James Procter [Tue, 29 Oct 2024 21:33:00 +0000 (21:33 +0000)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
James Procter [Tue, 29 Oct 2024 21:32:30 +0000 (21:32 +0000)]
JAL-4473 JAL-4467 release notes
James Procter [Tue, 29 Oct 2024 21:29:09 +0000 (21:29 +0000)]
Merge branch 'bug/JAL-4467_getdownArchive_task_fails' into develop
James Procter [Mon, 28 Oct 2024 16:57:38 +0000 (16:57 +0000)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
James Procter [Mon, 28 Oct 2024 16:57:12 +0000 (16:57 +0000)]
JAL-4473 release date 29th Oct 2024
James Procter [Mon, 28 Oct 2024 16:35:42 +0000 (16:35 +0000)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
James Procter [Mon, 28 Oct 2024 16:34:18 +0000 (16:34 +0000)]
JAL-4473 release notes for JAL-4380
Ben Soares [Tue, 2 Apr 2024 19:27:50 +0000 (20:27 +0100)]
JAL-4380 Improved annotation tooltips especially secondary structure tooltips
Ben Soares [Tue, 20 Feb 2024 15:35:22 +0000 (15:35 +0000)]
JAL-4380 Added information to annotation tooltips when description is not present
James Procter [Fri, 25 Oct 2024 14:42:09 +0000 (15:42 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
James Procter [Fri, 25 Oct 2024 14:41:49 +0000 (15:41 +0100)]
Merge branch 'patch/fix_JAL-4470_JAL-4471_for_2_11_4_1' into develop
Jim Procter [Fri, 4 Oct 2024 16:06:44 +0000 (17:06 +0100)]
JAL-4473 whatsNew 2.11.4.1
Jim Procter [Fri, 4 Oct 2024 15:08:23 +0000 (16:08 +0100)]
JAL-4473 new jalview patch release
Jim Procter [Fri, 4 Oct 2024 15:06:49 +0000 (16:06 +0100)]
fix for JAL-4471 - secondary structure similarity tree can only be computed for sequence-associated annotation(s)
Jim Procter [Fri, 4 Oct 2024 15:03:38 +0000 (16:03 +0100)]
JAL-4470 fix: check for workers!=null before checking its empty...
Ben Soares [Fri, 20 Sep 2024 15:42:53 +0000 (16:42 +0100)]
JAL-4467 Take account of presource and xresource in the getdownArchiveBuild task
Jim Procter [Wed, 18 Sep 2024 01:52:47 +0000 (02:52 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 18 Sep 2024 01:52:21 +0000 (02:52 +0100)]
JAL-4418 release notes typos
Jim Procter [Wed, 18 Sep 2024 00:28:05 +0000 (01:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 18 Sep 2024 00:27:36 +0000 (01:27 +0100)]
JAL-4418 bump release date to 18th September 2024
Jim Procter [Wed, 18 Sep 2024 00:26:47 +0000 (01:26 +0100)]
JAL-4418 fix up help TOC copypaste error
Jim Procter [Tue, 17 Sep 2024 22:55:58 +0000 (23:55 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 17 Sep 2024 22:53:40 +0000 (23:53 +0100)]
JAL-4418 more documentation tweaks - getting Jen Fleming's name correct
Jim Procter [Tue, 17 Sep 2024 22:24:54 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 17 Sep 2024 22:23:57 +0000 (23:23 +0100)]
JAL-4418 JAL-4428 CHANNEL=RELEASE has a different path for the jni jars
Jim Procter [Tue, 17 Sep 2024 20:41:41 +0000 (21:41 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 17 Sep 2024 20:39:49 +0000 (21:39 +0100)]
JAL-4418 fix link case for linkcheck and window menu documentation update
Jim Procter [Tue, 17 Sep 2024 20:21:28 +0000 (21:21 +0100)]
JAL-4159 pasimap viewer image for docs
Jim Procter [Tue, 17 Sep 2024 20:17:57 +0000 (21:17 +0100)]
JAL-4418 JAL-4090 known defect report for JAL-4349
Jim Procter [Tue, 17 Sep 2024 19:34:33 +0000 (20:34 +0100)]
JAL-4414 JAL-1054 fix irrelevant failing network test for JAL-4418 2.11.4.0 release
Jim Procter [Tue, 17 Sep 2024 16:57:42 +0000 (17:57 +0100)]
Merge branch 'bug/JAL-1054_broken_test' into develop
Jim Procter [Tue, 17 Sep 2024 16:05:09 +0000 (17:05 +0100)]
JAL-4418 documentation for 4461
Jim Procter [Tue, 17 Sep 2024 15:56:03 +0000 (16:56 +0100)]
JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL-4392)
Jim Procter [Tue, 17 Sep 2024 15:35:20 +0000 (16:35 +0100)]
JAL-4418 JAL-4442 quit racecondition patch
Jim Procter [Tue, 17 Sep 2024 15:32:55 +0000 (16:32 +0100)]
Merge branch 'JAL-4442_cant_quit_jalview_on_windows_11' into develop
Jim Procter [Tue, 17 Sep 2024 15:27:07 +0000 (16:27 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 17 Sep 2024 15:26:45 +0000 (16:26 +0100)]
JAL-4418 release 2.11.4.0 today!
Jim Procter [Tue, 17 Sep 2024 15:24:53 +0000 (16:24 +0100)]
JAL-4418 JAL-4392 show/hide group associated secondary structure consensus and document autohide of secondary structure consensus
JAL-4464 also knowndefect for not storing/restoring group associated secondary structure consensus
Jim Procter [Tue, 17 Sep 2024 11:09:00 +0000 (12:09 +0100)]
Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
Jim Procter [Mon, 16 Sep 2024 16:28:09 +0000 (17:28 +0100)]
JAL-4392 JAL-4425 commented out code to allow consensus to be hidden automatically when just one sequence is shown
Jim Procter [Mon, 16 Sep 2024 16:20:46 +0000 (17:20 +0100)]
Merge branch 'patch/JAL-4392_hide_ssconsensus_if_no_data' into develop
Jim Procter [Mon, 16 Sep 2024 15:57:33 +0000 (16:57 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Jim Procter [Mon, 16 Sep 2024 15:50:49 +0000 (16:50 +0100)]
JAL-4392 autohide the secondary structure consensus annotation by setting AlignmentAnnotation.hasData to false so it is not displayed in view
Renia Correya [Mon, 16 Sep 2024 14:59:55 +0000 (20:29 +0530)]
JAL-4427 Added test cases and a minor correction
Jim Procter [Mon, 16 Sep 2024 14:39:34 +0000 (15:39 +0100)]
JAL-4392 don't show SS consensus for DNA alignments
Ben Soares [Mon, 16 Sep 2024 08:18:44 +0000 (09:18 +0100)]
JAL-4461 Move SwingUtils to darrylbu.util.SwingUtils, more appropriate
Jim Procter [Fri, 13 Sep 2024 17:10:24 +0000 (18:10 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Fri, 13 Sep 2024 17:09:29 +0000 (18:09 +0100)]
JAL-4418 release notes for JAL-4461 - nb need to document the new option in the built in help
Jim Procter [Fri, 13 Sep 2024 17:06:36 +0000 (18:06 +0100)]
Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
Ben Soares [Fri, 13 Sep 2024 16:05:24 +0000 (17:05 +0100)]
JAL-4461 Tests for JalviewFileChooser.defaultSaveFileFormat() and a slight fix to the code
Ben Soares [Fri, 13 Sep 2024 14:26:23 +0000 (15:26 +0100)]
JAL-4461 Adding in a number of properties that control the default save_as format. See issue for details.
Jim Procter [Fri, 13 Sep 2024 13:38:50 +0000 (14:38 +0100)]
JAL-4418 sign off JAL-4454 and convert markdown header to html for whatsNew 'experimental'
Ben Soares [Fri, 13 Sep 2024 10:20:54 +0000 (11:20 +0100)]
JAL-4461 Change JalviewFileFilter to use LinkedHashSet for extensions. Add list of extensions to 'By extensions' tooltip.
Jim Procter [Thu, 12 Sep 2024 16:17:42 +0000 (17:17 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Thu, 12 Sep 2024 16:17:22 +0000 (17:17 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Jim Procter [Thu, 12 Sep 2024 16:16:43 +0000 (17:16 +0100)]
JAL-4418 sign off JAL-4427 JAL-4451 fix
Jim Procter [Thu, 12 Sep 2024 15:57:41 +0000 (16:57 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Ben Soares [Thu, 12 Sep 2024 15:52:01 +0000 (16:52 +0100)]
JAL-4461 Added a dynamic tooltip to give more information when 'By extension' is the selected File Type. Utilising MIT licensed SwingUtils.getDescendantsByClass() to delve into the JFileChooser.
Jim Procter [Thu, 12 Sep 2024 13:57:29 +0000 (14:57 +0100)]
JAL-4461 fix up formatting and remove old comment
Jim Procter [Thu, 12 Sep 2024 13:56:31 +0000 (14:56 +0100)]
JAL-4461 after autodetection, update the filechooser dialog and let the user hit OK again to confirm the autodetected format
Ben Soares [Thu, 12 Sep 2024 13:12:59 +0000 (14:12 +0100)]
JAL-4461 Change labelling of All-known-alignment-files to Select-format-from-extension for Save-as file chooser
Ben Soares [Thu, 12 Sep 2024 12:29:49 +0000 (13:29 +0100)]
JAL-4460 Don't display the All-known-alignment-files format when a JalviewFileChooser is made with acceptAny set to false (usually a Save-as dialog)
Jim Procter [Thu, 12 Sep 2024 10:05:03 +0000 (11:05 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Thu, 12 Sep 2024 10:04:37 +0000 (11:04 +0100)]
JAL-4454 make sure 2.11.4.0-test is stripped - *for reals*
Jim Procter [Wed, 11 Sep 2024 17:02:05 +0000 (18:02 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 11 Sep 2024 17:01:24 +0000 (18:01 +0100)]
JAL-4418 release notes for JAL-4460
Jim Procter [Wed, 11 Sep 2024 16:59:04 +0000 (17:59 +0100)]
Merge branch 'bug/JAL-4460_alignment_save_as_format_not_registering' into develop
Jim Procter [Wed, 11 Sep 2024 16:43:59 +0000 (17:43 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 11 Sep 2024 16:43:22 +0000 (17:43 +0100)]
JAL-4454 make sure 2.11.4.0-test is stripped
Ben Soares [Wed, 11 Sep 2024 16:24:33 +0000 (17:24 +0100)]
JAL-4460 In save as, set format from file extension if a multi-format file filter is selected
Ben Soares [Wed, 11 Sep 2024 15:51:49 +0000 (16:51 +0100)]
JAL-4460 Don't add .aln for an 'All known formats...' filename
Ben Soares [Wed, 11 Sep 2024 15:23:43 +0000 (16:23 +0100)]
JAL-4460 Update currentFileFormat /after/ new format selection
Jim Procter [Wed, 11 Sep 2024 14:44:03 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 11 Sep 2024 14:34:09 +0000 (15:34 +0100)]
JAL-4418 JAL-4428,JAL-4421,JAL-3393 release notes
Jim Procter [Wed, 11 Sep 2024 14:29:08 +0000 (15:29 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Wed, 11 Sep 2024 14:25:52 +0000 (15:25 +0100)]
JAL-4428 codesign jnilibs
Jim Procter [Wed, 11 Sep 2024 14:25:21 +0000 (15:25 +0100)]
JAL-4428 informational output (possibly needs verbosity control)
Jim Procter [Wed, 11 Sep 2024 14:24:54 +0000 (15:24 +0100)]
JAL-4428 giving another XXX
Jim Procter [Wed, 11 Sep 2024 14:23:46 +0000 (15:23 +0100)]
JAL-4428 add some XXXX for mktemp -t
Ben Soares [Wed, 11 Sep 2024 10:21:07 +0000 (11:21 +0100)]
JAL-4428 Fixes to -z's and mktemp
Jim Procter [Tue, 10 Sep 2024 16:21:35 +0000 (17:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 10 Sep 2024 16:17:17 +0000 (17:17 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Tue, 10 Sep 2024 15:25:27 +0000 (16:25 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 10 Sep 2024 15:24:26 +0000 (16:24 +0100)]
JAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their associated version
Jim Procter [Mon, 9 Sep 2024 17:13:49 +0000 (18:13 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Mon, 9 Sep 2024 17:12:06 +0000 (18:12 +0100)]
JAL-4418 initial pasimap documentation and updated release notes for recent merges
Jim Procter [Mon, 9 Sep 2024 14:37:16 +0000 (15:37 +0100)]
JAL-4418 postpone release to Thursday 12th Sept 2024
Jim Procter [Tue, 3 Sep 2024 14:08:47 +0000 (15:08 +0100)]
JAL-4386 remove magic string in registerScoreModel...
Jim Procter [Mon, 2 Sep 2024 16:53:11 +0000 (17:53 +0100)]
JAL-4418 fix linkCheck
Jim Procter [Mon, 2 Sep 2024 16:47:59 +0000 (17:47 +0100)]
JAL-4418 release 10th September
Jim Procter [Mon, 2 Sep 2024 16:46:56 +0000 (17:46 +0100)]
Merge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
Jim Procter [Mon, 2 Sep 2024 16:46:49 +0000 (17:46 +0100)]
Merge branch 'feature/JAL-4446_cancellable_pasimap_etal' into develop
Jim Procter [Mon, 2 Sep 2024 16:34:02 +0000 (17:34 +0100)]
JAL-4418 first pass at updating docs with pasimap, ssconservation, etc
Ben Soares [Mon, 2 Sep 2024 16:02:38 +0000 (17:02 +0100)]
JAL-1054 Add option to always follow redirects and not just http->https ones in jalview.util.HttpUtils. Fix tests for HttpUtils.followConnection,openConnection,openStream by checking with the followAnyway flag true and false.
Renia Correya [Fri, 30 Aug 2024 13:04:10 +0000 (18:34 +0530)]
Fix for JAL-4427
Sequence ID text showing html code - protein disorder.
Jim Procter [Thu, 29 Aug 2024 15:39:04 +0000 (16:39 +0100)]
JAL-4446 improved reporting of progress, and transition between cancelable and non-cancelable phases of pasimap calculation
Jim Procter [Thu, 29 Aug 2024 13:19:37 +0000 (14:19 +0100)]
JAL-4446 refactor progress listener handler code for reuse
Jim Procter [Thu, 29 Aug 2024 12:46:37 +0000 (13:46 +0100)]
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
Jim Procter [Wed, 28 Aug 2024 13:20:37 +0000 (14:20 +0100)]
JAL-4418 tweak release notes for JAL-4328
Jim Procter [Wed, 28 Aug 2024 13:19:34 +0000 (14:19 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
git://source.jalview.org / jalview.git / log