Ben Soares [Mon, 20 Feb 2023 10:09:46 +0000 (10:09 +0000)]
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
James Procter [Thu, 16 Feb 2023 12:25:41 +0000 (12:25 +0000)]
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
James Procter [Wed, 15 Feb 2023 15:25:53 +0000 (15:25 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Wed, 15 Feb 2023 14:43:32 +0000 (14:43 +0000)]
Passing test for JAL-4127 failing on the JAL-1713 branch
James Procter [Wed, 15 Feb 2023 13:59:29 +0000 (13:59 +0000)]
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
Ben Soares [Mon, 13 Feb 2023 22:42:58 +0000 (22:42 +0000)]
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Ben Soares [Mon, 13 Feb 2023 22:41:51 +0000 (22:41 +0000)]
JAL-4125 Spanish translations
Ben Soares [Mon, 13 Feb 2023 20:18:00 +0000 (20:18 +0000)]
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Ben Soares [Mon, 13 Feb 2023 19:16:08 +0000 (19:16 +0000)]
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
James Procter [Mon, 13 Feb 2023 17:28:45 +0000 (17:28 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Fri, 10 Feb 2023 17:05:30 +0000 (17:05 +0000)]
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
James Procter [Fri, 10 Feb 2023 16:26:37 +0000 (16:26 +0000)]
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
James Procter [Fri, 10 Feb 2023 16:23:53 +0000 (16:23 +0000)]
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
James Procter [Fri, 10 Feb 2023 16:03:32 +0000 (16:03 +0000)]
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
Ben Soares [Thu, 9 Feb 2023 01:38:20 +0000 (01:38 +0000)]
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
James Procter [Fri, 3 Feb 2023 14:18:44 +0000 (14:18 +0000)]
JAL-1551 remove temp file in src
James Procter [Fri, 3 Feb 2023 14:14:49 +0000 (14:14 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
James Procter [Tue, 31 Jan 2023 16:17:49 +0000 (16:17 +0000)]
JAL-1713 update from Jalview 2.11.3 develop
Merge branch 'develop' into feature/JAL-1713_overviewInProject
regenerated jaxb classes to resolve conflicts
Ben Soares [Mon, 30 Jan 2023 12:17:27 +0000 (12:17 +0000)]
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
Ben Soares [Thu, 26 Jan 2023 17:06:40 +0000 (17:06 +0000)]
JAL-4118 remove unnecessary sleep from QuitHandlerTest
Ben Soares [Thu, 26 Jan 2023 16:44:51 +0000 (16:44 +0000)]
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
Ben Soares [Thu, 26 Jan 2023 11:49:36 +0000 (11:49 +0000)]
JAL-1988 Add a sleep to file save test to give time for file to save
James Procter [Wed, 25 Jan 2023 15:28:48 +0000 (15:28 +0000)]
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
James Procter [Wed, 25 Jan 2023 13:05:54 +0000 (13:05 +0000)]
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
James Procter [Tue, 24 Jan 2023 18:20:55 +0000 (18:20 +0000)]
JAL-4090 Release 2.11.3.0 release notes and version bump
James Procter [Tue, 24 Jan 2023 17:41:02 +0000 (17:41 +0000)]
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
James Procter [Tue, 24 Jan 2023 06:26:15 +0000 (06:26 +0000)]
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
James Procter [Mon, 23 Jan 2023 20:17:42 +0000 (20:17 +0000)]
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
Jim Procter [Mon, 23 Jan 2023 09:32:43 +0000 (09:32 +0000)]
JAL-4102 whatsNew for 2.11.2.6
Jim Procter [Fri, 20 Jan 2023 23:40:08 +0000 (23:40 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 23:39:28 +0000 (23:39 +0000)]
JAL-4114 model_page_url not required in v2.0 response
Jim Procter [Fri, 20 Jan 2023 23:03:12 +0000 (23:03 +0000)]
JAL-4102 update date and release notes for 2.11.2.6
Jim Procter [Fri, 20 Jan 2023 22:53:26 +0000 (22:53 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 22:52:55 +0000 (22:52 +0000)]
Merge branch 'patch/Release_2_11_2_6_Branch' into develop
Jim Procter [Fri, 20 Jan 2023 20:48:43 +0000 (20:48 +0000)]
JAL-2353 primary ref candidates that should be promoted should preserve original version string
Jim Procter [Fri, 20 Jan 2023 20:44:47 +0000 (20:44 +0000)]
JAL-4114 missing mock server response
Jim Procter [Fri, 20 Jan 2023 17:53:48 +0000 (17:53 +0000)]
JAL-4114 only rank model qualities that are computed with the same method, and uprank models with pLDDT over other types of models in the same model type category
Jim Procter [Fri, 20 Jan 2023 17:52:52 +0000 (17:52 +0000)]
JAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories
Jim Procter [Fri, 20 Jan 2023 17:50:53 +0000 (17:50 +0000)]
JAL-4114 additional warnings when PDBe doesn’t return as many responses as queries made to it when adding in additional metadata
Jim Procter [Fri, 20 Jan 2023 17:49:38 +0000 (17:49 +0000)]
JAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API
Jim Procter [Fri, 20 Jan 2023 17:49:16 +0000 (17:49 +0000)]
JAL-4114 formatting
Jim Procter [Fri, 20 Jan 2023 17:48:04 +0000 (17:48 +0000)]
JAL-4114 updated mock tests and responses for v2.0 api
Ben Soares [Tue, 17 Jan 2023 17:01:45 +0000 (17:01 +0000)]
JAL-3416 No longer needed
Ben Soares [Tue, 17 Jan 2023 10:44:50 +0000 (10:44 +0000)]
Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Mon, 16 Jan 2023 23:21:25 +0000 (23:21 +0000)]
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
Ben Soares [Wed, 11 Jan 2023 13:04:47 +0000 (13:04 +0000)]
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
Ben Soares [Fri, 6 Jan 2023 17:36:42 +0000 (17:36 +0000)]
JAL-3416 More explicit setting of FlatLaf macOS theme
Ben Soares [Fri, 6 Jan 2023 17:09:11 +0000 (17:09 +0000)]
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
Ben Soares [Fri, 6 Jan 2023 16:50:24 +0000 (16:50 +0000)]
JAL-3416 remove a missed panel titlebar icon in TreePanel
Ben Soares [Fri, 6 Jan 2023 16:16:02 +0000 (16:16 +0000)]
JAL-3416 Fix file permissions on bundled macOS JREs
Jim Procter [Wed, 30 Nov 2022 11:51:02 +0000 (11:51 +0000)]
JAL-4102 bump version number
Jim Procter [Wed, 30 Nov 2022 11:34:45 +0000 (11:34 +0000)]
JAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL-2353
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Jim Procter [Sun, 30 Oct 2022 23:19:57 +0000 (23:19 +0000)]
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Ben Soares [Thu, 17 Nov 2022 09:39:38 +0000 (09:39 +0000)]
JAL-4019 Clarification of position on 'X' in help text
Ben Soares [Wed, 16 Nov 2022 11:52:30 +0000 (11:52 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 16 Nov 2022 11:23:00 +0000 (11:23 +0000)]
JAL-3416 make flatlaf default for linux
Ben Soares [Wed, 16 Nov 2022 09:27:49 +0000 (09:27 +0000)]
JAL-4019 finalised a boolean option and tidied some comments
Ben Soares [Mon, 14 Nov 2022 20:38:04 +0000 (20:38 +0000)]
JAL-4019 Put original test back
Ben Soares [Mon, 14 Nov 2022 09:07:32 +0000 (09:07 +0000)]
JAL-4019 Make diagnostic message debug level
Ben Soares [Sun, 13 Nov 2022 20:35:13 +0000 (20:35 +0000)]
JAL-4019 small colour fix for X in the documentation
Ben Soares [Sun, 13 Nov 2022 20:31:51 +0000 (20:31 +0000)]
JAL-4019 attribution to Suzanne
Ben Soares [Sun, 13 Nov 2022 10:51:22 +0000 (10:51 +0000)]
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme
Ben Soares [Sun, 13 Nov 2022 10:50:57 +0000 (10:50 +0000)]
JAL-4019 small but important corrections to array order, and X colour
Ben Soares [Sun, 13 Nov 2022 00:54:09 +0000 (00:54 +0000)]
JAL-4019 Added tests for new Nucleotide sequence detection
Ben Soares [Sun, 13 Nov 2022 00:53:27 +0000 (00:53 +0000)]
JAL-4019 improvement to short sequence nucleotide detection, and some tidying of unused parameters
Ben Soares [Thu, 10 Nov 2022 15:21:08 +0000 (15:21 +0000)]
JAL-4019 Nucleotide Ambiguity Colour Scheme added. Test for nucleotide sequence adapted to recognise nucleotide sequences with (more than 15%) ambiguity codes. Two tests fixed.
Ben Soares [Wed, 9 Nov 2022 18:11:42 +0000 (18:11 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 18:10:20 +0000 (18:10 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 18:10:10 +0000 (18:10 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 17:47:59 +0000 (17:47 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 17:45:21 +0000 (17:45 +0000)]
JAL-3416 Remove all JFrame/JInternalFrame icons (set to null)
Ben Soares [Wed, 9 Nov 2022 15:30:29 +0000 (15:30 +0000)]
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 15:30:09 +0000 (15:30 +0000)]
JAL-1988 JAL-3772 Test for FORCE_QUIT whilst saving a file
Ben Soares [Tue, 8 Nov 2022 17:47:25 +0000 (17:47 +0000)]
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into ben-big-merge
Ben Soares [Tue, 8 Nov 2022 17:47:14 +0000 (17:47 +0000)]
JAL-1988 JAL-3776 Formatting JvOptionPane
Ben Soares [Tue, 8 Nov 2022 17:42:33 +0000 (17:42 +0000)]
JAL-1988 JAL-3772 Tests for various quitting scenarios
Ben Soares [Tue, 8 Nov 2022 17:39:30 +0000 (17:39 +0000)]
JAL-1988 JAL-3772 Fixes highlighted by tests
Ben Soares [Fri, 4 Nov 2022 17:58:36 +0000 (17:58 +0000)]
Merge branch 'merge/JAL-4054+JAL-4064' into ben-big-merge
Ben Soares [Fri, 4 Nov 2022 17:54:14 +0000 (17:54 +0000)]
JAL-3416 Added logoIcon to quit (and potentially other) dialogs
Ben Soares [Fri, 4 Nov 2022 17:53:36 +0000 (17:53 +0000)]
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution of JalviewFileChooser and JvOptionPane
Ben Soares [Fri, 4 Nov 2022 09:58:02 +0000 (09:58 +0000)]
JAL-4064 JAL-4054 Combined install4j10 template with new architectures. Added scheme associations for macOS.
Ben Soares [Wed, 2 Nov 2022 21:36:46 +0000 (21:36 +0000)]
JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.
Ben Soares [Thu, 3 Nov 2022 19:53:56 +0000 (19:53 +0000)]
JAL-3416 File Chooser iconified, JvOptionPanes iconified, other internal frames and dialogs iconified
Jim Procter [Thu, 3 Nov 2022 16:27:10 +0000 (16:27 +0000)]
JAL-3855 JAL-4095 simple picking of ranges adjacent to a clicked region of the pAE that score less than the max pAE observed under the mouse
Ben Soares [Thu, 3 Nov 2022 13:26:20 +0000 (13:26 +0000)]
JAL-1988 JAL-3772 Allow other window closing dialogs to cancel quit handling
Ben Soares [Thu, 3 Nov 2022 13:14:43 +0000 (13:14 +0000)]
JAL-3416 More JInternalFrame icons
Ben Soares [Thu, 3 Nov 2022 09:10:24 +0000 (09:10 +0000)]
JAL-1988 JAL-3772 Tidying of unspecified Callable declarations. Use SwingUtilities.getAncestorOfClass()
Ben Soares [Thu, 3 Nov 2022 08:29:30 +0000 (08:29 +0000)]
JAL-3416 Start to add JInternalFrame icons (to replace default java Duke icon in frame decoration)
Ben Soares [Wed, 2 Nov 2022 14:34:11 +0000 (14:34 +0000)]
JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)
Ben Soares [Tue, 1 Nov 2022 18:29:09 +0000 (18:29 +0000)]
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
Ben Soares [Tue, 1 Nov 2022 16:50:36 +0000 (16:50 +0000)]
JAL-1988 JAL-3772 Change default alignmentviewport saved status and set to true when loaded from file
Ben Soares [Tue, 1 Nov 2022 14:22:21 +0000 (14:22 +0000)]
JAL-4064 tidying build.gradle
Ben Soares [Tue, 1 Nov 2022 14:21:19 +0000 (14:21 +0000)]
JAL-4064 re-added bundled macOS JREs as Filesets, which is the only way to get them in the DMG where we want them
Ben Soares [Tue, 1 Nov 2022 11:17:16 +0000 (11:17 +0000)]
JAL-4064 Cleaned up file sets in install4j template. New media installers for AARCH64 JVMs for macOS and Linux in install4j template. New variables passed to install4j by gradle.
Ben Soares [Tue, 1 Nov 2022 11:16:06 +0000 (11:16 +0000)]
JAL-4064 Download JRE/JDKs from Azul if not os/arch combination not available from Adoptium
Jim Procter [Sun, 30 Oct 2022 23:22:32 +0000 (23:22 +0000)]
JAL-2349 JAL-3855 bizarre resizing exception when resizing protein alignment for a linked CDS protein alignment
git://source.jalview.org / jalview.git / log