1517 dropped jnlp file in help documentation in favour of link to Jalview launchApp service
Jim Procter [Wed, 3 Dec 2014 07:48:02 +0000 (07:48 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 07:47:33 +0000 (07:47 +0000)]
JAL-1517 updated library licensing info
Jim Procter [Wed, 3 Dec 2014 07:39:56 +0000 (07:39 +0000)]
JAL-1517 release notes
Jim Procter [Tue, 2 Dec 2014 18:02:19 +0000 (18:02 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 18:02:00 +0000 (18:02 +0000)]
JAL-1517 typo
Jim Procter [Tue, 2 Dec 2014 16:53:17 +0000 (16:53 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 16:53:02 +0000 (16:53 +0000)]
JAL-1517 TOC items must be on one line for help2Website
Jim Procter [Tue, 2 Dec 2014 16:24:16 +0000 (16:24 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 16:23:52 +0000 (16:23 +0000)]
JAL-1602 tweak VM inclusion options
Jim Procter [Tue, 2 Dec 2014 13:22:20 +0000 (13:22 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 13:21:49 +0000 (13:21 +0000)]
JAL-1517 documentation for 2.8.2 release
Jim Procter [Tue, 2 Dec 2014 11:43:22 +0000 (11:43 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 11:43:00 +0000 (11:43 +0000)]
JAL-1602 typo in jsonsimple jar
Jim Procter [Tue, 2 Dec 2014 10:22:40 +0000 (10:22 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 10:22:21 +0000 (10:22 +0000)]
JAL-1602 add missing jars to install
Jim Procter [Mon, 1 Dec 2014 23:56:13 +0000 (23:56 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 23:55:44 +0000 (23:55 +0000)]
JAL-1602 upgrade to InstallAnywhere 2014 J17 runtimes
Jim Procter [Mon, 1 Dec 2014 21:49:16 +0000 (21:49 +0000)]
JAL-1199 JAL-1569 incremental patch allow non-standard annotation to be output
Jim Procter [Mon, 1 Dec 2014 21:47:37 +0000 (21:47 +0000)]
JAL-1517 updating author list
Jim Procter [Mon, 1 Dec 2014 21:47:13 +0000 (21:47 +0000)]
JAL-1517 updating authors list
Jim Procter [Mon, 1 Dec 2014 16:55:02 +0000 (16:55 +0000)]
JAL-795 hack to ignore black colour in annotation element.
Jim Procter [Mon, 1 Dec 2014 16:43:02 +0000 (16:43 +0000)]
JAL-1601 ignore the JABA Jpred client in Jalview 2.8.2 release
gmungoc [Mon, 1 Dec 2014 16:17:20 +0000 (16:17 +0000)]
JAL-429 Phylip added to help page
gmungoc [Mon, 1 Dec 2014 16:14:50 +0000 (16:14 +0000)]
JAL-1544 typos/formatting in help (and Phylip added)
Jim Procter [Mon, 1 Dec 2014 15:39:42 +0000 (15:39 +0000)]
Merge branch 'bug/JAL-1610refAnnotationsInViews' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 15:38:26 +0000 (15:38 +0000)]
file for JAL-1268 jalview.io.Jalview2xmlTests.testTCoffeeScores
Jim Procter [Fri, 28 Nov 2014 16:01:37 +0000 (16:01 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Fri, 28 Nov 2014 16:01:03 +0000 (16:01 +0000)]
JAL-1517 first stab at release notes... lots of documentation to go!
gmungoc [Fri, 28 Nov 2014 15:48:48 +0000 (15:48 +0000)]
JAL-1610 check reference annotations against alignment, not sequence
Jim Procter [Fri, 28 Nov 2014 14:58:00 +0000 (14:58 +0000)]
JAL-1522 output installation type to stdout
Jim Procter [Fri, 28 Nov 2014 14:47:37 +0000 (14:47 +0000)]
JAL-1522 remove build/deployment details imported from user preferences file
Jim Procter [Fri, 28 Nov 2014 14:46:41 +0000 (14:46 +0000)]
JAL-1517 formatting
Jim Procter [Fri, 28 Nov 2014 14:46:04 +0000 (14:46 +0000)]
JAL-1611 revise log level to reduce verbosity
Jim Procter [Fri, 28 Nov 2014 14:20:23 +0000 (14:20 +0000)]
JAL-1583 javadoc and fix constructor signature
Jim Procter [Fri, 28 Nov 2014 14:07:39 +0000 (14:07 +0000)]
JAL-1342 document argument to specify preferred JABA server
Jim Procter [Fri, 28 Nov 2014 14:06:08 +0000 (14:06 +0000)]
JAL-1604 formatting
Jim Procter [Fri, 28 Nov 2014 14:05:42 +0000 (14:05 +0000)]
JAL-1604 revised wording and internationalised dialog
Jim Procter [Fri, 28 Nov 2014 14:04:16 +0000 (14:04 +0000)]
JAL-1583 back out original fix and simply check MSAWSThread.hasValidInput flag before displaying job window and starting the web service job thread.
Jim Procter [Fri, 28 Nov 2014 14:01:27 +0000 (14:01 +0000)]
JAL-1583 formatting
Jim Procter [Fri, 28 Nov 2014 14:01:15 +0000 (14:01 +0000)]
JAL-1583 new validInput flag set according to validity of all MSA jobs prepared for submission
Jim Procter [Fri, 28 Nov 2014 13:58:51 +0000 (13:58 +0000)]
JAL-1583 refactored addInternalFrame to allow webservice job frame to be added but not automatically made visible
Jim Procter [Fri, 28 Nov 2014 13:55:05 +0000 (13:55 +0000)]
JAL-1517 formatting/tidy
Jim Procter [Tue, 25 Nov 2014 11:24:43 +0000 (11:24 +0000)]
JAL-1517 svg==scalable :)
Jim Procter [Thu, 27 Nov 2014 16:02:21 +0000 (16:02 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 15:59:39 +0000 (15:59 +0000)]
JAL-674 add sequence associated annotation rows to flanking alignment
Jim Procter [Thu, 27 Nov 2014 15:58:51 +0000 (15:58 +0000)]
JAL-1177 JAL-905 cannot recover sequences from dataset if dataset is currently being recovered
Jim Procter [Thu, 27 Nov 2014 14:56:35 +0000 (14:56 +0000)]
JAL-674 avoid writing \0 for chain code
Jim Procter [Thu, 27 Nov 2014 14:39:32 +0000 (14:39 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 14:32:52 +0000 (14:32 +0000)]
JAL-674 patch to fix bug with showing reference annotation for legacy jalview example file v2.7
Jim Procter [Thu, 27 Nov 2014 14:32:08 +0000 (14:32 +0000)]
JAL-674 formatting
Jim Procter [Thu, 27 Nov 2014 14:31:20 +0000 (14:31 +0000)]
JAL-674 unused variable
Jim Procter [Thu, 27 Nov 2014 14:31:05 +0000 (14:31 +0000)]
JAL-674 bug in test
gmungoc [Thu, 27 Nov 2014 11:56:25 +0000 (11:56 +0000)]
JAL-1603 if Chimera selected in Preferences, warn if not installed/found
gmungoc [Thu, 27 Nov 2014 11:53:50 +0000 (11:53 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 10:37:06 +0000 (10:37 +0000)]
JAL-674 test that PDB annotation created when importing a legacy jalview example file is mapped to the correct place as the manually created version (temperature factor in exampleFile_2_7.jar
Jim Procter [Thu, 27 Nov 2014 10:35:58 +0000 (10:35 +0000)]
JAL-674 patch NPE bug when test run in isolation
Jim Procter [Thu, 27 Nov 2014 10:35:23 +0000 (10:35 +0000)]
JAL-674 fix test properties path and add properties file
Jim Procter [Thu, 27 Nov 2014 10:31:31 +0000 (10:31 +0000)]
JAL-674 JAL-966 new method to retrieve all views
Jim Procter [Thu, 27 Nov 2014 10:29:55 +0000 (10:29 +0000)]
organise imports
Jim Procter [Thu, 27 Nov 2014 10:29:00 +0000 (10:29 +0000)]
JAL-966 promote getName to an api method
Charles Ofoegbu [Thu, 27 Nov 2014 10:15:59 +0000 (10:15 +0000)]
Merge branch 'bug/JAL-1604_Entire-alignment-submission' into Release_2_8_2_Branch
Charles Ofoegbu [Thu, 27 Nov 2014 10:13:39 +0000 (10:13 +0000)]
JAL-1604 Entire sequence submision for MSA job bugfix
Charles Ofoegbu [Thu, 27 Nov 2014 09:23:26 +0000 (09:23 +0000)]
Merge branch 'bug/JAL-1583_MSA_webservice_validation' into Release_2_8_2_Branch
Charles Ofoegbu [Thu, 27 Nov 2014 09:20:45 +0000 (09:20 +0000)]
modified regex for sequence validation
gmungoc [Thu, 27 Nov 2014 08:39:32 +0000 (08:39 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 26 Nov 2014 16:59:07 +0000 (16:59 +0000)]
Merge branch 'bug/JAL-207_pairwise-alignment-context-loss' into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 26 Nov 2014 16:57:23 +0000 (16:57 +0000)]
JAL-207 pairwise alignment sequence contexts propergation bugfix
git://source.jalview.org / jalview.git / log