jalview.git
4 months agoJAL-4386 move provider label into a new attribute on BinaryNodes so it can be recover...
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

4 months agoJAL-4386 account for null entries in sequence array passed to the score model - usual...
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

4 months agoMerge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation...
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

4 months agoJAL-4386 allow score models to generate additional labelled entities to cluster ...
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

4 months agoJAL-4386 JAL-4411 factored out the test for a particular annotation row being a secon...
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)

4 months agoJAL-4411 catch cases when 'ssStructFilePathNameInPDB' is null - this happens when...
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

4 months agoJAL-4411 handle Boolean from String when Jalview projects imported
Jim Procter [Thu, 27 Jun 2024 16:26:23 +0000 (17:26 +0100)]
JAL-4411 handle Boolean from String when Jalview projects imported

4 months agoJAL-4411 Fixed some test cases
Renia Correya [Thu, 27 Jun 2024 10:39:30 +0000 (11:39 +0100)]
JAL-4411 Fixed some test cases

4 months agoJAL-4411 Record source metadata in derived/transferred annotation rows
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.

4 months agoJAl-4392 Hide secondary structure consensus with no data to display
Renia Correya [Tue, 18 Jun 2024 12:26:21 +0000 (13:26 +0100)]
JAl-4392 Hide secondary structure consensus with no data to display

4 months agoJAL-4392 Fixed failed test cases
Renia Correya [Wed, 12 Jun 2024 15:01:12 +0000 (16:01 +0100)]
JAL-4392 Fixed failed test cases

4 months agoJAL-4392 Feature implementation of group consensus secondary structures
Renia Correya [Wed, 12 Jun 2024 13:59:17 +0000 (14:59 +0100)]
JAL-4392 Feature implementation of group consensus secondary structures

4 months agoJAL-4426 Fix when multiple secondary structure annotations are present
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

5 months agoJAL-4426 Defect fix to display number of sequences only for bar graph
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

5 months agoJAL-4426 Reword tool tip and status bar text
Renia Correya [Thu, 6 Jun 2024 10:17:59 +0000 (11:17 +0100)]
JAL-4426 Reword tool tip and status bar text

5 months agoJAL 4392 Reformat Secondary structure description text
Renia Correya [Thu, 6 Jun 2024 09:24:37 +0000 (10:24 +0100)]
JAL 4392 Reformat Secondary structure description text

5 months agoJAL-4426 Add feature to show number of sequences
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.

5 months agoJAL-4392 Bug fixing and code refactoring.
Renia Correya [Wed, 5 Jun 2024 10:03:04 +0000 (11:03 +0100)]
JAL-4392 Bug fixing and code refactoring.

5 months agoJAL-4386 Fixed some identified bugs in recent changes
Renia Correya [Tue, 28 May 2024 14:37:13 +0000 (15:37 +0100)]
JAL-4386 Fixed some identified bugs in recent changes

5 months agoMerge remote-tracking branch 'origin/feature/JAL-4386_calculate_tree_using_secondary_...
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

5 months agoJAL-4386 Added secondary structure providers check boxes in show
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.

5 months agoMerge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure...
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

5 months agoJAL-4356 bump release date to today, release notes for patching JAL-4407 and known...
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

5 months agoJAL-4386 Fixed failed test case
Renia Correya [Wed, 15 May 2024 16:30:44 +0000 (17:30 +0100)]
JAL-4386 Fixed failed test case

5 months agoMerge branch 'bug/JAL-4416_sview_not_shown_for_local_strucfile' into develop
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

5 months agoJAL-4386 Fixed failed test cases
Renia Correya [Wed, 15 May 2024 15:56:22 +0000 (16:56 +0100)]
JAL-4386 Fixed failed test cases

5 months agoJAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a test for this bug/JAL-4416_sview_not_shown_for_local_strucfile
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

5 months agoJAL-4416 ensure the structure view is shown and any added annotation is displayed
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

5 months agoJAL-4416 make sure the structure viewer is actually opened when handling local file...
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

5 months agoJAL-4386 Added preferences for secondary structure consensus and it is
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.

5 months agoMerge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_to_msa' into develop
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

5 months agoJAL-4386 - Implementation of retrieving secondary structure
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.

5 months agoJAL-4217 Upped the main testTask0 timeout to 15 minutes for build server's benefit improvement/JAL-4217_added_a_timeout_to_tests
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

5 months agoJAL-4356 fix release note
Jim Procter [Tue, 14 May 2024 13:41:03 +0000 (14:41 +0100)]
JAL-4356 fix release note

5 months agoJAL-4356 set release date to Weds 15th May and update release notes
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

5 months agoJAL-4356 JAL-518 JAL-4413 release notes
Jim Procter [Mon, 13 May 2024 16:22:06 +0000 (17:22 +0100)]
JAL-4356 JAL-518 JAL-4413 release notes

5 months agoMerge branch 'features/JAL-518_justify_seqs_in_region' into develop
Jim Procter [Mon, 13 May 2024 16:14:08 +0000 (17:14 +0100)]
Merge branch 'features/JAL-518_justify_seqs_in_region' into develop

5 months agoJAL-518 better test coverage and support for case preservation features/JAL-518_justify_seqs_in_region
Jim Procter [Mon, 13 May 2024 16:05:11 +0000 (17:05 +0100)]
JAL-518 better test coverage and support for case preservation

5 months agoJAL-518 failing test for case preservation on justify
Jim Procter [Mon, 13 May 2024 15:01:36 +0000 (16:01 +0100)]
JAL-518 failing test for case preservation on justify

5 months agoMerge remote-tracking branch 'origin/develop' into feature/JAL-4386_calculate_tree_us...
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

5 months agoMerge branch 'develop' into features/JAL-518_justify_seqs_in_region
Jim Procter [Mon, 13 May 2024 14:10:03 +0000 (15:10 +0100)]
Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

5 months agoJAL-4413 timeouts Merge branch 'improvement/JAL-4217_added_a_timeout_to_tests' into...
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

5 months agoMerge branch 'develop' into features/JAL-518_justify_seqs_in_region
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

5 months agoMerge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation...
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

5 months agoJAL-4386 - Implementation of substitution matrix and test cases.
Renia Correya [Mon, 13 May 2024 09:23:02 +0000 (10:23 +0100)]
JAL-4386 - Implementation of substitution matrix and test cases.

5 months agoJAL-4411 fix typo :(
Jim Procter [Fri, 10 May 2024 14:52:00 +0000 (15:52 +0100)]
JAL-4411 fix typo :(

5 months agoJAL-4411 store class of provider in PDBEntry
Jim Procter [Fri, 10 May 2024 14:50:55 +0000 (15:50 +0100)]
JAL-4411 store class of provider in PDBEntry

6 months agoJAL-4217 Sensible timeout for testTask0
Ben Soares [Thu, 2 May 2024 18:48:41 +0000 (19:48 +0100)]
JAL-4217 Sensible timeout for testTask0

6 months agoJAL-4217 Added a timeout for testTasks. If timeout is exceeded then test execution...
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.

6 months agoMerge remote-tracking branch 'origin/bug/JAL-4407_no_sec_str_from_draganddrop_to_msa...
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

6 months agoJAL-4407 don't transfer 'local' settings - leave as default 3d-structure annotation... bug/JAL-4407_no_sec_str_from_draganddrop_to_msa
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

6 months agoJAL-4407 failing test checking for secondary structure is added when calling the...
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

6 months agoJAL-4392 Merging consensus secondary structure
Renia Correya [Tue, 30 Apr 2024 14:37:13 +0000 (15:37 +0100)]
JAL-4392 Merging consensus secondary structure

6 months agoJAL-4386 Comparing secondary structure similarity directly with a basic
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.

6 months agoJAL-4386 Drop down for secondary structure sources in calculate window
Renia Correya [Fri, 26 Apr 2024 09:27:28 +0000 (10:27 +0100)]
JAL-4386 Drop down for secondary structure sources in calculate window

6 months agoJAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown...
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.

6 months agoJAL-4386 Calculate tree using secondary structure annotation - Documentation, Changes...
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.

7 months agoJAL-4386_Added changes in similarity score calculation for different cases of sequenc...
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

8 months agoJAL-4386 Corrected failed test case.
Renia Correya [Fri, 8 Mar 2024 14:49:48 +0000 (14:49 +0000)]
JAL-4386 Corrected failed test case.

8 months agoJAL-4386 Added further checks for sequences that have no secondary structure.
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.

8 months agoJAL-4386 Calculate tree using secondary structure annotation
Renia Correya [Fri, 8 Mar 2024 09:16:44 +0000 (09:16 +0000)]
JAL-4386 Calculate tree using secondary structure annotation

9 months agoJAL-4356 release notes
James Procter [Tue, 23 Jan 2024 17:27:24 +0000 (17:27 +0000)]
JAL-4356 release notes

9 months agoJAL-4356 update release notes for 2.11.3.3
James Procter [Tue, 23 Jan 2024 17:08:28 +0000 (17:08 +0000)]
JAL-4356 update release notes for 2.11.3.3

9 months agoMerge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesn...
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

9 months agoMerge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_ann...
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

9 months agoJAL-4367 Limit right and top adjustments
Ben Soares [Wed, 20 Dec 2023 13:23:07 +0000 (13:23 +0000)]
JAL-4367 Limit right and top adjustments

9 months agoJAL-4290 Fix image comparison between gui and headless output. Images are now the...
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

9 months agoJAL-4290 fixed tests
Ben Soares [Wed, 20 Dec 2023 00:08:56 +0000 (00:08 +0000)]
JAL-4290 fixed tests

9 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
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

9 months agoMerge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_i...
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

9 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
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

9 months agoJAL-4353 wait for files to be written fully before comparing size with older file
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

9 months agoJAL-4353 singleThread all tests
James Procter [Tue, 12 Dec 2023 17:18:48 +0000 (17:18 +0000)]
JAL-4353 singleThread all tests

9 months agoJAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is...
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

9 months agoJAL-4369 uniprotkb - try to avoid another redirect response
James Procter [Wed, 10 Jan 2024 10:26:26 +0000 (10:26 +0000)]
JAL-4369 uniprotkb - try to avoid another redirect response

9 months agoJAL-4369 use rest.uniprot.org as fetch domain
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

9 months agoMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executa...
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

9 months agoMerge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into...
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

9 months agoJAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consis... bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch
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.

9 months agoJAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It...
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.

10 months agoJAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately
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

10 months agoJAL-4290 Fixed one test
Ben Soares [Tue, 19 Dec 2023 17:50:33 +0000 (17:50 +0000)]
JAL-4290 Fixed one test

10 months agoJAL-4290 not quite working tests
Ben Soares [Mon, 18 Dec 2023 13:58:28 +0000 (13:58 +0000)]
JAL-4290 not quite working tests

10 months agoJAL-4290 incorrect usage of main()
Ben Soares [Mon, 18 Dec 2023 13:58:15 +0000 (13:58 +0000)]
JAL-4290 incorrect usage of main()

10 months agoMerge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesn...
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

10 months agoJAL-4290 Add method to allow for specific settings. Revert setting show annotations.
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.

10 months agoJAL-4290 Set structureSelectionManager settings more generically and when no desktop...
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

10 months agoMerge branch 'bug/JAL-4290_headless_alignment_figure_with_sse' into bug/JAL-4290_head...
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

10 months agoJAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations... bug/JAL-4290_headless_alignment_figure_with_sse
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

10 months agoJAL-4290 Move some annotation visibility settings to after opening a structure. Set...
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.

10 months agoJAL-4356 update release notes
James Procter [Thu, 14 Dec 2023 15:39:20 +0000 (15:39 +0000)]
JAL-4356 update release notes

10 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
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

10 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
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

10 months agoJAL-4353 wait for files to be written fully before comparing size with older file
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

10 months agoJAL-4217 singleThread all tests
James Procter [Tue, 12 Dec 2023 17:18:48 +0000 (17:18 +0000)]
JAL-4217 singleThread all tests

10 months agoMerge branch 'bug/JAL-2934proportionalScrolling' into develop
James Procter [Thu, 14 Dec 2023 14:16:38 +0000 (14:16 +0000)]
Merge branch 'bug/JAL-2934proportionalScrolling' into develop

10 months agoMerge branch 'develop' into bug/JAL-2934proportionalScrolling bug/JAL-2934proportionalScrolling
James Procter [Thu, 14 Dec 2023 14:14:15 +0000 (14:14 +0000)]
Merge branch 'develop' into bug/JAL-2934proportionalScrolling

10 months agoJAL-4353 bigger tighter test
Ben Soares [Tue, 12 Dec 2023 17:49:35 +0000 (17:49 +0000)]
JAL-4353 bigger tighter test

10 months agoJAL-4217 don’t try and export an image when Jmol is also trying to repaint
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

10 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
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