Ben Soares [Wed, 29 Nov 2023 16:34:10 +0000 (16:34 +0000)]
JAL-4059 Fixed a test for adding jalview.bin.JalviewJS
Ben Soares [Wed, 29 Nov 2023 16:27:15 +0000 (16:27 +0000)]
Merge branch 'bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS' into bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square
Ben Soares [Wed, 29 Nov 2023 16:21:08 +0000 (16:21 +0000)]
JAL-4344 Some fixes of waiting blocks, and headless mode for export. Control logging of Jmol.
Ben Soares [Mon, 27 Nov 2023 19:53:58 +0000 (19:53 +0000)]
JAL-4238 minor errors fixed for JalviewJS structure colouring
Ben Soares [Fri, 24 Nov 2023 15:40:05 +0000 (15:40 +0000)]
JAL-4059 Allow form-created querystring style values for boolean values
Ben Soares [Thu, 23 Nov 2023 20:07:42 +0000 (20:07 +0000)]
JAL-4059 Storing important thisApplet information in java. Some CSS loading indicators.
Ben Soares [Thu, 23 Nov 2023 17:47:03 +0000 (17:47 +0000)]
JAL-4059 Made jalview.bin.JalviewJS to use new command-line args in querystring. See jalview_bin_JalviewJS-corenamespace.html for example.
Ben Soares [Thu, 23 Nov 2023 15:24:50 +0000 (15:24 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 23 Nov 2023 15:04:52 +0000 (15:04 +0000)]
JAL-4059 rename vars to j2s_ this and that for clarity
Ben Soares [Wed, 22 Nov 2023 20:11:43 +0000 (20:11 +0000)]
JAL-4059 Send bespoke Info hash parameters into jalview.bin.Jalview instance. Set 'splash' div exemplified in jalview_bin_Jalview-namespace.html. Add to core_jalview classlist.
James Procter [Wed, 22 Nov 2023 10:43:58 +0000 (10:43 +0000)]
JAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1
James Procter [Wed, 22 Nov 2023 10:38:41 +0000 (10:38 +0000)]
JAL-4343 release today, update notes for JAL-4348 and what’s new for release
James Procter [Wed, 22 Nov 2023 10:28:18 +0000 (10:28 +0000)]
Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
James Procter [Tue, 21 Nov 2023 18:02:57 +0000 (18:02 +0000)]
JAL-4345 patch and release notes
Ben Soares [Tue, 21 Nov 2023 16:00:25 +0000 (16:00 +0000)]
JAL-4238 an attempt to set JalviewJS desktop overflow to visible (not working)
Ben Soares [Tue, 21 Nov 2023 15:59:09 +0000 (15:59 +0000)]
JAL-4238 Changing visibility of locateInRange(int) bizarrely fixes a PAE viewing problem
Ben Soares [Tue, 21 Nov 2023 15:55:59 +0000 (15:55 +0000)]
JAL-4238 example file added to exmaples
Ben Soares [Tue, 21 Nov 2023 15:54:40 +0000 (15:54 +0000)]
JAL-4238 test files for PAE in jalviewjs
Ben Soares [Tue, 21 Nov 2023 15:54:12 +0000 (15:54 +0000)]
JAL-4059 updated swingjs, Jmol-SwingJS.zip. Insignificantly altered build.gradle.
Ben Soares [Mon, 20 Nov 2023 13:40:53 +0000 (13:40 +0000)]
JAL-4348 Add newer versions of Chimera and ChimeraX to the version whitelist
James Procter [Mon, 20 Nov 2023 11:34:03 +0000 (11:34 +0000)]
JAL-4343 patch for JAL-4347 uniprot non-pos feature parsing
James Procter [Fri, 17 Nov 2023 16:05:27 +0000 (16:05 +0000)]
JAL-4343 release notes for JAL-4340 and JAL-4243
James Procter [Fri, 17 Nov 2023 16:01:01 +0000 (16:01 +0000)]
JAL-4343 bump version
Ben Soares [Thu, 16 Nov 2023 20:03:30 +0000 (20:03 +0000)]
JAL-4243 Updated bio.tools record for 2.11.3.0
Ben Soares [Thu, 16 Nov 2023 11:35:05 +0000 (11:35 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 16 Nov 2023 11:34:50 +0000 (11:34 +0000)]
JAL-4340 Change launch scripts to be xresources to set executable permission bit where needed
Ben Soares [Thu, 16 Nov 2023 10:41:03 +0000 (10:41 +0000)]
JAL-4238 ignore thread.sleeps in jalviewjs. Added a simple PAE example file.
Ben Soares [Thu, 16 Nov 2023 09:56:27 +0000 (09:56 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Thu, 16 Nov 2023 09:56:13 +0000 (09:56 +0000)]
JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference to java.beans.Beans which is not in swingjs. Settle on miglayout-4.2 jars.
James Procter [Wed, 15 Nov 2023 16:16:27 +0000 (16:16 +0000)]
JAL-4090 JAL-4334 patch in release notes
James Procter [Wed, 15 Nov 2023 16:10:02 +0000 (16:10 +0000)]
Merge branch 'bug/JAL-4334_unknownstartenduniprotfeatures' into develop
James Procter [Wed, 15 Nov 2023 16:09:35 +0000 (16:09 +0000)]
Merge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop
Ben Soares [Wed, 15 Nov 2023 15:35:44 +0000 (15:35 +0000)]
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
James Procter [Wed, 15 Nov 2023 15:33:06 +0000 (15:33 +0000)]
JAL-4273 actually pass startSeq etc on to rendering code when rendering for image export
James Procter [Wed, 15 Nov 2023 15:24:40 +0000 (15:24 +0000)]
JAL-4090 fix up release notes new known issues
James Procter [Wed, 15 Nov 2023 15:02:43 +0000 (15:02 +0000)]
JAL-4222 bail if we wait too long for Jmol to save an image
James Procter [Wed, 15 Nov 2023 14:54:31 +0000 (14:54 +0000)]
JAL-4090 blocker patch JAL-3772 tidy up groovy console when closed rather than calling its exit and hanging
James Procter [Wed, 15 Nov 2023 14:31:08 +0000 (14:31 +0000)]
JAL-4090 JAL-4334 position status when start, end or pos is unknown is stored in start_status,end_status,pos_status properties
Ben Soares [Wed, 15 Nov 2023 13:29:19 +0000 (13:29 +0000)]
JAL-3836 Allow .ext.gz files to be recognised in the File Chooser if .ext is a recognised extension.
James Procter [Wed, 15 Nov 2023 11:54:33 +0000 (11:54 +0000)]
JAL-4090 JAL-4338 known defect
James Procter [Wed, 15 Nov 2023 11:48:43 +0000 (11:48 +0000)]
JAL-4090 release 15th November 2023
James Procter [Wed, 15 Nov 2023 11:48:30 +0000 (11:48 +0000)]
JAL-4090 JAL-3858 fix up PAE docs - drop the EBI image example
Ben Soares [Wed, 15 Nov 2023 10:46:34 +0000 (10:46 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
Ben Soares [Wed, 15 Nov 2023 10:46:13 +0000 (10:46 +0000)]
JAL-4059 update intervalstore-1.2-site.zip transpiled with new j2s
Ben Soares [Wed, 15 Nov 2023 10:36:56 +0000 (10:36 +0000)]
Merge branch 'feature/JAL-3576intervalStore_1_2' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Tue, 14 Nov 2023 12:11:34 +0000 (12:11 +0000)]
JAL-4238 examples files for PAE
Ben Soares [Tue, 14 Nov 2023 10:38:29 +0000 (10:38 +0000)]
JAL-4059 added test for <br/> break
Ben Soares [Mon, 13 Nov 2023 23:05:48 +0000 (23:05 +0000)]
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' of https://source.jalview.org/git/jalview into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 22:58:49 +0000 (22:58 +0000)]
JAL-4059 fix other PopupMenuTest
James Procter [Mon, 13 Nov 2023 22:43:54 +0000 (22:43 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 22:42:57 +0000 (22:42 +0000)]
JAL-4059 revert to intervalstore 1.1 for VCFLoader
Ben Soares [Mon, 13 Nov 2023 19:53:17 +0000 (19:53 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 19:51:40 +0000 (19:51 +0000)]
JAL-4059 fixed a test that is now working as expected due to <br/>. Better calculation of long line with HTML tags.
Ben Soares [Mon, 13 Nov 2023 19:03:03 +0000 (19:03 +0000)]
JAL-4059 Fix the tooltip formatting for when, e.g. enclose=false
Ben Soares [Mon, 13 Nov 2023 19:02:34 +0000 (19:02 +0000)]
JAL-4059 redo these tests as TestNG asserts to add message
James Procter [Mon, 13 Nov 2023 18:36:35 +0000 (18:36 +0000)]
JAL-4090 JAL-1551 source license
Ben Soares [Mon, 13 Nov 2023 18:33:36 +0000 (18:33 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
Ben Soares [Mon, 13 Nov 2023 18:29:04 +0000 (18:29 +0000)]
JAL-4059 Updates to miglayout, varna, intervalstore, with re-transpiled javascript libs. Some failing tests
James Procter [Mon, 13 Nov 2023 18:16:46 +0000 (18:16 +0000)]
JAL-4090 relese date 14th Nov 2023
James Procter [Mon, 13 Nov 2023 17:19:45 +0000 (17:19 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
James Procter [Mon, 13 Nov 2023 17:19:11 +0000 (17:19 +0000)]
JAL-4236 don’t look for headers in JalviewJS
James Procter [Mon, 13 Nov 2023 17:18:14 +0000 (17:18 +0000)]
JAL-4336 set preferred dimensions for JTextBox workaround in JalviewJS
James Procter [Mon, 13 Nov 2023 16:17:27 +0000 (16:17 +0000)]
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
James Procter [Mon, 13 Nov 2023 16:11:29 +0000 (16:11 +0000)]
JAL-4090 fix JAL-4236 - just put the name of the class in rather than look it up in a fancy way
James Procter [Mon, 13 Nov 2023 16:05:09 +0000 (16:05 +0000)]
JAL-4331 construct and pass on overview title before asking desktop to open the window…
Ben Soares [Mon, 13 Nov 2023 12:16:48 +0000 (12:16 +0000)]
JAL-4059 updated intervalstore jars to match updating util/jalviewjs/libjs/intervalstore-site.zip
James Procter [Mon, 13 Nov 2023 10:28:37 +0000 (10:28 +0000)]
JAL-4334 failing test using whole of Q29079 accession. Can be trimmed.
Ben Soares [Fri, 10 Nov 2023 22:27:09 +0000 (22:27 +0000)]
JAL-4240 Remove unnecessary whitespace, being rendered in JalviewJS. Split on both <br> <br/>. Should make consistent at source, mea culpa.
Ben Soares [Fri, 10 Nov 2023 21:49:28 +0000 (21:49 +0000)]
JAL-4059 tidyup
Ben Soares [Fri, 10 Nov 2023 21:29:02 +0000 (21:29 +0000)]
JAL-4059 Change long querystringnamespace to namespace as it's being used for more than query string now. Add a spinner image for proof of concept loading indicator.
Ben Soares [Fri, 10 Nov 2023 21:27:54 +0000 (21:27 +0000)]
JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance for retrieval within Java. If namespace exists when desktop appears, remove a div by id ns:jalviewSplash from the HTML page.
Ben Soares [Fri, 10 Nov 2023 21:26:06 +0000 (21:26 +0000)]
JAL-4059 fix not merging html files to the final site from libs
Ben Soares [Fri, 10 Nov 2023 14:50:27 +0000 (14:50 +0000)]
JAL-4059 SwingJS from java2script github repo. It works\!
Ben Soares [Fri, 10 Nov 2023 14:43:29 +0000 (14:43 +0000)]
JAL-4059 Checked through and fixed build tasks
Ben Soares [Thu, 9 Nov 2023 23:44:30 +0000 (23:44 +0000)]
JAL-4059 Fix up Jsmol calls and delete html files from JS zips in build.gradle. Improve closure-compiler core creation with merged swingjs. Change startup file for core example page. Add querystringnamepspace to example pages. Remove unnecessary core lists.
Ben Soares [Thu, 9 Nov 2023 12:31:05 +0000 (12:31 +0000)]
JAL-4090 minor missing word correction to whatsnew
Ben Soares [Tue, 7 Nov 2023 17:02:41 +0000 (17:02 +0000)]
JAL-4059 fix that boolean for non-value query string args
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
git://source.jalview.org / jalview.git / log