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.
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
Ben Soares [Tue, 21 Nov 2023 15:54:40 +0000 (15:54 +0000)]
JAL-4238 test files for PAE in jalviewjs
Ben Soares [Tue, 21 Nov 2023 15:54:12 +0000 (15:54 +0000)]
JAL-4059 updated swingjs, Jmol-SwingJS.zip. Insignificantly altered build.gradle.
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 11:35:05 +0000 (11:35 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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
Ben Soares [Thu, 16 Nov 2023 10:41:03 +0000 (10:41 +0000)]
JAL-4238 ignore thread.sleeps in jalviewjs. Added a simple PAE example file.
Ben Soares [Thu, 16 Nov 2023 09:56:27 +0000 (09:56 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 16 Nov 2023 09:56:13 +0000 (09:56 +0000)]
JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference to java.beans.Beans which is not in swingjs. Settle on miglayout-4.2 jars.
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
Ben Soares [Wed, 15 Nov 2023 15:35:44 +0000 (15:35 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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
Ben Soares [Wed, 15 Nov 2023 13:29:19 +0000 (13:29 +0000)]
JAL-3836 Allow .ext.gz files to be recognised in the File Chooser if .ext is a recognised extension.
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
Ben Soares [Wed, 15 Nov 2023 10:46:34 +0000 (10:46 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Wed, 15 Nov 2023 10:46:13 +0000 (10:46 +0000)]
JAL-4059 update intervalstore-1.2-site.zip transpiled with new j2s
Ben Soares [Wed, 15 Nov 2023 10:36:56 +0000 (10:36 +0000)]
Merge branch 'feature/JAL-3576intervalStore_1_2' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Tue, 14 Nov 2023 12:11:34 +0000 (12:11 +0000)]
JAL-4238 examples files for PAE
Ben Soares [Tue, 14 Nov 2023 10:38:29 +0000 (10:38 +0000)]
JAL-4059 added test for <br/> break
Ben Soares [Mon, 13 Nov 2023 23:05:48 +0000 (23:05 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' of https://source.jalview.org/git/jalview into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 22:58:49 +0000 (22:58 +0000)]
JAL-4059 fix other PopupMenuTest
James Procter [Mon, 13 Nov 2023 22:43:54 +0000 (22:43 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 22:42:57 +0000 (22:42 +0000)]
JAL-4059 revert to intervalstore 1.1 for VCFLoader
Ben Soares [Mon, 13 Nov 2023 19:53:17 +0000 (19:53 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 19:51:40 +0000 (19:51 +0000)]
JAL-4059 fixed a test that is now working as expected due to <br/>. Better calculation of long line with HTML tags.
Ben Soares [Mon, 13 Nov 2023 19:03:03 +0000 (19:03 +0000)]
JAL-4059 Fix the tooltip formatting for when, e.g. enclose=false
Ben Soares [Mon, 13 Nov 2023 19:02:34 +0000 (19:02 +0000)]
JAL-4059 redo these tests as TestNG asserts to add message
James Procter [Mon, 13 Nov 2023 18:36:35 +0000 (18:36 +0000)]
JAL-4090 JAL-1551 source license
Ben Soares [Mon, 13 Nov 2023 18:33:36 +0000 (18:33 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 18:29:04 +0000 (18:29 +0000)]
JAL-4059 Updates to miglayout, varna, intervalstore, with re-transpiled javascript libs. Some failing tests
git://source.jalview.org / jalview.git / log