Ben Soares [Tue, 7 Nov 2023 15:57:20 +0000 (15:57 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Tue, 7 Nov 2023 08:22:19 +0000 (08:22 +0000)]
JAL-4059 --timeout not needed with --virtual-time-budget
Ben Soares [Fri, 3 Nov 2023 15:37:07 +0000 (15:37 +0000)]
JAL-4239 Using own id generation to avoid Random.nextLong() not implemented in jalviewjs
James Procter [Fri, 3 Nov 2023 07:29:04 +0000 (07:29 +0000)]
JAL-4090 JAL-1551 spotlessApply
James Procter [Fri, 3 Nov 2023 07:28:39 +0000 (07:28 +0000)]
JAL-4090 tweak what’s new
Ben Soares [Thu, 2 Nov 2023 23:25:04 +0000 (23:25 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
James Procter [Thu, 2 Nov 2023 23:23:41 +0000 (23:23 +0000)]
JAL-4090 reported new known issue JAL-4328
Ben Soares [Thu, 2 Nov 2023 23:08:33 +0000 (23:08 +0000)]
JAL-4059 updated _j2sclasslist.txt
Ben Soares [Thu, 2 Nov 2023 23:07:55 +0000 (23:07 +0000)]
JAL-4059 updated test for StringUtils
James Procter [Thu, 2 Nov 2023 23:07:15 +0000 (23:07 +0000)]
JAL-4192 minimal specification of gradle version in building.md
Ben Soares [Thu, 2 Nov 2023 23:06:49 +0000 (23:06 +0000)]
JAL-4059 New namespaced query string parameters.
James Procter [Thu, 2 Nov 2023 23:03:14 +0000 (23:03 +0000)]
JAL-4090 fix up release notes - add notes or JAL-4216 JAL-4169 JAL-4250 JAL-4327 and remove erroneous note for JAL-3776 (targeted for 2.12 release not this one)
James Procter [Thu, 2 Nov 2023 23:00:03 +0000 (23:00 +0000)]
JAL-4169 fix up urls to faq and documentation
Ben Soares [Thu, 2 Nov 2023 22:44:38 +0000 (22:44 +0000)]
JAL-4059 swingjs and Jmol-SwingJS.zip from Jmol github.
Ben Soares [Thu, 2 Nov 2023 22:35:17 +0000 (22:35 +0000)]
JAL-4059 Update closure-compiler.
James Procter [Thu, 2 Nov 2023 21:34:01 +0000 (21:34 +0000)]
JAL-4090 known issue report for JAL-4517
James Procter [Thu, 2 Nov 2023 21:23:32 +0000 (21:23 +0000)]
JAL-4090 release notes for JAL-1713 JAL-2528 and known issue report for JAL-4127
James Procter [Thu, 2 Nov 2023 21:07:41 +0000 (21:07 +0000)]
JAL-4090 JAL-3921 release notes
James Procter [Thu, 2 Nov 2023 21:05:53 +0000 (21:05 +0000)]
Merge branch 'patch/JAL-3921_jmol_session_save' into develop
James Procter [Thu, 2 Nov 2023 21:01:22 +0000 (21:01 +0000)]
Merge branch 'develop' into patch/JAL-3921_jmol_session_save
James Procter [Thu, 2 Nov 2023 19:43:01 +0000 (19:43 +0000)]
JAL-4217 wrap progress bar creation in an invokeLater to avoid setFont deadlock with other ops
James Procter [Thu, 2 Nov 2023 19:14:06 +0000 (19:14 +0000)]
JAL-3088 release notes JAL-4090
James Procter [Thu, 2 Nov 2023 19:13:53 +0000 (19:13 +0000)]
JAL-1551 formatting
James Procter [Thu, 2 Nov 2023 19:01:40 +0000 (19:01 +0000)]
Merge branch 'patch/JAL-3088_finalbracenotinrightplace' into develop
James Procter [Thu, 2 Nov 2023 18:49:04 +0000 (18:49 +0000)]
Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace
Conflicts: - JAL-4250
src/jalview/renderer/AnnotationRenderer.java
James Procter [Thu, 2 Nov 2023 18:43:42 +0000 (18:43 +0000)]
JAL-4090 update release date to friday 3rd November
Release notes for JAL-4252 JAL-3858 JAL-2292 JAL-4288 JAL-4151
James Procter [Thu, 2 Nov 2023 17:24:27 +0000 (17:24 +0000)]
JAL-4090 JAL-4293 JAL-4325 release notes
James Procter [Thu, 2 Nov 2023 17:07:25 +0000 (17:07 +0000)]
JAL-4090 JAL-4218 patch and release notes - don’t include dist in tarball
James Procter [Thu, 2 Nov 2023 16:51:01 +0000 (16:51 +0000)]
JAL-4090 marked JAL-4290 as a knowndefect
James Procter [Thu, 2 Nov 2023 16:40:41 +0000 (16:40 +0000)]
JAL-4090 JAL-4110 JAL-3599 release notes
James Procter [Thu, 2 Nov 2023 16:32:18 +0000 (16:32 +0000)]
JAL-4090 JAL-4310 JAL-4298 JAL-4282 JAL-4223 release notes
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
Ben Soares [Wed, 1 Nov 2023 12:18:15 +0000 (12:18 +0000)]
JAL-4059 Add the newest exampleFile_2_7.jar to the JalviewJS examples (I want the structure\!).
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.
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
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 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
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
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
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
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
git://source.jalview.org / jalview.git / log