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).
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.
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
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
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
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
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
Ben Soares [Tue, 28 May 2024 14:33:54 +0000 (15:33 +0100)]
JAL-4417 Use a specified props file for consistent output
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
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
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
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
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
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
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
Ben Soares [Tue, 21 May 2024 14:55:57 +0000 (15:55 +0100)]
JAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'
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
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)
Ben Soares [Mon, 20 May 2024 20:11:02 +0000 (21:11 +0100)]
JAL-4397 Another fix on linux
Ben Soares [Fri, 17 May 2024 16:26:30 +0000 (17:26 +0100)]
JAL-4420 Add some debugging statements
Ben Soares [Fri, 17 May 2024 14:56:11 +0000 (15:56 +0100)]
JAL-4420 Tests for new FileUtils methods
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.
Ben Soares [Fri, 17 May 2024 14:11:48 +0000 (15:11 +0100)]
JAL-4409 Checking getdown jars up to date
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
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
Ben Soares [Thu, 16 May 2024 23:57:29 +0000 (00:57 +0100)]
JAL-4409 Added remote JVL files for Linux/Windows
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.
Jim Procter [Thu, 16 May 2024 14:13:40 +0000 (15:13 +0100)]
JAL-4356 release notes for JAL-3978 patch
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
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
Ben Soares [Thu, 16 May 2024 13:44:36 +0000 (14:44 +0100)]
JAL-4409 Easier full install from source for macOS
Ben Soares [Thu, 16 May 2024 13:44:04 +0000 (14:44 +0100)]
JAL-4409 more places to check for jalviewd://
Jim Procter [Thu, 16 May 2024 07:31:29 +0000 (08:31 +0100)]
JAL-4418 bump release to 2.11.4.0
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
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
Ben Soares [Wed, 15 May 2024 17:27:07 +0000 (18:27 +0100)]
JAL-4397 IdWidth tests slightly less restrictive for platform/scaling variations
Ben Soares [Wed, 15 May 2024 16:59:45 +0000 (17:59 +0100)]
JAL-4409 extra schemes now opening correctly in macos
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.
Ben Soares [Wed, 15 May 2024 15:23:43 +0000 (16:23 +0100)]
JAL-4409 minor change for mac testing
Ben Soares [Wed, 15 May 2024 14:48:41 +0000 (15:48 +0100)]
JAL-4409 Updated getdown classes
Ben Soares [Wed, 15 May 2024 14:48:14 +0000 (15:48 +0100)]
JAL-4409 Refactoring to allow easier reuse of classes with getdown
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 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().
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
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
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
Ben Soares [Tue, 14 May 2024 16:37:49 +0000 (17:37 +0100)]
JAL-1054 Tests for the HttpUtils redirection wrappers
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
Ben Soares [Tue, 14 May 2024 14:27:28 +0000 (15:27 +0100)]
Merge branch 'develop' into bug/JAL-4397_failing_idWidth_tests
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
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
Ben Soares [Mon, 13 May 2024 16:12:49 +0000 (17:12 +0100)]
JAL-1054 Fix wrappers for following http->https redirects
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
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
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
Ben Soares [Mon, 13 May 2024 13:33:12 +0000 (14:33 +0100)]
JAL-4409 Fix some file extensions (including remove .txt)
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
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 [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.
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.
Ben Soares [Sat, 27 Apr 2024 21:22:01 +0000 (22:22 +0100)]
JAL-4397 Removed debugging statement
Ben Soares [Fri, 26 Apr 2024 17:41:40 +0000 (18:41 +0100)]
JAL-4397 Adjustments for macOS HiDPI
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.
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.
Ben Soares [Mon, 22 Apr 2024 16:36:20 +0000 (17:36 +0100)]
JAL-4397 Allow some leeway in automatically calculated id width tests
Ben Soares [Thu, 18 Apr 2024 15:01:46 +0000 (16:01 +0100)]
JAL-4397 fixed testresetIdWidth() test on macos
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