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 [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 [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 [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, 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
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
Ben Soares [Sat, 29 Oct 2022 18:38:23 +0000 (19:38 +0100)]
JAL-1988 JAL-3772 removed a debugging log line
Ben Soares [Fri, 28 Oct 2022 23:16:20 +0000 (00:16 +0100)]
JAL-1988 JAL-3772 Removed 'Wait' button from waitDialog, no iterations for GUI. Added bulletpoint to files saving list. Added use of passed in button objects to modal JvOptionPane, so buttons can be controlled (e.g. setEnabled, setVisible) outside of JvOptionPane.
Ben Soares [Fri, 28 Oct 2022 11:48:56 +0000 (12:48 +0100)]
JAL-1988 JAL-3772 Fixed wait between waitDialog appearances, ensuring all files saving will quit straight away. Goodbye message to user if waitDialog still visible.
Ben Soares [Thu, 27 Oct 2022 17:51:22 +0000 (18:51 +0100)]
JAL-1988 Allow generic Container object in JvOptionPane showDialog. Fix dynamically saving files in the wait for save dialog
Ben Soares [Thu, 27 Oct 2022 15:20:14 +0000 (16:20 +0100)]
Merge branch 'develop' into bug/JAL-1988_JAL-3772_improved_quit_handling
Ben Soares [Wed, 26 Oct 2022 08:13:24 +0000 (09:13 +0100)]
JAL-3416 (and others) increasing number of STDERR lines used for jalview.bin.CommandLineOperations tests for increased robustness
Ben Soares [Tue, 25 Oct 2022 22:03:17 +0000 (23:03 +0100)]
JAL-3772 silly NPE error fixed
Ben Soares [Tue, 25 Oct 2022 12:07:19 +0000 (13:07 +0100)]
JAL-3416 Making FlatLaF default for macs due to a problem with VAqua not starting on macs
Ben Soares [Mon, 24 Oct 2022 17:08:00 +0000 (18:08 +0100)]
JAL-1988 JAL-3772 wait timer working first time but blocking desktop gui updates
Ben Soares [Mon, 24 Oct 2022 14:41:18 +0000 (15:41 +0100)]
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsaved changes and saving files. Wait timer not working. Wait dialog update/close on files saved not working.
Jim Procter [Tue, 11 Oct 2022 15:54:16 +0000 (16:54 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:53:25 +0000 (16:53 +0100)]
JAL-4065 final fix for 2.11.2.5 - 5pm BST release
Jim Procter [Tue, 11 Oct 2022 15:16:37 +0000 (16:16 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:16:01 +0000 (16:16 +0100)]
JAL-4065 revised to avoid a visit from the apostrophe police
Jim Procter [Tue, 11 Oct 2022 14:44:01 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:43:36 +0000 (15:43 +0100)]
JAL-4073 update tests
Jim Procter [Tue, 11 Oct 2022 14:28:03 +0000 (15:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:26:59 +0000 (15:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 11 Oct 2022 14:24:32 +0000 (15:24 +0100)]
JAL-4073 fix PEBCAK failure
Ben Soares [Tue, 11 Oct 2022 13:43:10 +0000 (14:43 +0100)]
JAL-4014 Changed gecos display names to match labels in help
Jim Procter [Tue, 11 Oct 2022 12:10:56 +0000 (13:10 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 12:10:29 +0000 (13:10 +0100)]
JAL-4065 revised whatsNew to make sense !
Jim Procter [Tue, 11 Oct 2022 10:32:29 +0000 (11:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 10:32:05 +0000 (11:32 +0100)]
JAL-4065 release 2.11.2.5 date is 11th Oct
Jim Procter [Fri, 7 Oct 2022 14:53:01 +0000 (15:53 +0100)]
JAL-4065 update citations for Pfam and Rfam and added the Interpro citation
Jim Procter [Fri, 7 Oct 2022 14:19:54 +0000 (15:19 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:19:21 +0000 (15:19 +0100)]
JAL-4065 2.11.2.5 release version bump
Jim Procter [Fri, 7 Oct 2022 14:14:42 +0000 (15:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:14:08 +0000 (15:14 +0100)]
JAL-4065 release notes and updated release date for 2.11.2.5
Jim Procter [Thu, 6 Oct 2022 17:14:19 +0000 (18:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 17:13:09 +0000 (18:13 +0100)]
stable url for PFAM retrieval via interpro api :) JAL-4073
Jim Procter [Thu, 6 Oct 2022 11:36:33 +0000 (12:36 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 11:31:14 +0000 (12:31 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 11:22:09 +0000 (12:22 +0100)]
JAL-4065 release notes for JAL-4073 JAL-4074
Jim Procter [Thu, 6 Oct 2022 11:21:28 +0000 (12:21 +0100)]
JAL-4073 Pfam retrieval now works via a template including $PFAMID$ and $ALTYPE$ (full, seed, etc). Also changed name of PFAM_BASEURL_KEY to PFAM_INTERPRO_URL_TEMPLATE to avoid misconfiguration
Jim Procter [Thu, 6 Oct 2022 11:19:13 +0000 (12:19 +0100)]
Patch for JAL-4074 - any content ending in ‘gzip’ recognised as a gzipped stream to decompress
Ben Soares [Thu, 29 Sep 2022 14:55:25 +0000 (15:55 +0100)]
Merge branch 'develop' into bug/JAL-1988_JAL-3772_improved_quit_handling
Ben Soares [Mon, 26 Sep 2022 19:17:14 +0000 (20:17 +0100)]
JAL-1988 JAL-3772 linked undostack to saved changes flags. No confirmation if all viewports have been saved individually
Ben Soares [Mon, 26 Sep 2022 19:16:23 +0000 (20:16 +0100)]
JAL-1988 better wording for quit dialog
Ben Soares [Fri, 23 Sep 2022 17:34:12 +0000 (18:34 +0100)]
JAL-1988 JAL-3772 Quit confirmation dialog boxes with saving files check and wait
Ben Soares [Fri, 23 Sep 2022 17:33:36 +0000 (18:33 +0100)]
JAL-3676 extra information about jalview_properties file being used in Java Console
Ben Soares [Fri, 23 Sep 2022 17:28:14 +0000 (18:28 +0100)]
JAL-1988 property based fake delay whilst saving project file
git://source.jalview.org / jalview.git / log