Ben Soares [Fri, 15 Mar 2024 12:40:40 +0000 (12:40 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Fri, 15 Mar 2024 12:39:49 +0000 (12:39 +0000)]
JAL-4320 Improve the inputs and outputs dependencies of jalviewjs build tasks
Ben Soares [Fri, 15 Mar 2024 12:38:54 +0000 (12:38 +0000)]
JAL-3225 Force gradle version in eclipse settings
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
Ben Soares [Tue, 23 Jan 2024 17:07:58 +0000 (17:07 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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
Ben Soares [Tue, 23 Jan 2024 16:42:24 +0000 (16:42 +0000)]
Merge branch 'bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Tue, 23 Jan 2024 15:05:33 +0000 (15:05 +0000)]
Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
Ben Soares [Tue, 23 Jan 2024 14:54:05 +0000 (14:54 +0000)]
Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
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 [Fri, 5 Jan 2024 14:47:38 +0000 (14:47 +0000)]
JAL-4328 Example html 'form' launch in examples.html
Ben Soares [Wed, 20 Dec 2023 20:28:49 +0000 (20:28 +0000)]
JAL-4238 Marked where JalviewJS is hanging on 3DBeacons search.
Ben Soares [Wed, 20 Dec 2023 20:28:11 +0000 (20:28 +0000)]
JAL-4059 Added some more Platform.addJ2SDirectDatabaseCall web service URLs in static blocks in appropriate classes. Altered addJ2SDirectDatabaseCall to only add scheme://host:port and not path.
Ben Soares [Wed, 20 Dec 2023 14:49:27 +0000 (14:49 +0000)]
JAL-4328 Move the examples links to a sensible place. Add pae-example.jvp
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
Ben Soares [Fri, 15 Dec 2023 13:06:52 +0000 (13:06 +0000)]
JAL-4059 Only run this once
Ben Soares [Fri, 15 Dec 2023 12:58:03 +0000 (12:58 +0000)]
JAL-4059 Use namespaced query parameters in preference to Info.args. Report what's being used.
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.
Ben Soares [Thu, 14 Dec 2023 16:40:02 +0000 (16:40 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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 15:24:05 +0000 (15:24 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 14 Dec 2023 14:25:16 +0000 (14:25 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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 [Thu, 14 Dec 2023 12:38:15 +0000 (12:38 +0000)]
JAL-4059 Improvement to launch indicator
Ben Soares [Thu, 14 Dec 2023 12:37:35 +0000 (12:37 +0000)]
JAL-4059 Updated swingjs and removed spare library .zip
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 [Mon, 4 Dec 2023 23:12:13 +0000 (23:12 +0000)]
JAL-4059 Attempts to set JalviewJS desktop geometry from Info hash
Ben Soares [Mon, 4 Dec 2023 20:32:04 +0000 (20:32 +0000)]
JAL-4059 rename files from jsmol j2s zip from jsmol to swingjs
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 13:43:11 +0000 (13:43 +0000)]
Merge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square-FIXED_from_develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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.
Ben Soares [Wed, 29 Nov 2023 16:34:10 +0000 (16:34 +0000)]
JAL-4059 Fixed a test for adding jalview.bin.JalviewJS
Ben Soares [Wed, 29 Nov 2023 16:27:15 +0000 (16:27 +0000)]
Merge branch 'bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS' into bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square
Ben Soares [Wed, 29 Nov 2023 16:21:08 +0000 (16:21 +0000)]
JAL-4344 Some fixes of waiting blocks, and headless mode for export. Control logging of Jmol.
Ben Soares [Mon, 27 Nov 2023 19:53:58 +0000 (19:53 +0000)]
JAL-4238 minor errors fixed for JalviewJS structure colouring
Ben Soares [Fri, 24 Nov 2023 15:40:05 +0000 (15:40 +0000)]
JAL-4059 Allow form-created querystring style values for boolean values
Ben Soares [Thu, 23 Nov 2023 20:07:42 +0000 (20:07 +0000)]
JAL-4059 Storing important thisApplet information in java. Some CSS loading indicators.
Ben Soares [Thu, 23 Nov 2023 17:47:03 +0000 (17:47 +0000)]
JAL-4059 Made jalview.bin.JalviewJS to use new command-line args in querystring. See jalview_bin_JalviewJS-corenamespace.html for example.
Ben Soares [Thu, 23 Nov 2023 15:24:50 +0000 (15:24 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 23 Nov 2023 15:04:52 +0000 (15:04 +0000)]
JAL-4059 rename vars to j2s_ this and that for clarity
Ben Soares [Wed, 22 Nov 2023 20:11:43 +0000 (20:11 +0000)]
JAL-4059 Send bespoke Info hash parameters into jalview.bin.Jalview instance. Set 'splash' div exemplified in jalview_bin_Jalview-namespace.html. Add to core_jalview classlist.
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 [Tue, 21 Nov 2023 16:00:25 +0000 (16:00 +0000)]
JAL-4238 an attempt to set JalviewJS desktop overflow to visible (not working)
Ben Soares [Tue, 21 Nov 2023 15:59:09 +0000 (15:59 +0000)]
JAL-4238 Changing visibility of locateInRange(int) bizarrely fixes a PAE viewing problem
Ben Soares [Tue, 21 Nov 2023 15:55:59 +0000 (15:55 +0000)]
JAL-4238 example file added to exmaples
git://source.jalview.org / jalview.git / log