Renia Correya [Tue, 28 May 2024 10:13:00 +0000 (11:13 +0100)]
JAL-4386 Added secondary structure providers check boxes in show
secondary structure menu. Implemented displaying of secondary structure
and consensus based on user selection. Added secondary structure
providers option in calculate window. Added provider label in pca panel
and tree panel for secondary structure similarity.
Renia Correya [Wed, 15 May 2024 16:30:44 +0000 (17:30 +0100)]
JAL-4386 Fixed failed test case
Renia Correya [Wed, 15 May 2024 15:56:22 +0000 (16:56 +0100)]
JAL-4386 Fixed failed test cases
Renia Correya [Wed, 15 May 2024 15:37:39 +0000 (16:37 +0100)]
JAL-4386 Added preferences for secondary structure consensus and it is
set as false by default to skip failed test cases.
Renia Correya [Wed, 15 May 2024 09:58:52 +0000 (10:58 +0100)]
JAL-4386 - Implementation of retrieving secondary structure
source/provider from matching the annotation description and PDB entry.
Implementation of Show secondary structure menu option. Updated
calculation of secondary structure consensus.
Renia Correya [Mon, 13 May 2024 14:30:06 +0000 (15:30 +0100)]
Merge remote-tracking branch 'origin/develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
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
Renia Correya [Mon, 13 May 2024 09:43:44 +0000 (10:43 +0100)]
Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' of https://source.jalview.org/git/jalview.git into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
Renia Correya [Mon, 13 May 2024 09:23:02 +0000 (10:23 +0100)]
JAL-4386 - Implementation of substitution matrix and test cases.
Jim Procter [Fri, 10 May 2024 14:52:00 +0000 (15:52 +0100)]
JAL-4411 fix typo :(
Jim Procter [Fri, 10 May 2024 14:50:55 +0000 (15:50 +0100)]
JAL-4411 store class of provider in PDBEntry
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.
Renia Correya [Wed, 1 May 2024 16:47:36 +0000 (17:47 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-4407_no_sec_str_from_draganddrop_to_msa' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
Jim Procter [Wed, 1 May 2024 15:15:15 +0000 (16:15 +0100)]
JAL-4407 don't transfer 'local' settings - leave as default 3d-structure annotation processing
Jim Procter [Wed, 1 May 2024 14:58:21 +0000 (15:58 +0100)]
JAL-4407 failing test checking for secondary structure is added when calling the associate pdb file routine
Renia Correya [Tue, 30 Apr 2024 14:37:13 +0000 (15:37 +0100)]
JAL-4392 Merging consensus secondary structure
Renia Correya [Tue, 30 Apr 2024 14:34:18 +0000 (15:34 +0100)]
JAL-4386 Comparing secondary structure similarity directly with a basic
substitution matrix. Some code refactoring.
Renia Correya [Fri, 26 Apr 2024 09:27:28 +0000 (10:27 +0100)]
JAL-4386 Drop down for secondary structure sources in calculate window
Renia Correya [Wed, 24 Apr 2024 14:26:35 +0000 (15:26 +0100)]
JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown in Calculate window.
Renia Correya [Tue, 16 Apr 2024 16:28:21 +0000 (17:28 +0100)]
JAL-4386 Calculate tree using secondary structure annotation - Documentation, Changes to include Secondary structure from JPred.
Renia Correya [Wed, 13 Mar 2024 11:50:16 +0000 (11:50 +0000)]
JAL-4386_Added changes in similarity score calculation for different cases of sequences with undefined secondary structure
Renia Correya [Fri, 8 Mar 2024 14:49:48 +0000 (14:49 +0000)]
JAL-4386 Corrected failed test case.
Renia Correya [Fri, 8 Mar 2024 14:31:51 +0000 (14:31 +0000)]
JAL-4386 Added further checks for sequences that have no secondary structure.
Renia Correya [Fri, 8 Mar 2024 09:16:44 +0000 (09:16 +0000)]
JAL-4386 Calculate tree using secondary structure annotation
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
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
git://source.jalview.org / jalview.git / log