Ben Soares [Thu, 26 Jan 2023 11:10:04 +0000 (11:10 +0000)]
JAL-629 helper eclipse CLI run
Ben Soares [Thu, 26 Jan 2023 11:09:47 +0000 (11:09 +0000)]
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
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 08:18:39 +0000 (08:18 +0000)]
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
James Procter [Tue, 24 Jan 2023 07:51:00 +0000 (07:51 +0000)]
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
James Procter [Tue, 24 Jan 2023 07:49:39 +0000 (07:49 +0000)]
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
James Procter [Tue, 24 Jan 2023 07:48:54 +0000 (07:48 +0000)]
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
James Procter [Tue, 24 Jan 2023 07:48:07 +0000 (07:48 +0000)]
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
James Procter [Tue, 24 Jan 2023 07:46:53 +0000 (07:46 +0000)]
JAL-629 don’t complain for Unary args
James Procter [Tue, 24 Jan 2023 07:46:34 +0000 (07:46 +0000)]
JAL-629 labelled breaks are frowned upon by everyone
James Procter [Tue, 24 Jan 2023 06:27:46 +0000 (06:27 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
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
Ben Soares [Mon, 23 Jan 2023 23:57:06 +0000 (23:57 +0000)]
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
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 [Wed, 18 Jan 2023 15:52:10 +0000 (15:52 +0000)]
JAL-629 make sequence id key 'seqid'
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 [Wed, 11 Jan 2023 11:55:53 +0000 (11:55 +0000)]
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
Ben Soares [Wed, 11 Jan 2023 11:55:14 +0000 (11:55 +0000)]
JAL-629 refactoring TFType. Remove i18n identification of annotation.
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
Ben Soares [Fri, 6 Jan 2023 13:53:44 +0000 (13:53 +0000)]
JAL-4111 Added commit and date text to splashscreens of all channels
Ben Soares [Thu, 5 Jan 2023 20:18:57 +0000 (20:18 +0000)]
JAL-4111 improvement to convert -draw argument
Ben Soares [Thu, 5 Jan 2023 20:07:00 +0000 (20:07 +0000)]
JAL-4111 Use ImageMagick to add commit and build time text to DMG and getdown splash images
Ben Soares [Thu, 5 Jan 2023 13:38:00 +0000 (13:38 +0000)]
JAL-4111 Fixed channel.props to allow replacement of __SUFFIX__. Generic background images with 'branch version' for getdown and DMG
Benedict Soares (Staff) [Thu, 5 Jan 2023 00:19:00 +0000 (00:19 +0000)]
JAL-4111 fixed DMG background image for generic Develop-X.XX app name, and new DS_Store
Ben Soares [Thu, 22 Dec 2022 00:51:44 +0000 (00:51 +0000)]
JAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase. Add a utils/channel/develop-2.12 dir with new getdown images.
Ben Soares [Mon, 19 Dec 2022 18:18:40 +0000 (18:18 +0000)]
JAL-629 Add image output and quit
Ben Soares [Thu, 15 Dec 2022 14:25:40 +0000 (14:25 +0000)]
JAL-629 move SubId to more logical place. Attempt removal of annotations in a better way (commented out).
Ben Soares [Wed, 14 Dec 2022 10:45:27 +0000 (10:45 +0000)]
JAL-629 Open Structure Viewer from cmdline
Ben Soares [Fri, 9 Dec 2022 13:05:10 +0000 (13:05 +0000)]
JAL-629 null check, fixed tests!
Ben Soares [Thu, 8 Dec 2022 17:29:38 +0000 (17:29 +0000)]
JAL-629 fix opening files
Ben Soares [Thu, 8 Dec 2022 17:08:49 +0000 (17:08 +0000)]
JAL-629 stray code deleted
Ben Soares [Thu, 8 Dec 2022 14:19:23 +0000 (14:19 +0000)]
JAL-629 Allow attachment of pAE file to a particular sequence
Ben Soares [Mon, 5 Dec 2022 09:32:24 +0000 (09:32 +0000)]
JAL-629 implementation of --tempfac options
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, 23 Nov 2022 17:19:43 +0000 (17:19 +0000)]
JAL-629 Doing things with the command line arguments
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)
git://source.jalview.org / jalview.git / log