Ben Soares [Tue, 12 Dec 2023 17:13:45 +0000 (17:13 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' of https://source.jalview.org/git/jalview into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
James Procter [Tue, 12 Dec 2023 16:02:14 +0000 (16:02 +0000)]
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
James Procter [Tue, 12 Dec 2023 15:48:32 +0000 (15:48 +0000)]
JAL-4217 close internal frame on the swing thread to avoid deadlock
Ben Soares [Tue, 12 Dec 2023 15:47:26 +0000 (15:47 +0000)]
JAL-4353 helper method and test for primary/secondary and auxiliary arguments with --structure pdb0 --structureimage png0a --bgcolour col0a --structureimagepng0b --bgcolour col0b --structure pdb1 --...
James Procter [Tue, 12 Dec 2023 12:37:04 +0000 (12:37 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop
James Procter [Tue, 12 Dec 2023 12:36:51 +0000 (12:36 +0000)]
JAL-4353 failing test
James Procter [Tue, 12 Dec 2023 12:36:36 +0000 (12:36 +0000)]
JAL-4353 fix assert that successive test output files get bigger in structureImageOutputTest and argFilesGlobAndSubstitutionsTest
James Procter [Mon, 11 Dec 2023 17:31:38 +0000 (17:31 +0000)]
JAL-4192 more specific info about versions needed
Ben Soares [Wed, 6 Dec 2023 22:00:06 +0000 (22:00 +0000)]
JAL-4353 re-used random color code
Ben Soares [Wed, 6 Dec 2023 17:41:35 +0000 (17:41 +0000)]
JAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding if user deliberately set a wildcard linkedId (or --all), to inform value of sub-args.
James Procter [Wed, 6 Dec 2023 14:37:04 +0000 (14:37 +0000)]
JAL-4356 bump RELEASE
James Procter [Wed, 6 Dec 2023 14:21:11 +0000 (14:21 +0000)]
JAL-4356 new release notes and whats new for 2.11.3.3 and JAL-840 release notes
James Procter [Wed, 6 Dec 2023 14:14:12 +0000 (14:14 +0000)]
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop
Ben Soares [Wed, 6 Dec 2023 11:02:32 +0000 (11:02 +0000)]
JAL-4353 Add a 'random' colour to produce a random colour.
Ben Soares [Tue, 5 Dec 2023 14:15:53 +0000 (14:15 +0000)]
JAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE Type and restrict structureimages between structures on the same open alignment
Ben Soares [Fri, 1 Dec 2023 12:05:27 +0000 (12:05 +0000)]
JAL-4243 Updated bio.tools record and JSON (version number)
James Procter [Thu, 30 Nov 2023 16:55:24 +0000 (16:55 +0000)]
JAL-4351 update release notes for JAL-4342
James Procter [Thu, 30 Nov 2023 16:51:09 +0000 (16:51 +0000)]
Merge branch 'patch/JAL-4342_emptyannotationsexport' into develop
James Procter [Thu, 30 Nov 2023 15:39:14 +0000 (15:39 +0000)]
JAL-4342 test and patch checking annotation csv export contains the annotations on the alignment or a specific exported annotation
James Procter [Thu, 30 Nov 2023 15:17:41 +0000 (15:17 +0000)]
Patch fixes JAL-4165 - added to release notes JAL-4351
James Procter [Thu, 30 Nov 2023 15:06:04 +0000 (15:06 +0000)]
JAL-4351 2.11.3.2 scheduled for 1st December release
James Procter [Thu, 30 Nov 2023 14:32:45 +0000 (14:32 +0000)]
Merge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square-FIXED_from_develop' into develop
Ben Soares [Thu, 30 Nov 2023 12:51:54 +0000 (12:51 +0000)]
JAL-4344 careful application of -Djava.awt.headless=true to avoid Jmol problem. Using -Dapple.awt.headless=true instead for macOS. Fixed in install and conda shell scripts and also in jalview.bin.Launcher.
James Procter [Wed, 22 Nov 2023 10:43:58 +0000 (10:43 +0000)]
JAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1
James Procter [Wed, 22 Nov 2023 10:38:41 +0000 (10:38 +0000)]
JAL-4343 release today, update notes for JAL-4348 and what’s new for release
James Procter [Wed, 22 Nov 2023 10:28:18 +0000 (10:28 +0000)]
Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
James Procter [Tue, 21 Nov 2023 18:02:57 +0000 (18:02 +0000)]
JAL-4345 patch and release notes
Ben Soares [Mon, 20 Nov 2023 13:40:53 +0000 (13:40 +0000)]
JAL-4348 Add newer versions of Chimera and ChimeraX to the version whitelist
James Procter [Mon, 20 Nov 2023 11:34:03 +0000 (11:34 +0000)]
JAL-4343 patch for JAL-4347 uniprot non-pos feature parsing
James Procter [Fri, 17 Nov 2023 16:05:27 +0000 (16:05 +0000)]
JAL-4343 release notes for JAL-4340 and JAL-4243
James Procter [Fri, 17 Nov 2023 16:01:01 +0000 (16:01 +0000)]
JAL-4343 bump version
Ben Soares [Thu, 16 Nov 2023 20:03:30 +0000 (20:03 +0000)]
JAL-4243 Updated bio.tools record for 2.11.3.0
Ben Soares [Thu, 16 Nov 2023 11:34:50 +0000 (11:34 +0000)]
JAL-4340 Change launch scripts to be xresources to set executable permission bit where needed
James Procter [Wed, 15 Nov 2023 16:16:27 +0000 (16:16 +0000)]
JAL-4090 JAL-4334 patch in release notes
James Procter [Wed, 15 Nov 2023 16:10:02 +0000 (16:10 +0000)]
Merge branch 'bug/JAL-4334_unknownstartenduniprotfeatures' into develop
James Procter [Wed, 15 Nov 2023 16:09:35 +0000 (16:09 +0000)]
Merge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop
James Procter [Wed, 15 Nov 2023 15:33:06 +0000 (15:33 +0000)]
JAL-4273 actually pass startSeq etc on to rendering code when rendering for image export
James Procter [Wed, 15 Nov 2023 15:24:40 +0000 (15:24 +0000)]
JAL-4090 fix up release notes new known issues
James Procter [Wed, 15 Nov 2023 15:02:43 +0000 (15:02 +0000)]
JAL-4222 bail if we wait too long for Jmol to save an image
James Procter [Wed, 15 Nov 2023 14:54:31 +0000 (14:54 +0000)]
JAL-4090 blocker patch JAL-3772 tidy up groovy console when closed rather than calling its exit and hanging
James Procter [Wed, 15 Nov 2023 14:31:08 +0000 (14:31 +0000)]
JAL-4090 JAL-4334 position status when start, end or pos is unknown is stored in start_status,end_status,pos_status properties
James Procter [Wed, 15 Nov 2023 11:54:33 +0000 (11:54 +0000)]
JAL-4090 JAL-4338 known defect
James Procter [Wed, 15 Nov 2023 11:48:43 +0000 (11:48 +0000)]
JAL-4090 release 15th November 2023
James Procter [Wed, 15 Nov 2023 11:48:30 +0000 (11:48 +0000)]
JAL-4090 JAL-3858 fix up PAE docs - drop the EBI image example
James Procter [Mon, 13 Nov 2023 18:36:35 +0000 (18:36 +0000)]
JAL-4090 JAL-1551 source license
James Procter [Mon, 13 Nov 2023 18:16:46 +0000 (18:16 +0000)]
JAL-4090 relese date 14th Nov 2023
James Procter [Mon, 13 Nov 2023 17:19:11 +0000 (17:19 +0000)]
JAL-4236 don’t look for headers in JalviewJS
James Procter [Mon, 13 Nov 2023 17:18:14 +0000 (17:18 +0000)]
JAL-4336 set preferred dimensions for JTextBox workaround in JalviewJS
James Procter [Mon, 13 Nov 2023 16:11:29 +0000 (16:11 +0000)]
JAL-4090 fix JAL-4236 - just put the name of the class in rather than look it up in a fancy way
James Procter [Mon, 13 Nov 2023 16:05:09 +0000 (16:05 +0000)]
JAL-4331 construct and pass on overview title before asking desktop to open the window…
James Procter [Mon, 13 Nov 2023 10:28:37 +0000 (10:28 +0000)]
JAL-4334 failing test using whole of Q29079 accession. Can be trimmed.
Ben Soares [Thu, 9 Nov 2023 12:31:05 +0000 (12:31 +0000)]
JAL-4090 minor missing word correction to whatsnew
James Procter [Fri, 3 Nov 2023 07:29:04 +0000 (07:29 +0000)]
JAL-4090 JAL-1551 spotlessApply
James Procter [Fri, 3 Nov 2023 07:28:39 +0000 (07:28 +0000)]
JAL-4090 tweak what’s new
James Procter [Thu, 2 Nov 2023 23:23:41 +0000 (23:23 +0000)]
JAL-4090 reported new known issue JAL-4328
James Procter [Thu, 2 Nov 2023 23:07:15 +0000 (23:07 +0000)]
JAL-4192 minimal specification of gradle version in building.md
James Procter [Thu, 2 Nov 2023 23:03:14 +0000 (23:03 +0000)]
JAL-4090 fix up release notes - add notes or JAL-4216 JAL-4169 JAL-4250 JAL-4327 and remove erroneous note for JAL-3776 (targeted for 2.12 release not this one)
James Procter [Thu, 2 Nov 2023 23:00:03 +0000 (23:00 +0000)]
JAL-4169 fix up urls to faq and documentation
James Procter [Thu, 2 Nov 2023 21:34:01 +0000 (21:34 +0000)]
JAL-4090 known issue report for JAL-4517
James Procter [Thu, 2 Nov 2023 21:23:32 +0000 (21:23 +0000)]
JAL-4090 release notes for JAL-1713 JAL-2528 and known issue report for JAL-4127
James Procter [Thu, 2 Nov 2023 21:07:41 +0000 (21:07 +0000)]
JAL-4090 JAL-3921 release notes
James Procter [Thu, 2 Nov 2023 21:05:53 +0000 (21:05 +0000)]
Merge branch 'patch/JAL-3921_jmol_session_save' into develop
James Procter [Thu, 2 Nov 2023 21:01:22 +0000 (21:01 +0000)]
Merge branch 'develop' into patch/JAL-3921_jmol_session_save
James Procter [Thu, 2 Nov 2023 19:43:01 +0000 (19:43 +0000)]
JAL-4217 wrap progress bar creation in an invokeLater to avoid setFont deadlock with other ops
James Procter [Thu, 2 Nov 2023 19:14:06 +0000 (19:14 +0000)]
JAL-3088 release notes JAL-4090
James Procter [Thu, 2 Nov 2023 19:13:53 +0000 (19:13 +0000)]
JAL-1551 formatting
James Procter [Thu, 2 Nov 2023 19:01:40 +0000 (19:01 +0000)]
Merge branch 'patch/JAL-3088_finalbracenotinrightplace' into develop
James Procter [Thu, 2 Nov 2023 18:49:04 +0000 (18:49 +0000)]
Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace
Conflicts: - JAL-4250
src/jalview/renderer/AnnotationRenderer.java
James Procter [Thu, 2 Nov 2023 18:43:42 +0000 (18:43 +0000)]
JAL-4090 update release date to friday 3rd November
Release notes for JAL-4252 JAL-3858 JAL-2292 JAL-4288 JAL-4151
James Procter [Thu, 2 Nov 2023 17:24:27 +0000 (17:24 +0000)]
JAL-4090 JAL-4293 JAL-4325 release notes
James Procter [Thu, 2 Nov 2023 17:07:25 +0000 (17:07 +0000)]
JAL-4090 JAL-4218 patch and release notes - don’t include dist in tarball
James Procter [Thu, 2 Nov 2023 16:51:01 +0000 (16:51 +0000)]
JAL-4090 marked JAL-4290 as a knowndefect
James Procter [Thu, 2 Nov 2023 16:40:41 +0000 (16:40 +0000)]
JAL-4090 JAL-4110 JAL-3599 release notes
James Procter [Thu, 2 Nov 2023 16:32:18 +0000 (16:32 +0000)]
JAL-4090 JAL-4310 JAL-4298 JAL-4282 JAL-4223 release notes
James Procter [Thu, 2 Nov 2023 16:29:19 +0000 (16:29 +0000)]
JAL-4090 JAL-4147 documentation for revised sequence associated annotation display and pop-up menu
James Procter [Thu, 2 Nov 2023 16:02:07 +0000 (16:02 +0000)]
JAL-4090 release notes for JAL-4304,JAL-4305 and JAL-3783 and marking JAL-4323 as known issue (groovy scripts colourschemes and file formats)
James Procter [Thu, 2 Nov 2023 12:43:12 +0000 (12:43 +0000)]
JAL-4289 JAL-4253 lower end of group boundary vertical needs to be flush with horizontal
James Procter [Wed, 1 Nov 2023 23:36:05 +0000 (23:36 +0000)]
JAL-4090 JAL-4281 JAL-4311 release notes
James Procter [Wed, 1 Nov 2023 20:47:20 +0000 (20:47 +0000)]
Merge branch 'patch/JAL-4281_idwidthandannotHeight_in_project' into develop
James Procter [Wed, 1 Nov 2023 20:34:23 +0000 (20:34 +0000)]
JAL-4281 patch test so it passes on build server and accepts different legacy idwidth on macs
James Procter [Wed, 1 Nov 2023 19:20:10 +0000 (19:20 +0000)]
JAL-4090 release notes for JAL-4315
James Procter [Wed, 1 Nov 2023 19:16:55 +0000 (19:16 +0000)]
Merge branch 'feature/JAL-4315_fc_draganddrop' into develop
James Procter [Wed, 1 Nov 2023 19:15:15 +0000 (19:15 +0000)]
JAL-4090 JAL-4317 release notes
James Procter [Wed, 1 Nov 2023 19:12:43 +0000 (19:12 +0000)]
Merge branch 'patch/JAL-4317_enablefeaturewhenadjustingstyle' into develop
James Procter [Wed, 1 Nov 2023 19:08:58 +0000 (19:08 +0000)]
Merge branch 'develop' into patch/JAL-4281_idwidthandannotHeight_in_project
Conflicts:
src/jalview/gui/AlignmentPanel.java
and regenerated schema binding
James Procter [Wed, 1 Nov 2023 16:40:55 +0000 (16:40 +0000)]
Merge branch 'patch/JAL-4260_fix_up_select_via_ruler_in_wrapped' into develop
James Procter [Wed, 1 Nov 2023 16:23:30 +0000 (16:23 +0000)]
JAL-4260 encapsulate logic for resolving nearest column and do better using it in wrapped mode for drags/clicks/popups on alignment
James Procter [Wed, 1 Nov 2023 16:18:36 +0000 (16:18 +0000)]
JAL-4260 reinstate annotation auto-id-width for wrapped view in headless mode (JAL-244) whilst still right-aligning labels
James Procter [Tue, 31 Oct 2023 13:22:30 +0000 (13:22 +0000)]
JAL-4260 fix up click/drags on ruler area in wrapped mode.
James Procter [Tue, 31 Oct 2023 12:33:03 +0000 (12:33 +0000)]
JAL-4260 right align the annotation labels regardless of width in wrapped mode.
James Procter [Tue, 31 Oct 2023 12:01:03 +0000 (12:01 +0000)]
JAL-244 noticed NPE exception was possible when visibility was adjusted in wrapped mode
James Procter [Tue, 31 Oct 2023 12:00:38 +0000 (12:00 +0000)]
JAL-244 knock on - make sure alignPanel is laid out properly after adjusting height. Probably a better
Ben Soares [Tue, 31 Oct 2023 10:55:30 +0000 (10:55 +0000)]
JAL-4319 Downgrade shadow(Jar) module to stop triggering clover
James Procter [Mon, 30 Oct 2023 12:14:20 +0000 (12:14 +0000)]
JAL-4317 enable display of feature when showing its colour or filter settings dialog, and restore original visibility if cancel is pressed.
James Procter [Mon, 30 Oct 2023 11:24:22 +0000 (11:24 +0000)]
Handle feature settings files loaded via drag and drop or import
James Procter [Mon, 30 Oct 2023 11:24:07 +0000 (11:24 +0000)]
JAL-4315 allow feature settings to be loaded from a file or input stream without the dialog being open
James Procter [Mon, 30 Oct 2023 11:23:05 +0000 (11:23 +0000)]
JAL-4315 identify feature settings file from its xml schema header
James Procter [Thu, 26 Oct 2023 11:44:31 +0000 (12:44 +0100)]
Merge branch 'patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources' into develop
James Procter [Thu, 26 Oct 2023 11:43:48 +0000 (12:43 +0100)]
Merge branch 'bug/JAL-4313_cme_in_tests' into patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources
Ben Soares [Wed, 25 Oct 2023 10:28:15 +0000 (11:28 +0100)]
Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint
git://source.jalview.org / jalview.git / log