Ben Soares [Tue, 14 May 2024 16:57:01 +0000 (17:57 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Tue, 14 May 2024 16:38:54 +0000 (17:38 +0100)]
JAL-4217 Upped the main testTask0 timeout to 15 minutes for build server's benefit
Ben Soares [Tue, 14 May 2024 16:37:49 +0000 (17:37 +0100)]
JAL-1054 Tests for the HttpUtils redirection wrappers
Ben Soares [Tue, 14 May 2024 14:44:49 +0000 (15:44 +0100)]
Merge branch 'bug/JAL-4397_failing_idWidth_tests' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Tue, 14 May 2024 14:27:28 +0000 (15:27 +0100)]
Merge branch 'develop' into bug/JAL-4397_failing_idWidth_tests
Ben Soares [Tue, 14 May 2024 14:26:51 +0000 (15:26 +0100)]
JAL-4414 Add a FileNotFoundException when identifying URL file formats and catch to change error message appropriately
Jim Procter [Tue, 14 May 2024 13:41:03 +0000 (14:41 +0100)]
JAL-4356 fix release note
Jim Procter [Tue, 14 May 2024 13:26:49 +0000 (14:26 +0100)]
JAL-4356 set release date to Weds 15th May and update release notes
Jim Procter [Mon, 13 May 2024 16:22:06 +0000 (17:22 +0100)]
JAL-4356 JAL-518 JAL-4413 release notes
Jim Procter [Mon, 13 May 2024 16:14:08 +0000 (17:14 +0100)]
Merge branch 'features/JAL-518_justify_seqs_in_region' into develop
Ben Soares [Mon, 13 May 2024 16:12:49 +0000 (17:12 +0100)]
JAL-1054 Fix wrappers for following http->https redirects
Jim Procter [Mon, 13 May 2024 16:05:11 +0000 (17:05 +0100)]
JAL-518 better test coverage and support for case preservation
Jim Procter [Mon, 13 May 2024 15:01:36 +0000 (16:01 +0100)]
JAL-518 failing test for case preservation on justify
Ben Soares [Mon, 13 May 2024 14:36:01 +0000 (15:36 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Jim Procter [Mon, 13 May 2024 14:10:03 +0000 (15:10 +0100)]
Merge branch 'develop' into features/JAL-518_justify_seqs_in_region
Jim Procter [Mon, 13 May 2024 14:03:52 +0000 (15:03 +0100)]
JAL-4413 timeouts Merge branch 'improvement/JAL-4217_added_a_timeout_to_tests' into develop
Ben Soares [Mon, 13 May 2024 13:33:12 +0000 (14:33 +0100)]
JAL-4409 Fix some file extensions (including remove .txt)
Ben Soares [Mon, 13 May 2024 13:31:58 +0000 (14:31 +0100)]
JAL-1054 Add wrappers for URL.openConnection(), URL.openStream() to allow following redirect from http to https
Jim Procter [Mon, 13 May 2024 12:44:27 +0000 (13:44 +0100)]
Merge branch 'develop' into features/JAL-518_justify_seqs_in_region
Conflicts:
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/controller/AlignViewController.java
Ben Soares [Fri, 10 May 2024 11:14:27 +0000 (12:14 +0100)]
JAL-4409 Add jalviewhttp and jalviewhttps schemes to register in install4j. Recognise all extra schemes in getdown.
Ben Soares [Thu, 2 May 2024 18:48:41 +0000 (19:48 +0100)]
JAL-4217 Sensible timeout for testTask0
Ben Soares [Thu, 2 May 2024 18:29:43 +0000 (19:29 +0100)]
JAL-4217 Added a timeout for testTasks. If timeout is exceeded then test execution should be interrupted.
Ben Soares [Sat, 27 Apr 2024 21:22:01 +0000 (22:22 +0100)]
JAL-4397 Removed debugging statement
Ben Soares [Fri, 26 Apr 2024 17:41:40 +0000 (18:41 +0100)]
JAL-4397 Adjustments for macOS HiDPI
Ben Soares [Fri, 26 Apr 2024 17:23:04 +0000 (18:23 +0100)]
JAL-4397 Test all fixed on linux. Given leeway to some tests, platform dependent expected values on some tests, HiDPI dependent expected values on some tests. Still to test on macOS.
Ben Soares [Mon, 22 Apr 2024 16:36:20 +0000 (17:36 +0100)]
JAL-4397 Allow some leeway in automatically calculated id width tests
Ben Soares [Thu, 18 Apr 2024 15:01:46 +0000 (16:01 +0100)]
JAL-4397 fixed testresetIdWidth() test on macos
James Procter [Tue, 23 Jan 2024 17:27:24 +0000 (17:27 +0000)]
JAL-4356 release notes
James Procter [Tue, 23 Jan 2024 17:08:28 +0000 (17:08 +0000)]
JAL-4356 update release notes for 2.11.3.3
James Procter [Tue, 23 Jan 2024 16:51:04 +0000 (16:51 +0000)]
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' into develop
James Procter [Tue, 23 Jan 2024 14:21:59 +0000 (14:21 +0000)]
Merge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
Ben Soares [Wed, 20 Dec 2023 13:23:07 +0000 (13:23 +0000)]
JAL-4367 Limit right and top adjustments
Ben Soares [Wed, 20 Dec 2023 13:14:26 +0000 (13:14 +0000)]
JAL-4290 Fix image comparison between gui and headless output. Images are now the same
Ben Soares [Wed, 20 Dec 2023 00:08:56 +0000 (00:08 +0000)]
JAL-4290 fixed tests
Ben Soares [Tue, 19 Dec 2023 17:52:45 +0000 (17:52 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
Ben Soares [Thu, 14 Dec 2023 15:40:48 +0000 (15:40 +0000)]
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
James Procter [Tue, 12 Dec 2023 20:55:49 +0000 (20:55 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
James Procter [Tue, 12 Dec 2023 17:20:04 +0000 (17:20 +0000)]
JAL-4353 wait for files to be written fully before comparing size with older file
James Procter [Tue, 12 Dec 2023 17:18:48 +0000 (17:18 +0000)]
JAL-4353 singleThread all tests
James Procter [Wed, 10 Jan 2024 15:51:52 +0000 (15:51 +0000)]
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress
James Procter [Wed, 10 Jan 2024 10:26:26 +0000 (10:26 +0000)]
JAL-4369 uniprotkb - try to avoid another redirect response
James Procter [Tue, 9 Jan 2024 18:36:12 +0000 (18:36 +0000)]
JAL-4369 use rest.uniprot.org as fetch domain
t pu# Please enter the commit message for your changes. Lines starting
James Procter [Tue, 23 Jan 2024 13:39:04 +0000 (13:39 +0000)]
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop
James Procter [Tue, 23 Jan 2024 13:34:35 +0000 (13:34 +0000)]
Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop
Ben Soares [Fri, 19 Jan 2024 17:00:46 +0000 (17:00 +0000)]
JAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consistency. Updated some comments.
Ben Soares [Fri, 19 Jan 2024 16:11:14 +0000 (16:11 +0000)]
JAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It requires a 'dummy' Jar task with the correct settings.
Ben Soares [Fri, 5 Jan 2024 17:28:36 +0000 (17:28 +0000)]
JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file
Ben Soares [Tue, 19 Dec 2023 17:50:33 +0000 (17:50 +0000)]
JAL-4290 Fixed one test
Ben Soares [Mon, 18 Dec 2023 13:58:28 +0000 (13:58 +0000)]
JAL-4290 not quite working tests
Ben Soares [Mon, 18 Dec 2023 13:58:15 +0000 (13:58 +0000)]
JAL-4290 incorrect usage of main()
Ben Soares [Fri, 15 Dec 2023 21:30:13 +0000 (21:30 +0000)]
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' of https://source.jalview.org/git/jalview into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
Ben Soares [Fri, 15 Dec 2023 21:29:59 +0000 (21:29 +0000)]
JAL-4290 Add method to allow for specific settings. Revert setting show annotations.
Ben Soares [Fri, 15 Dec 2023 15:18:23 +0000 (15:18 +0000)]
JAL-4290 Set structureSelectionManager settings more generically and when no desktop exists
James Procter [Fri, 15 Dec 2023 11:31:30 +0000 (11:31 +0000)]
Merge branch 'bug/JAL-4290_headless_alignment_figure_with_sse' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
James Procter [Fri, 15 Dec 2023 11:30:11 +0000 (11:30 +0000)]
JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations.Worker to run jalview as a separate process to verify headless alignment image export should be same size as when launched with —gui
Ben Soares [Fri, 15 Dec 2023 01:08:11 +0000 (01:08 +0000)]
JAL-4290 Move some annotation visibility settings to after opening a structure. Set synchronously if in headless mode.
James Procter [Thu, 14 Dec 2023 15:39:20 +0000 (15:39 +0000)]
JAL-4356 update release notes
James Procter [Thu, 14 Dec 2023 15:28:08 +0000 (15:28 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop
James Procter [Tue, 12 Dec 2023 20:55:49 +0000 (20:55 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
James Procter [Tue, 12 Dec 2023 17:20:04 +0000 (17:20 +0000)]
JAL-4353 wait for files to be written fully before comparing size with older file
James Procter [Tue, 12 Dec 2023 17:18:48 +0000 (17:18 +0000)]
JAL-4217 singleThread all tests
James Procter [Thu, 14 Dec 2023 14:16:38 +0000 (14:16 +0000)]
Merge branch 'bug/JAL-2934proportionalScrolling' into develop
James Procter [Thu, 14 Dec 2023 14:14:15 +0000 (14:14 +0000)]
Merge branch 'develop' into bug/JAL-2934proportionalScrolling
Ben Soares [Tue, 12 Dec 2023 17:49:35 +0000 (17:49 +0000)]
JAL-4353 bigger tighter test
James Procter [Tue, 12 Dec 2023 17:17:17 +0000 (17:17 +0000)]
JAL-4217 don’t try and export an image when Jmol is also trying to repaint
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
James Procter [Wed, 6 Dec 2023 13:48:54 +0000 (13:48 +0000)]
Merge branch 'bug/JAL-2934proportionalScrolling' 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
git://source.jalview.org / jalview.git / log