James Procter [Thu, 2 Nov 2023 16:29:19 +0000 (16:29 +0000)]
JAL-4090 JAL-4147 documentation for revised sequence associated annotation display and pop-up menu
James Procter [Thu, 2 Nov 2023 16:02:07 +0000 (16:02 +0000)]
JAL-4090 release notes for JAL-4304,JAL-4305 and JAL-3783 and marking JAL-4323 as known issue (groovy scripts colourschemes and file formats)
James Procter [Thu, 2 Nov 2023 12:43:12 +0000 (12:43 +0000)]
JAL-4289 JAL-4253 lower end of group boundary vertical needs to be flush with horizontal
James Procter [Wed, 1 Nov 2023 23:36:05 +0000 (23:36 +0000)]
JAL-4090 JAL-4281 JAL-4311 release notes
James Procter [Wed, 1 Nov 2023 20:47:20 +0000 (20:47 +0000)]
Merge branch 'patch/JAL-4281_idwidthandannotHeight_in_project' into develop
James Procter [Wed, 1 Nov 2023 20:34:23 +0000 (20:34 +0000)]
JAL-4281 patch test so it passes on build server and accepts different legacy idwidth on macs
James Procter [Wed, 1 Nov 2023 19:20:10 +0000 (19:20 +0000)]
JAL-4090 release notes for JAL-4315
James Procter [Wed, 1 Nov 2023 19:16:55 +0000 (19:16 +0000)]
Merge branch 'feature/JAL-4315_fc_draganddrop' into develop
James Procter [Wed, 1 Nov 2023 19:15:15 +0000 (19:15 +0000)]
JAL-4090 JAL-4317 release notes
James Procter [Wed, 1 Nov 2023 19:12:43 +0000 (19:12 +0000)]
Merge branch 'patch/JAL-4317_enablefeaturewhenadjustingstyle' into develop
James Procter [Wed, 1 Nov 2023 19:08:58 +0000 (19:08 +0000)]
Merge branch 'develop' into patch/JAL-4281_idwidthandannotHeight_in_project
Conflicts:
src/jalview/gui/AlignmentPanel.java
and regenerated schema binding
James Procter [Wed, 1 Nov 2023 16:40:55 +0000 (16:40 +0000)]
Merge branch 'patch/JAL-4260_fix_up_select_via_ruler_in_wrapped' into develop
James Procter [Wed, 1 Nov 2023 16:23:30 +0000 (16:23 +0000)]
JAL-4260 encapsulate logic for resolving nearest column and do better using it in wrapped mode for drags/clicks/popups on alignment
James Procter [Wed, 1 Nov 2023 16:18:36 +0000 (16:18 +0000)]
JAL-4260 reinstate annotation auto-id-width for wrapped view in headless mode (JAL-244) whilst still right-aligning labels
James Procter [Tue, 31 Oct 2023 13:22:30 +0000 (13:22 +0000)]
JAL-4260 fix up click/drags on ruler area in wrapped mode.
James Procter [Tue, 31 Oct 2023 12:33:03 +0000 (12:33 +0000)]
JAL-4260 right align the annotation labels regardless of width in wrapped mode.
James Procter [Tue, 31 Oct 2023 12:01:03 +0000 (12:01 +0000)]
JAL-244 noticed NPE exception was possible when visibility was adjusted in wrapped mode
James Procter [Tue, 31 Oct 2023 12:00:38 +0000 (12:00 +0000)]
JAL-244 knock on - make sure alignPanel is laid out properly after adjusting height. Probably a better
Ben Soares [Tue, 31 Oct 2023 10:55:30 +0000 (10:55 +0000)]
JAL-4319 Downgrade shadow(Jar) module to stop triggering clover
James Procter [Mon, 30 Oct 2023 12:14:20 +0000 (12:14 +0000)]
JAL-4317 enable display of feature when showing its colour or filter settings dialog, and restore original visibility if cancel is pressed.
James Procter [Mon, 30 Oct 2023 11:24:22 +0000 (11:24 +0000)]
Handle feature settings files loaded via drag and drop or import
James Procter [Mon, 30 Oct 2023 11:24:07 +0000 (11:24 +0000)]
JAL-4315 allow feature settings to be loaded from a file or input stream without the dialog being open
James Procter [Mon, 30 Oct 2023 11:23:05 +0000 (11:23 +0000)]
JAL-4315 identify feature settings file from its xml schema header
James Procter [Thu, 26 Oct 2023 11:44:31 +0000 (12:44 +0100)]
Merge branch 'patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources' into develop
James Procter [Thu, 26 Oct 2023 11:43:48 +0000 (12:43 +0100)]
Merge branch 'bug/JAL-4313_cme_in_tests' into patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources
Ben Soares [Wed, 25 Oct 2023 10:28:15 +0000 (11:28 +0100)]
Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint
James Procter [Wed, 25 Oct 2023 10:17:06 +0000 (11:17 +0100)]
JAL-4312 defend against ConcurrentModificationException
James Procter [Wed, 25 Oct 2023 10:16:01 +0000 (11:16 +0100)]
JAL-4312 call AlignFrame.setAnnotationsVisibility on AWT thread from Commands
James Procter [Mon, 23 Oct 2023 17:31:06 +0000 (18:31 +0100)]
JAL-4311 fix ranking so models with like scores are sorted in their own group - AlphaFold 2 now selected as highest scoring model (58) over levyLab (50)
James Procter [Mon, 23 Oct 2023 17:29:33 +0000 (18:29 +0100)]
JAL-4311 failing test case for 3d-beacons epas1_human including levyLab alphaFold2 pLDDT scored result
James Procter [Mon, 23 Oct 2023 13:03:45 +0000 (14:03 +0100)]
JAL-4310 let the user know when model pages are not available for a 3d-beacons structure (and log URLs when they are opened).
James Procter [Mon, 23 Oct 2023 11:14:13 +0000 (12:14 +0100)]
Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews
James Procter [Mon, 23 Oct 2023 11:06:19 +0000 (12:06 +0100)]
JAL-4090 release weds 25th Oct 23 - JAL-4308 release notes
James Procter [Mon, 23 Oct 2023 11:02:42 +0000 (12:02 +0100)]
Merge branch 'feature/JAL-4307_hetatm_showhide' into develop
James Procter [Mon, 23 Oct 2023 11:02:14 +0000 (12:02 +0100)]
Merge branch 'improvement/JAL-4308_smalleridtooltip' into develop
James Procter [Mon, 23 Oct 2023 08:25:34 +0000 (09:25 +0100)]
JAL-4090 defensive check for featureSettings redraws when feature filter attrbute is null (noticed whilst testing)
James Procter [Mon, 23 Oct 2023 08:24:43 +0000 (09:24 +0100)]
JAL-4308 reduce number of refs to 5, always have canonical reference first.
James Procter [Sun, 22 Oct 2023 11:31:19 +0000 (12:31 +0100)]
JAL-4153 avoid use of invokeAndWait, increase wait time and add timeout for the cache update test
James Procter [Sun, 22 Oct 2023 11:02:56 +0000 (12:02 +0100)]
JAL-1551 errant tab and import
James Procter [Sun, 22 Oct 2023 10:59:21 +0000 (11:59 +0100)]
Merge branch 'patch/JAL-4298_synchronize_consoledoc' into develop
Conflicts:
src/jalview/gui/Console.java
still needs some tidying up
James Procter [Sun, 22 Oct 2023 10:53:42 +0000 (11:53 +0100)]
Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into develop
James Procter [Sun, 22 Oct 2023 10:53:04 +0000 (11:53 +0100)]
Merge branch 'jims/bug/JAL-4298_java_console_causing_hang_at_startup' into develop
James Procter [Sun, 22 Oct 2023 10:44:08 +0000 (11:44 +0100)]
Merge branch 'develop' into improvement/JAL-3783_upgrade_to_groovy-4
James Procter [Sun, 22 Oct 2023 10:42:47 +0000 (11:42 +0100)]
Merge branch 'jims/bug/JAL-4298_java_console_causing_hang_at_startup' into develop
James Procter [Sun, 22 Oct 2023 10:42:24 +0000 (11:42 +0100)]
JAL-4090 update docs for changed gradle -P options for testng
James Procter [Sat, 21 Oct 2023 12:25:36 +0000 (13:25 +0100)]
JAL-1332 JAL-4298 JAL-3772 rejig the quit handler so we have a JVM-exit safe way of closing Jalview and all its merry console threads for test suite and when used as plugin
James Procter [Sat, 21 Oct 2023 11:54:06 +0000 (12:54 +0100)]
Merge branch 'patch/JAL-4110_stdout_for_tests' into jims/bug/JAL-4298_java_console_causing_hang_at_startup
James Procter [Sat, 21 Oct 2023 11:48:10 +0000 (12:48 +0100)]
JAL-4110 allow configuration of stdout/err test output via -Ptest_output=1 and update building.md
James Procter [Sat, 21 Oct 2023 11:30:42 +0000 (12:30 +0100)]
Merge branch 'develop' into patch/JAL-4110_stdout_for_tests
Ben Soares [Fri, 20 Oct 2023 17:17:04 +0000 (18:17 +0100)]
JAL-4298 Update help docs to reflect Groovy changes
James Procter [Fri, 20 Oct 2023 16:00:05 +0000 (17:00 +0100)]
Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into jims/bug/JAL-4298_java_console_causing_hang_at_startup
Ben Soares [Fri, 20 Oct 2023 15:57:29 +0000 (16:57 +0100)]
JAL-4298 Remove a stray return in the processGroovyScript method. Mildy improve a groovy example. Ensure consistent setting of groovy variables with JalviewObjectI fields. Update the currentAlFrame when run from Calculate menu.
James Procter [Fri, 20 Oct 2023 15:35:27 +0000 (16:35 +0100)]
JAL-4298 reuse existing log level preference method
James Procter [Fri, 20 Oct 2023 13:17:18 +0000 (14:17 +0100)]
JAL-4307 also report molecule name in tooltip for show/hide HETATM
Ben Soares [Fri, 20 Oct 2023 13:16:50 +0000 (14:16 +0100)]
JAL-4298 another implicated line
James Procter [Fri, 20 Oct 2023 13:02:53 +0000 (14:02 +0100)]
Merge branch 'feature/JAL-4307_hetatm_showhide' into develop
James Procter [Fri, 20 Oct 2023 13:02:26 +0000 (14:02 +0100)]
Merge branch 'patch/JAL-4298_synchronize_consoledoc' into develop
James Procter [Fri, 20 Oct 2023 12:56:01 +0000 (13:56 +0100)]
JAL-4307 some models return null for hetatm list
James Procter [Fri, 20 Oct 2023 11:55:57 +0000 (12:55 +0100)]
JAL-4298 try much harder to avoid modifying console gui anywhere outside swing worker threads
Ben Soares [Thu, 19 Oct 2023 20:06:00 +0000 (21:06 +0100)]
Merge branch 'patch/JAL-4298_synchronize_consoledoc' into bug/JAL-4298_java_console_causing_hang_at_startup
Ben Soares [Thu, 19 Oct 2023 19:40:14 +0000 (20:40 +0100)]
JAL-629 Fix --nodebug turning off debug mode from properties
Ben Soares [Thu, 19 Oct 2023 17:35:06 +0000 (18:35 +0100)]
JAL-4298 comment markers
Ben Soares [Thu, 19 Oct 2023 17:34:39 +0000 (18:34 +0100)]
Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into bug/JAL-4298_java_console_causing_hang_at_startup
James Procter [Thu, 19 Oct 2023 17:33:57 +0000 (18:33 +0100)]
JAL-4298 avoid deadlock waiting to update doc when doc is being used by gui thread waiting for thread to update the doc
Ben Soares [Thu, 19 Oct 2023 17:33:56 +0000 (18:33 +0100)]
JAL-4305 Isolate and unify the Jalview object from all the gubbins in jalview.bin.Jalview or jalview.gui.Desktop with a JalviewObject interface. Adjust/fix some example groovy scripts.
James Procter [Thu, 19 Oct 2023 17:27:33 +0000 (18:27 +0100)]
JAL-4307 View->Ligands submenu, implementation for Jmol and documentation
Ben Soares [Thu, 19 Oct 2023 10:33:02 +0000 (11:33 +0100)]
Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into bug/JAL-4298_java_console_causing_hang_at_startup
Ben Soares [Wed, 18 Oct 2023 13:57:27 +0000 (14:57 +0100)]
JAL-629 Run non-alignframe linked groovy scripts. Use multiple specified groovy scripts. Don't add a warning for image and output if not asked for
Ben Soares [Wed, 18 Oct 2023 11:28:11 +0000 (12:28 +0100)]
JAL-4262 Fix the nonblockingdialog so that Jalview desktop isn't left set to alwaysOnTop
James Procter [Wed, 18 Oct 2023 09:39:50 +0000 (10:39 +0100)]
Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
James Procter [Wed, 18 Oct 2023 09:39:13 +0000 (10:39 +0100)]
JAL-4090 JAL-4303 as known defect
James Procter [Tue, 17 Oct 2023 16:30:08 +0000 (17:30 +0100)]
Merge branch 'bug/JAL-4302_treeheightrendererbroke' into develop
James Procter [Tue, 17 Oct 2023 16:29:49 +0000 (17:29 +0100)]
Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
James Procter [Tue, 17 Oct 2023 16:27:14 +0000 (17:27 +0100)]
JAL-4090 JAL-4302 marked as known defect
James Procter [Tue, 17 Oct 2023 16:26:56 +0000 (17:26 +0100)]
JAL-4134 TODO printNode update for columnTrees
James Procter [Tue, 17 Oct 2023 16:25:28 +0000 (17:25 +0100)]
JAL-4134 JAL-4302 remove unnecessary casts
James Procter [Tue, 17 Oct 2023 15:11:15 +0000 (16:11 +0100)]
JAL-4090 JAL-4089 document use of selected columns for superposition, and add links to Pymol for individual viewer capabilities
James Procter [Tue, 17 Oct 2023 10:40:18 +0000 (11:40 +0100)]
Merge branch 'bug/JAL-4089_selectedcolshiddenregions' into develop
James Procter [Tue, 17 Oct 2023 09:53:13 +0000 (10:53 +0100)]
JAL-4089 selected columns are reported in absolute column numbers, not visible columns
James Procter [Mon, 16 Oct 2023 13:41:28 +0000 (14:41 +0100)]
Merge branch 'bug/JAL-4295_hangjmolandmouseovers' into develop
Ben Soares [Fri, 13 Oct 2023 17:21:04 +0000 (18:21 +0100)]
JAL-3783 Updated groovy jars. Requires javaparser-core library to run too
James Procter [Fri, 13 Oct 2023 16:45:17 +0000 (17:45 +0100)]
JAL-4295 concatenate all mouseover highlights into one call to jmolScript - so we don’t need to invoke scriptWait and risk blocking UI
Ben Soares [Fri, 13 Oct 2023 15:09:11 +0000 (16:09 +0100)]
JAL-3783 Updated build process to allow multiple groovy-* jars to work within the shadowJar. Updated groovy jars to 2.5.23.
Ben Soares [Thu, 12 Oct 2023 15:01:12 +0000 (16:01 +0100)]
JAL-3772 Fix the logic of prompt to save URL loaded alignments preference
Ben Soares [Thu, 12 Oct 2023 09:54:02 +0000 (10:54 +0100)]
JAL-629 null check and neatening code
Ben Soares [Wed, 11 Oct 2023 22:11:46 +0000 (23:11 +0100)]
JAL-629 correct a timeout. Correct passing html flag.
Ben Soares [Wed, 11 Oct 2023 16:55:09 +0000 (17:55 +0100)]
JAL-629 Add a timeout to modal dialogs for command line warning
Ben Soares [Wed, 11 Oct 2023 12:35:26 +0000 (13:35 +0100)]
JAL-629 Change getdown not to add -open argument
Ben Soares [Wed, 11 Oct 2023 12:14:30 +0000 (13:14 +0100)]
JAL-629 Remove argfiles from the hashset of used argfiles once it has been used. More like (though not) a stack of argfiles
Ben Soares [Wed, 11 Oct 2023 11:12:28 +0000 (12:12 +0100)]
JAL-3772 Preference to NOT prompt to save remotely loaded alignments
Ben Soares [Wed, 11 Oct 2023 11:11:09 +0000 (12:11 +0100)]
JAL-4298 Added diagnostics and minor dimension changes to Java Console. Added a --javaconsole Arg.
Ben Soares [Thu, 5 Oct 2023 14:18:07 +0000 (15:18 +0100)]
JAL-4298 Fixed initial log level to see .jalview_properties setting. Moved Java Console startup to before Desktop startup.
James Procter [Thu, 5 Oct 2023 07:07:25 +0000 (08:07 +0100)]
Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
James Procter [Thu, 5 Oct 2023 07:04:49 +0000 (08:04 +0100)]
JAL-4090 JAL-3858 paedocs
Ben Soares [Tue, 3 Oct 2023 17:31:08 +0000 (18:31 +0100)]
JAL-4001 Only use acquireDialogQueue and releaseDialogQueue when SplashScreen is transient. Fixes macOS About dialog
Ben Soares [Tue, 3 Oct 2023 13:18:08 +0000 (14:18 +0100)]
Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint
James Procter [Sat, 30 Sep 2023 14:04:11 +0000 (15:04 +0100)]
JAL-4217 move CommandsTest to testTask3 involving structure image export and random NPE in commandsOpen test on osx
James Procter [Tue, 3 Oct 2023 12:19:02 +0000 (13:19 +0100)]
Merge branch 'patch/JAL-4062_sort_and_merge_contiguousregions' into develop
James Procter [Tue, 3 Oct 2023 12:18:02 +0000 (13:18 +0100)]
JAL-4090 fix up release notes and what’s new (inc removing 2.11.2 cruft from template)
James Procter [Tue, 3 Oct 2023 11:12:37 +0000 (12:12 +0100)]
Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0
git://source.jalview.org / jalview.git / log