jalview.git
5 months agoJAL-4420 Allow associated files to be dragged on separately from the alignment (but...
Ben Soares [Wed, 5 Jun 2024 20:20:32 +0000 (21:20 +0100)]
JAL-4420 Allow associated files to be dragged on separately from the alignment (but afterwards).

5 months agoJAL-4409 Small refactoring of ArgParserUtils to allow processFiles to work on drag...
Ben Soares [Wed, 5 Jun 2024 19:39:27 +0000 (20:39 +0100)]
JAL-4409 Small refactoring of ArgParserUtils to allow processFiles to work on drag-and-dropped files list.

5 months agoJAL-4409 Allow more URI schemes (e.g. file) to be opened in Jalview
Ben Soares [Wed, 29 May 2024 15:25:34 +0000 (16:25 +0100)]
JAL-4409 Allow more URI schemes (e.g. file) to be opened in Jalview

5 months agoJAL-4409 Allow more URI schemes (e.g. file) to filter through to Jalview
Ben Soares [Wed, 29 May 2024 15:11:38 +0000 (16:11 +0100)]
JAL-4409 Allow more URI schemes (e.g. file) to filter through to Jalview

5 months agoJAL-4414 Add SocketTimeoutException to exceptions that trigger File Not Found rather...
Ben Soares [Wed, 29 May 2024 12:08:09 +0000 (13:08 +0100)]
JAL-4414 Add SocketTimeoutException to exceptions that trigger File Not Found rather than Format Not Recognised

5 months agoJAL-3196 Need more memory for the install4j process run by gradle
Ben Soares [Wed, 29 May 2024 11:58:57 +0000 (12:58 +0100)]
JAL-3196 Need more memory for the install4j process run by gradle

5 months agoJAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file...
Ben Soares [Tue, 28 May 2024 21:14:17 +0000 (22:14 +0100)]
JAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file paths. Allow getdown CLI memory setting with double-dash --jvmmemX

5 months agoJAL-4417 Use a specified props file for consistent output
Ben Soares [Tue, 28 May 2024 14:33:54 +0000 (15:33 +0100)]
JAL-4417 Use a specified props file for consistent output

5 months agoJAL-4409 TEMPORARY don't clean up image files from jalview.bin.CommandsTest.headlessO...
Ben Soares [Tue, 28 May 2024 13:40:03 +0000 (14:40 +0100)]
JAL-4409 TEMPORARY don't clean up image files from jalview.bin.CommandsTest.headlessOrGuiImageOutputTest failing on build server

5 months agoJAL-4409 Ensure the specific scheme jalviewx is only for the release version
Ben Soares [Tue, 28 May 2024 12:21:24 +0000 (13:21 +0100)]
JAL-4409 Ensure the specific scheme jalviewx is only for the release version

5 months agoJAL-4409 Don't insist on HttpURLConnection, allows for file:/ protocol connection
Ben Soares [Tue, 28 May 2024 12:03:31 +0000 (13:03 +0100)]
JAL-4409 Don't insist on HttpURLConnection, allows for file:/ protocol connection

5 months agoMerge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Mon, 27 May 2024 09:06:01 +0000 (10:06 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown

5 months agoJAL-1054 Change one more (unused) url.openStream to use the HttpUtils wrapper for...
Ben Soares [Tue, 21 May 2024 17:02:14 +0000 (18:02 +0100)]
JAL-1054 Change one more (unused) url.openStream to use the HttpUtils wrapper for completeness

5 months agoJAL-1054 Change the rest of the url.openConnection() calls to use the HttpUtils.openC...
Ben Soares [Tue, 21 May 2024 16:56:44 +0000 (17:56 +0100)]
JAL-1054 Change the rest of the url.openConnection() calls to use the HttpUtils.openConnection(url) wrapper

5 months agoJAL-4409 Adjust usage of HttpUtils.equivalentJalviewURLString() and pass jalviewX...
Ben Soares [Tue, 21 May 2024 15:31:00 +0000 (16:31 +0100)]
JAL-4409 Adjust usage of HttpUtils.equivalentJalviewURLString() and pass jalviewX:// URL files to Jalview without changing them as Jalview now deals with them

5 months agoJAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'
Ben Soares [Tue, 21 May 2024 14:55:57 +0000 (15:55 +0100)]
JAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'

5 months agoJAL-4356 release date for 2.11.3.3 is 22nd May 2025
Jim Procter [Tue, 21 May 2024 14:19:13 +0000 (15:19 +0100)]
JAL-4356 release date for 2.11.3.3 is 22nd May 2025

5 months agoJAL-4409 Also interpret jalviewX:// URIs in Jalview itself (for executable jar or...
Ben Soares [Mon, 20 May 2024 20:19:21 +0000 (21:19 +0100)]
JAL-4409 Also interpret jalviewX:// URIs in Jalview itself (for executable jar or command line start)

5 months agoJAL-4397 Another fix on linux
Ben Soares [Mon, 20 May 2024 20:11:02 +0000 (21:11 +0100)]
JAL-4397 Another fix on linux

5 months agoJAL-4420 Add some debugging statements
Ben Soares [Fri, 17 May 2024 16:26:30 +0000 (17:26 +0100)]
JAL-4420 Add some debugging statements

5 months agoJAL-4420 Tests for new FileUtils methods
Ben Soares [Fri, 17 May 2024 14:56:11 +0000 (15:56 +0100)]
JAL-4420 Tests for new FileUtils methods

5 months agoJAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs...
Ben Soares [Fri, 17 May 2024 14:55:52 +0000 (15:55 +0100)]
JAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs).  Preprocessing involves adding --open arguments, and spotting and regrouping associated files such as annotations, features and tree files.  These get --annotations argument etc.  Add FileUtils tools to get basepath and extension of filename or URL whilst only in String form.

5 months agoJAL-4409 Checking getdown jars up to date
Ben Soares [Fri, 17 May 2024 14:11:48 +0000 (15:11 +0100)]
JAL-4409 Checking getdown jars up to date

5 months agoJAL-3409 Add newline back into Buffered Reader in getdown launcher.log
Ben Soares [Fri, 17 May 2024 13:48:01 +0000 (14:48 +0100)]
JAL-3409 Add newline back into Buffered Reader in getdown launcher.log

5 months agoJAL-4409 corrected the umount of dmg to hdiutil detach to allow subsequent opening...
Ben Soares [Fri, 17 May 2024 09:03:30 +0000 (10:03 +0100)]
JAL-4409 corrected the umount of dmg to hdiutil detach to allow subsequent opening with other improvements

5 months agoJAL-4409 Added remote JVL files for Linux/Windows
Ben Soares [Thu, 16 May 2024 23:57:29 +0000 (00:57 +0100)]
JAL-4409 Added remote JVL files for Linux/Windows

5 months agoJAL-4409 Added multiple file open to getdown. Added URL source of JVL file ability...
Ben Soares [Thu, 16 May 2024 19:01:01 +0000 (20:01 +0100)]
JAL-4409 Added multiple file open to getdown. Added URL source of JVL file ability to getdown. Convert jalviewX:// type schemed URIs consistently.

5 months agoJAL-4356 release notes for JAL-3978 patch
Jim Procter [Thu, 16 May 2024 14:13:40 +0000 (15:13 +0100)]
JAL-4356 release notes for JAL-3978 patch

5 months agoMerge branch 'bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task' into develop
Jim Procter [Thu, 16 May 2024 14:09:54 +0000 (15:09 +0100)]
Merge branch 'bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task' into develop

5 months agoJAL-3978 Add the bin dir to be copied from website appdir to archive appdir bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task
Ben Soares [Thu, 16 May 2024 13:59:17 +0000 (14:59 +0100)]
JAL-3978 Add the bin dir to be copied from website appdir to archive appdir

5 months agoJAL-4409 Easier full install from source for macOS
Ben Soares [Thu, 16 May 2024 13:44:36 +0000 (14:44 +0100)]
JAL-4409 Easier full install from source for macOS

5 months agoJAL-4409 more places to check for jalviewd://
Ben Soares [Thu, 16 May 2024 13:44:04 +0000 (14:44 +0100)]
JAL-4409 more places to check for jalviewd://

5 months agoJAL-4418 bump release to 2.11.4.0
Jim Procter [Thu, 16 May 2024 07:31:29 +0000 (08:31 +0100)]
JAL-4418 bump release to 2.11.4.0

5 months agoMerge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation...
Jim Procter [Thu, 16 May 2024 06:54:13 +0000 (07:54 +0100)]
Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into develop

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-4397 IdWidth tests slightly less restrictive for platform/scaling variations
Ben Soares [Wed, 15 May 2024 17:27:07 +0000 (18:27 +0100)]
JAL-4397 IdWidth tests slightly less restrictive for platform/scaling variations

5 months agoJAL-4409 extra schemes now opening correctly in macos
Ben Soares [Wed, 15 May 2024 16:59:45 +0000 (17:59 +0100)]
JAL-4409 extra schemes now opening correctly in macos

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 agoJAL-4409 minor change for mac testing
Ben Soares [Wed, 15 May 2024 15:23:43 +0000 (16:23 +0100)]
JAL-4409 minor change for mac testing

5 months agoJAL-4409 Updated getdown classes
Ben Soares [Wed, 15 May 2024 14:48:41 +0000 (15:48 +0100)]
JAL-4409 Updated getdown classes

5 months agoJAL-4409 Refactoring to allow easier reuse of classes with getdown
Ben Soares [Wed, 15 May 2024 14:48:14 +0000 (15:48 +0100)]
JAL-4409 Refactoring to allow easier reuse of classes with getdown

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-1054 JAL-4414 Tests for the HttpUtils redirect wrapper methods. Tests for the...
Ben Soares [Tue, 14 May 2024 20:09:38 +0000 (21:09 +0100)]
JAL-1054 JAL-4414 Tests for the HttpUtils redirect wrapper methods.  Tests for the different exceptions from IdentityFile.identify().

5 months agoJAL-1054 Also recognise UnknownHostException as a file not found at URL
Ben Soares [Tue, 14 May 2024 20:07:09 +0000 (21:07 +0100)]
JAL-1054 Also recognise UnknownHostException as a file not found at URL

5 months agoMerge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Tue, 14 May 2024 16:57:01 +0000 (17:57 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown

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-1054 Tests for the HttpUtils redirection wrappers
Ben Soares [Tue, 14 May 2024 16:37:49 +0000 (17:37 +0100)]
JAL-1054 Tests for the HttpUtils redirection wrappers

5 months agoMerge branch 'bug/JAL-4397_failing_idWidth_tests' into improvement/JAL-4409_implement...
Ben Soares [Tue, 14 May 2024 14:44:49 +0000 (15:44 +0100)]
Merge branch 'bug/JAL-4397_failing_idWidth_tests' into improvement/JAL-4409_implement_extra_schemes_in_getdown

5 months agoMerge branch 'develop' into bug/JAL-4397_failing_idWidth_tests bug/JAL-4397_failing_idWidth_tests
Ben Soares [Tue, 14 May 2024 14:27:28 +0000 (15:27 +0100)]
Merge branch 'develop' into bug/JAL-4397_failing_idWidth_tests

5 months agoJAL-4414 Add a FileNotFoundException when identifying URL file formats and catch...
Ben Soares [Tue, 14 May 2024 14:26:51 +0000 (15:26 +0100)]
JAL-4414 Add a FileNotFoundException when identifying URL file formats and catch to change error message appropriately

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-1054 Fix wrappers for following http->https redirects
Ben Soares [Mon, 13 May 2024 16:12:49 +0000 (17:12 +0100)]
JAL-1054 Fix wrappers for following http->https redirects

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 branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Mon, 13 May 2024 14:36:01 +0000 (15:36 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown

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 agoJAL-4409 Fix some file extensions (including remove .txt)
Ben Soares [Mon, 13 May 2024 13:33:12 +0000 (14:33 +0100)]
JAL-4409 Fix some file extensions (including remove .txt)

5 months agoJAL-1054 Add wrappers for URL.openConnection(), URL.openStream() to allow following...
Ben Soares [Mon, 13 May 2024 13:31:58 +0000 (14:31 +0100)]
JAL-1054 Add wrappers for URL.openConnection(), URL.openStream() to allow following redirect from http to https

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

5 months agoJAL-4409 Add jalviewhttp and jalviewhttps schemes to register in install4j. Recognis...
Ben Soares [Fri, 10 May 2024 11:14:27 +0000 (12:14 +0100)]
JAL-4409 Add jalviewhttp and jalviewhttps schemes to register in install4j.  Recognise all extra schemes in getdown.

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-4397 Removed debugging statement
Ben Soares [Sat, 27 Apr 2024 21:22:01 +0000 (22:22 +0100)]
JAL-4397 Removed debugging statement

6 months agoJAL-4397 Adjustments for macOS HiDPI
Ben Soares [Fri, 26 Apr 2024 17:41:40 +0000 (18:41 +0100)]
JAL-4397 Adjustments for macOS HiDPI

6 months agoJAL-4397 Test all fixed on linux. Given leeway to some tests, platform dependent...
Ben Soares [Fri, 26 Apr 2024 17:23:04 +0000 (18:23 +0100)]
JAL-4397 Test all fixed on linux.  Given leeway to some tests, platform dependent expected values on some tests, HiDPI dependent expected values on some tests.  Still to test on macOS.

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-4397 Allow some leeway in automatically calculated id width tests
Ben Soares [Mon, 22 Apr 2024 16:36:20 +0000 (17:36 +0100)]
JAL-4397 Allow some leeway in automatically calculated id width tests

6 months agoJAL-4397 fixed testresetIdWidth() test on macos
Ben Soares [Thu, 18 Apr 2024 15:01:46 +0000 (16:01 +0100)]
JAL-4397 fixed testresetIdWidth() test on macos

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