Ben Soares [Tue, 31 Oct 2023 12:57:25 +0000 (12:57 +0000)]
JAL-4059 simpler reimplementation of StringUtils.separatorListToArray to avoid unnecessary use of Pattern and regex because of possible jalviewjs Pattern incompatibility
Ben Soares [Tue, 31 Oct 2023 12:54:26 +0000 (12:54 +0000)]
JAL-4059 Actually fix the order of js lib syncs to site.
Ben Soares [Tue, 31 Oct 2023 12:53:43 +0000 (12:53 +0000)]
JAL-4059 upgraded Jmol
Ben Soares [Tue, 31 Oct 2023 11:27:15 +0000 (11:27 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Tue, 31 Oct 2023 10:55:30 +0000 (10:55 +0000)]
JAL-4319 Downgrade shadow(Jar) module to stop triggering clover
Ben Soares [Tue, 31 Oct 2023 09:31:07 +0000 (09:31 +0000)]
JAL-4059 Just keeping these jsmol versions handy. Remove these files before merging to develop.
Ben Soares [Tue, 31 Oct 2023 09:29:44 +0000 (09:29 +0000)]
JAL-4059 If we upgrade Jsmol, do we want to upgrade Jmol to the same version?
Ben Soares [Tue, 31 Oct 2023 09:28:36 +0000 (09:28 +0000)]
JAL-4059 Converting Pattern/Matcher methods that are possibly incompatible with JS regex equivalents
Ben Soares [Tue, 31 Oct 2023 09:26:20 +0000 (09:26 +0000)]
JAL-4059 rename jsmol zip file for clarity
Ben Soares [Tue, 31 Oct 2023 09:25:26 +0000 (09:25 +0000)]
JAL-4059 ensure order of transferring JS lib zip files to site is consistent
Ben Soares [Thu, 26 Oct 2023 16:12:48 +0000 (17:12 +0100)]
JAL-4059 Now using "Google Chrome for Testing" https://googlechromelabs.github.io/chrome-for-testing/ . Adjusted timeouts. Removed window.console.err fix \(no longer needed\).
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
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
Ben Soares [Tue, 24 Oct 2023 21:08:37 +0000 (22:08 +0100)]
JAL-4059 Updated jmoljs and _j2sclasslist.txt
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
Ben Soares [Mon, 23 Oct 2023 16:08:43 +0000 (17:08 +0100)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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
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
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 17:41:03 +0000 (18:41 +0100)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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
git://source.jalview.org / jalview.git / log