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
James Procter [Thu, 19 Oct 2023 13:03:37 +0000 (14:03 +0100)]
Merge branch 'develop' into releases/Release_2_11_3_Branch
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 07:07:55 +0000 (08:07 +0100)]
Merge branch 'develop' into releases/Release_2_11_3_Branch
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 07:05:32 +0000 (08:05 +0100)]
Merge branch 'develop' into releases/Release_2_11_3_Branch
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
James Procter [Tue, 3 Oct 2023 10:45:55 +0000 (11:45 +0100)]
JAL-4061 JAL-4062 update find box image and docs in help
James Procter [Tue, 3 Oct 2023 06:57:40 +0000 (07:57 +0100)]
Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0
James Procter [Tue, 3 Oct 2023 06:57:14 +0000 (07:57 +0100)]
Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig' into develop
James Procter [Tue, 3 Oct 2023 06:56:37 +0000 (07:56 +0100)]
JAL-4090 tweak pae doc
jprocter [Mon, 2 Oct 2023 19:33:59 +0000 (20:33 +0100)]
JAL-4090 more JAL-3858 docs
Ben Soares [Mon, 2 Oct 2023 19:15:30 +0000 (20:15 +0100)]
JAL-4289 In fastPaint(), don't render one more than necessary sequence when scrolling up or down. Adjust transY for this one fewer sequence render. Draw group lower boundary within the sequence boundary -- makes things much simple, and also is visible on bottom row. Don't use -1 for lower boundary y-value.
jprocter [Mon, 2 Oct 2023 14:36:53 +0000 (15:36 +0100)]
Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0
James Procter [Sun, 1 Oct 2023 19:29:49 +0000 (20:29 +0100)]
JAL-4090 JAL-3855 updated figure and doc.. a little
James Procter [Sun, 1 Oct 2023 19:06:28 +0000 (20:06 +0100)]
JAL-244 ensure background is completely filled with white
James Procter [Sun, 1 Oct 2023 16:42:42 +0000 (17:42 +0100)]
JAL-4090 JAL-4291 disable failing test and note as new knowndefect
James Procter [Sun, 1 Oct 2023 16:06:47 +0000 (17:06 +0100)]
JAL-244 attempt to fix broken test - still needs to be fixed!
James Procter [Sun, 1 Oct 2023 16:06:27 +0000 (17:06 +0100)]
JAL-244 export image with full width IDs regardless of UI
James Procter [Sun, 1 Oct 2023 13:03:57 +0000 (14:03 +0100)]
JAL-244 JAL-4091 allow calculation of label id width off screen including sequence ids for sequence associated annotation
James Procter [Sun, 1 Oct 2023 12:26:54 +0000 (13:26 +0100)]
JAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculateIdWidth_withMaxWidth test for new annotation label marks
James Procter [Sun, 1 Oct 2023 12:24:08 +0000 (13:24 +0100)]
JAL-4160 update args used in test suite for new CLI framework
James Procter [Fri, 29 Sep 2023 17:25:10 +0000 (18:25 +0100)]
Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig' into develop
James Procter [Fri, 29 Sep 2023 17:23:06 +0000 (18:23 +0100)]
JAL-629 JAL-4265 JAL-4286 report the filename for the exported structure image like we do for exported alignment images
James Procter [Fri, 29 Sep 2023 16:59:02 +0000 (17:59 +0100)]
JAL-4090 JAL-629 FER1+SPIOL -> FER1_SPIOL in command line example
James Procter [Fri, 29 Sep 2023 16:57:41 +0000 (17:57 +0100)]
JAL-244 JAL-4090 use current IdWidth when exporting unwrapped alignment image.
James Procter [Fri, 29 Sep 2023 12:46:36 +0000 (13:46 +0100)]
JAL-4090 figures in paematrix doc
James Procter [Fri, 29 Sep 2023 12:46:36 +0000 (13:46 +0100)]
JAL-4288 fix up gradle generated getdown launch jvl for bamboo channel builds
James Procter [Fri, 29 Sep 2023 11:59:53 +0000 (12:59 +0100)]
JAL-4090 fix url to new cli docs
James Procter [Fri, 29 Sep 2023 11:09:05 +0000 (12:09 +0100)]
JAL-4153 move JvCacheableInputBoxTest to testTask2
James Procter [Fri, 29 Sep 2023 07:28:03 +0000 (08:28 +0100)]
JAL-3858 fix check annotation row and column positioning in case we have been called during an annotation height change operation
James Procter [Thu, 28 Sep 2023 17:06:30 +0000 (18:06 +0100)]
JAL-4090 JAL-3855 figure showing PAEs for epas1 homolog structures
James Procter [Thu, 28 Sep 2023 17:05:17 +0000 (18:05 +0100)]
JAL-1556 JAL-4090 colour by annotation options on annotation label popup menu
James Procter [Thu, 28 Sep 2023 16:59:17 +0000 (17:59 +0100)]
JAL-3858 don’t divide if we only had one value to count
git://source.jalview.org / jalview.git / log