Jim Procter [Fri, 28 Jun 2024 16:03:09 +0000 (17:03 +0100)]
JAL-4386 move provider label into a new attribute on BinaryNodes so it can be recovered easily
Jim Procter [Thu, 27 Jun 2024 16:52:01 +0000 (17:52 +0100)]
JAL-4386 account for null entries in sequence array passed to the score model - usually only for the tests
Jim Procter [Thu, 27 Jun 2024 16:45:08 +0000 (17:45 +0100)]
Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into spike/JAL-4386_generate_multiple_leaves_for_ss_sources
Jim Procter [Thu, 27 Jun 2024 16:36:47 +0000 (17:36 +0100)]
JAL-4386 allow score models to generate additional labelled entities to cluster - and do so for sequences with multiple secondary structure lines
Jim Procter [Thu, 27 Jun 2024 16:32:24 +0000 (17:32 +0100)]
JAL-4386 JAL-4411 factored out the test for a particular annotation row being a secondary structure row and from specified provider (if needbe)
Jim Procter [Thu, 27 Jun 2024 16:28:18 +0000 (17:28 +0100)]
JAL-4411 catch cases when 'ssStructFilePathNameInPDB' is null - this happens when files are imported from Jalview project - which may mean provider is not conserved in round trip to project
Jim Procter [Thu, 27 Jun 2024 16:26:23 +0000 (17:26 +0100)]
JAL-4411 handle Boolean from String when Jalview projects imported
Renia Correya [Thu, 27 Jun 2024 10:39:30 +0000 (11:39 +0100)]
JAL-4411 Fixed some test cases
Renia Correya [Thu, 27 Jun 2024 10:01:05 +0000 (11:01 +0100)]
JAL-4411 Record source metadata in derived/transferred annotation rows
Add secondary structure provider as a property in the annotation rows
when searched and added from 3d beacons.
Renia Correya [Tue, 18 Jun 2024 12:26:21 +0000 (13:26 +0100)]
JAl-4392 Hide secondary structure consensus with no data to display
Renia Correya [Wed, 12 Jun 2024 15:01:12 +0000 (16:01 +0100)]
JAL-4392 Fixed failed test cases
Renia Correya [Wed, 12 Jun 2024 13:59:17 +0000 (14:59 +0100)]
JAL-4392 Feature implementation of group consensus secondary structures
Renia Correya [Wed, 12 Jun 2024 13:54:28 +0000 (14:54 +0100)]
JAL-4426 Fix when multiple secondary structure annotations are present
for a sequence
Renia Correya [Fri, 7 Jun 2024 14:16:09 +0000 (15:16 +0100)]
JAL-4426 Defect fix to display number of sequences only for bar graph
annotations
Renia Correya [Thu, 6 Jun 2024 10:17:59 +0000 (11:17 +0100)]
JAL-4426 Reword tool tip and status bar text
Renia Correya [Thu, 6 Jun 2024 09:24:37 +0000 (10:24 +0100)]
JAL 4392 Reformat Secondary structure description text
Renia Correya [Thu, 6 Jun 2024 09:22:01 +0000 (10:22 +0100)]
JAL-4426 Add feature to show number of sequences
Add feature to show number of sequences contributing to the consensus
secondary structure in the status bar/tool tip.
Renia Correya [Wed, 5 Jun 2024 10:03:04 +0000 (11:03 +0100)]
JAL-4392 Bug fixing and code refactoring.
Renia Correya [Tue, 28 May 2024 14:37:13 +0000 (15:37 +0100)]
JAL-4386 Fixed some identified bugs in recent changes
Renia Correya [Tue, 28 May 2024 10:18:34 +0000 (11:18 +0100)]
Merge remote-tracking branch 'origin/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
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.
Jim Procter [Thu, 16 May 2024 06:53:50 +0000 (07:53 +0100)]
Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
Jim Procter [Thu, 16 May 2024 06:52:10 +0000 (07:52 +0100)]
JAL-4356 bump release date to today, release notes for patching JAL-4407 and known issue report for JAL-3124 and JAL-4415
Renia Correya [Wed, 15 May 2024 16:30:44 +0000 (17:30 +0100)]
JAL-4386 Fixed failed test case
Jim Procter [Wed, 15 May 2024 16:15:05 +0000 (17:15 +0100)]
Merge branch 'bug/JAL-4416_sview_not_shown_for_local_strucfile' into develop
Renia Correya [Wed, 15 May 2024 15:56:22 +0000 (16:56 +0100)]
JAL-4386 Fixed failed test cases
Jim Procter [Wed, 15 May 2024 15:54:47 +0000 (16:54 +0100)]
JAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a test for this
Jim Procter [Wed, 15 May 2024 15:53:18 +0000 (16:53 +0100)]
JAL-4416 ensure the structure view is shown and any added annotation is displayed
Jim Procter [Wed, 15 May 2024 15:44:23 +0000 (16:44 +0100)]
JAL-4416 make sure the structure viewer is actually opened when handling local file view
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.
Jim Procter [Wed, 15 May 2024 13:28:59 +0000 (14:28 +0100)]
Merge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_to_msa' into develop
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.
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
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
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
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 14:10:03 +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
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
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