Ben Soares [Fri, 18 Mar 2022 16:55:17 +0000 (16:55 +0000)]
JAL-3978 New tasks to build archive 'old' dir with appropriate getdown resources, JVL file and digest
Ben Soares [Wed, 16 Mar 2022 17:29:56 +0000 (17:29 +0000)]
JAL-3978 task stub and getdown splash screens
Jalview Development Admin [Thu, 10 Mar 2022 01:29:53 +0000 (01:29 +0000)]
JAL-3746 bump release date to 10th March - after UoD network maintenance
Jalview Development Admin [Thu, 10 Mar 2022 01:28:58 +0000 (01:28 +0000)]
JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(
Jalview Development Admin [Wed, 9 Mar 2022 16:51:38 +0000 (16:51 +0000)]
JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert
Jim Procter [Wed, 9 Mar 2022 10:11:56 +0000 (10:11 +0000)]
JAL-3746 JAL-3841 fix README typo
Jim Procter [Wed, 9 Mar 2022 08:09:45 +0000 (08:09 +0000)]
JAL-3746 more docs tweaking and release notes
Jim Procter [Wed, 9 Mar 2022 07:59:03 +0000 (07:59 +0000)]
Merge branch 'spike/try_spotless_JAL-3438' into develop
Jim Procter [Tue, 8 Mar 2022 21:58:37 +0000 (21:58 +0000)]
JAL-3746 apply copyright to tests
Jim Procter [Tue, 8 Mar 2022 21:56:25 +0000 (21:56 +0000)]
JAL-3746 apply copyright to source
Jim Procter [Tue, 8 Mar 2022 21:30:05 +0000 (21:30 +0000)]
JAL-3438 spotless for 2.11.2.0
Jim Procter [Tue, 8 Mar 2022 20:39:47 +0000 (20:39 +0000)]
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes
Jim Procter [Tue, 8 Mar 2022 18:53:09 +0000 (18:53 +0000)]
JAL-3108 updated Ensembl client and model species names
Jim Procter [Tue, 8 Mar 2022 18:18:56 +0000 (18:18 +0000)]
JAL-3746 new release date for 2.11.2
Jim Procter [Tue, 8 Mar 2022 18:13:27 +0000 (18:13 +0000)]
JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes
Jim Procter [Tue, 8 Mar 2022 17:41:04 +0000 (17:41 +0000)]
Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop
Ben Soares [Tue, 8 Mar 2022 12:26:28 +0000 (12:26 +0000)]
JAL-3103 updated help doc to remove default browser choice
Ben Soares [Tue, 8 Mar 2022 12:14:45 +0000 (12:14 +0000)]
JAL-3103 Removed code and unused widgets for defaultBrowser
Ben Soares [Tue, 8 Mar 2022 12:03:11 +0000 (12:03 +0000)]
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods
Ben Soares [Tue, 8 Mar 2022 00:39:04 +0000 (00:39 +0000)]
JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS
Ben Soares [Tue, 8 Mar 2022 00:34:55 +0000 (00:34 +0000)]
JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2
Jim Procter [Mon, 7 Mar 2022 20:07:36 +0000 (20:07 +0000)]
JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633 and report JAL-3764 as a known issue
Jim Procter [Mon, 7 Mar 2022 17:52:44 +0000 (17:52 +0000)]
JAL-3685 - two single quotes when replacements are present in i18n message
Ben Soares [Mon, 7 Mar 2022 17:51:47 +0000 (17:51 +0000)]
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
Jim Procter [Fri, 4 Mar 2022 17:19:17 +0000 (17:19 +0000)]
JAL-3647 release notes for hdpi/laf scaling JAL-3608 JAL-3609 JAL-3552
Jim Procter [Fri, 4 Mar 2022 16:38:01 +0000 (16:38 +0000)]
JAL-3746 structure mapping preference docs for JAL-3817
Jim Procter [Fri, 5 Feb 2021 17:03:12 +0000 (17:03 +0000)]
JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.
Jim Procter [Fri, 5 Feb 2021 17:05:03 +0000 (17:05 +0000)]
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository
Jim Procter [Fri, 5 Feb 2021 17:07:18 +0000 (17:07 +0000)]
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences
Jim Procter [Fri, 5 Feb 2021 17:07:54 +0000 (17:07 +0000)]
JAL-3746 JAL-3814 don’t automatically launch the news browser when the desktop is first opened
Jim Procter [Fri, 5 Feb 2021 17:01:09 +0000 (17:01 +0000)]
JAL-3746 JAL-3814 NONEWS property
Jim Procter [Fri, 4 Mar 2022 15:41:06 +0000 (15:41 +0000)]
JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC
Jim Procter [Fri, 4 Mar 2022 15:26:03 +0000 (15:26 +0000)]
JAL-3608 JAL-3830 simplified command line docs a bit
Jim Procter [Fri, 4 Mar 2022 14:36:11 +0000 (14:36 +0000)]
Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop
Ben Soares [Fri, 4 Mar 2022 13:48:54 +0000 (13:48 +0000)]
JAL-3830 added command line to whatsnew and releases
Ben Soares [Fri, 4 Mar 2022 13:38:29 +0000 (13:38 +0000)]
JAL-3830 Added new command line usage to docs
Ben Soares [Fri, 4 Mar 2022 12:19:35 +0000 (12:19 +0000)]
JAL-3608 added to LaF documentation
Ben Soares [Thu, 3 Mar 2022 15:38:47 +0000 (15:38 +0000)]
JAL-3830 fix broken/buggy install4j9 setting of executeSetupApp=false still running setupApp
Jim Procter [Wed, 2 Mar 2022 20:50:54 +0000 (20:50 +0000)]
Merge branch 'bug/JAL-3962_awt_dll_problem' into develop
Jim Procter [Wed, 2 Mar 2022 20:50:02 +0000 (20:50 +0000)]
JAL-3746 release notes for JAL-3867
Jim Procter [Wed, 2 Mar 2022 18:12:13 +0000 (18:12 +0000)]
JAL-3746 release note for JAL-3907 building Jalview with j17
Jim Procter [Wed, 2 Mar 2022 18:09:45 +0000 (18:09 +0000)]
JAL-3746 release note for JAL-3618 Vaqua config so app directories can be opened
Jim Procter [Wed, 2 Mar 2022 17:59:33 +0000 (17:59 +0000)]
Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebuilds' into develop
Jim Procter [Wed, 2 Mar 2022 17:55:41 +0000 (17:55 +0000)]
JAL-3594 release notes and mention jalview develop app in release notes
Jim Procter [Wed, 2 Mar 2022 17:49:37 +0000 (17:49 +0000)]
Release notes for JAL—3728 - waiting for ben to sign off or leave issue open
Jim Procter [Wed, 2 Mar 2022 17:28:55 +0000 (17:28 +0000)]
JAL-3208 release notes and docs for setprop
Jim Procter [Wed, 2 Mar 2022 17:10:06 +0000 (17:10 +0000)]
JAL-3746 release notes and cli arg docs for JAL-3530
Ben Soares [Wed, 2 Mar 2022 17:00:48 +0000 (17:00 +0000)]
JAL-3691 bumped the version to 1.8.3-1.2.12 in source and libraries
Jim Procter [Wed, 2 Mar 2022 16:14:59 +0000 (16:14 +0000)]
JAL-3746 release notes JAL-3391 JAL-3829 improved 3dbeacons docs, including documenting ‘best’ and ‘multiple best’ options in 3D-beacons
Jim Procter [Wed, 2 Mar 2022 15:58:48 +0000 (15:58 +0000)]
JAL-3746 release notes for JAL-3929
Jim Procter [Wed, 2 Mar 2022 15:11:20 +0000 (15:11 +0000)]
JAL-3746 more what’s new
Jim Procter [Wed, 2 Mar 2022 15:10:53 +0000 (15:10 +0000)]
JAL-3619 fix up error messages and try to bail quietly if the viewer doesn’t open
Jim Procter [Wed, 2 Mar 2022 14:49:56 +0000 (14:49 +0000)]
JAL-3619 fix up warning message and minimal patch to make sure failed-to-launch viewers tidy up after themselves.
Ben Soares [Wed, 2 Mar 2022 14:39:32 +0000 (14:39 +0000)]
JAL-3962 Added jre/bin and dist folders to the native library path to try and fix the awt.dll problem
Ben Soares [Wed, 2 Mar 2022 14:38:34 +0000 (14:38 +0000)]
JAL-3130 updated download_jres.sh
Jim Procter [Wed, 2 Mar 2022 14:22:56 +0000 (14:22 +0000)]
JAL-3746 what’s new..
Jim Procter [Wed, 2 Mar 2022 13:05:39 +0000 (13:05 +0000)]
JAL-3746 release notes for JAL-3202 (JalviewJS)
Jim Procter [Wed, 2 Mar 2022 12:30:53 +0000 (12:30 +0000)]
JAL-3746 update release date and release notes/docs for JAL-1260, JAL-3821, JAL-3144, JAL-2226
Jim Procter [Mon, 28 Feb 2022 18:57:07 +0000 (18:57 +0000)]
JAL-3746 more what’s new and release notes
Jim Procter [Mon, 28 Feb 2022 18:30:02 +0000 (18:30 +0000)]
JAL-3503 2.11.2.0 release notes and docs
Jim Procter [Mon, 28 Feb 2022 17:57:49 +0000 (17:57 +0000)]
JAL-3746 JAL-3551 update pymol docs and what’s new text
Jim Procter [Mon, 28 Feb 2022 11:59:28 +0000 (11:59 +0000)]
JAL-3746 document -no-annotation cli arg
Jalview Development Admin [Wed, 23 Feb 2022 18:55:37 +0000 (18:55 +0000)]
Merge branch 'improvement/JAL-3830_install4j9_macos_setup_application' of source.jalview.org/git/jalview into improvement/JAL-3830_install4j9_macos_setup_application
Jalview Development Admin [Wed, 23 Feb 2022 18:54:57 +0000 (18:54 +0000)]
JAL-3830 temporarily disable the setup screen for OSX dmgs until we can properly document its use
Jalview Development Admin [Wed, 23 Feb 2022 17:23:42 +0000 (17:23 +0000)]
JAL-3796 additional steps for notarization
Jim Procter [Thu, 17 Feb 2022 17:28:24 +0000 (17:28 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Jim Procter [Thu, 17 Feb 2022 17:15:38 +0000 (17:15 +0000)]
JAL-3551 patch superpose test for additional undo dis/enable commands
Jim Procter [Thu, 17 Feb 2022 17:10:50 +0000 (17:10 +0000)]
JAL-3823 JAL-3830 update gradle plugin for install4j to 9.0.6
Jim Procter [Thu, 17 Feb 2022 17:04:14 +0000 (17:04 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Jim Procter [Thu, 17 Feb 2022 15:05:21 +0000 (15:05 +0000)]
JAL-3959 add key retrieval urls that support CORS needed by JalviewJS
Jim Procter [Thu, 17 Feb 2022 12:58:37 +0000 (12:58 +0000)]
JAL-3746 more release notes and docs: JAL-3863 JAL-3745
Jim Procter [Thu, 17 Feb 2022 11:00:52 +0000 (11:00 +0000)]
JAL-3691 rebuilt getdown jars
Jim Procter [Thu, 17 Feb 2022 10:55:18 +0000 (10:55 +0000)]
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 getdown - needs rebuild / redacting
Jim Procter [Thu, 17 Feb 2022 10:36:26 +0000 (10:36 +0000)]
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
Jim Procter [Wed, 16 Feb 2022 18:43:48 +0000 (18:43 +0000)]
JAL-3746 release notes.. in progress
Jim Procter [Wed, 16 Feb 2022 18:43:23 +0000 (18:43 +0000)]
JAL-3551 - wrap pair_fit with undo_disable and undo_enable
Jim Procter [Wed, 16 Feb 2022 16:34:56 +0000 (16:34 +0000)]
JAL-3837 GPL license on splashscreen (finally !) and added link to discourse.jalview.org to replace mailing list
Jim Procter [Wed, 16 Feb 2022 15:51:23 +0000 (15:51 +0000)]
JAL-3949 report Pymol XMLRPC port via log.info
Jim Procter [Tue, 15 Feb 2022 17:35:16 +0000 (17:35 +0000)]
JAL-1761 backbone type parameter for configuring which atoms are used for superposition of structures
Jim Procter [Tue, 15 Feb 2022 16:55:17 +0000 (16:55 +0000)]
JAL-1761 need to pass molecule type when generating superposition commands
Jim Procter [Tue, 15 Feb 2022 16:54:26 +0000 (16:54 +0000)]
JAL-3551 patch test for altloc handling atom spec in superposition code
Jim Procter [Tue, 15 Feb 2022 16:47:32 +0000 (16:47 +0000)]
JAL-1761 need to pass molecule type when generating superposition commands
Jim Procter [Tue, 15 Feb 2022 16:46:02 +0000 (16:46 +0000)]
JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol view
Jim Procter [Tue, 15 Feb 2022 16:45:11 +0000 (16:45 +0000)]
JAL-3746 update release date to later in Feb 2022
Jim Procter [Tue, 15 Feb 2022 16:44:40 +0000 (16:44 +0000)]
JAL-3551 pymol documentation
Jim Procter [Mon, 14 Feb 2022 23:02:41 +0000 (23:02 +0000)]
Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative_IDs' into develop
Jim Procter [Mon, 14 Feb 2022 22:58:01 +0000 (22:58 +0000)]
JAL-3551
Jim Procter [Mon, 14 Feb 2022 14:03:39 +0000 (14:03 +0000)]
JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs
Jim Procter [Sat, 12 Feb 2022 11:49:56 +0000 (11:49 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop
Conflicts:
test/jalview/bin/CommandLineOperations.java
Ben Soares [Sat, 12 Feb 2022 10:09:07 +0000 (10:09 +0000)]
JAL-3949 fix testProps path and make line count more accurate
Jim Procter [Fri, 11 Feb 2022 18:52:17 +0000 (18:52 +0000)]
JAL-3949 increase command line ops test timeout
Jim Procter [Fri, 11 Feb 2022 18:44:19 +0000 (18:44 +0000)]
JAL-3949 ensure Jalview command line ops setup actually quits after SETUP_TIME milliseconds - seems there’s less stderr noise than before !
Jim Procter [Fri, 11 Feb 2022 17:27:42 +0000 (17:27 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop
Jim Procter [Fri, 11 Feb 2022 17:09:04 +0000 (17:09 +0000)]
JAL-3931 fix - escape % symbols after urlencoding
Ben Soares [Fri, 11 Feb 2022 15:43:34 +0000 (15:43 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' of https://source.jalview.org/git/jalview into update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
Ben Soares [Fri, 11 Feb 2022 15:43:30 +0000 (15:43 +0000)]
JLogger loglevel check on whether to call the actual logger or not. New factory methods with Class.
Jim Procter [Fri, 11 Feb 2022 15:27:51 +0000 (15:27 +0000)]
JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console
Conflicts:
src/jalview/bin/Jalview.java
Ben Soares [Fri, 11 Feb 2022 14:15:09 +0000 (14:15 +0000)]
JAL-3949 fixed failing commandlinetests due to more output and line count limit
Ben Soares [Fri, 11 Feb 2022 14:14:39 +0000 (14:14 +0000)]
JAL-3949 added Java Console autoscrolling help paragraph
Ben Soares [Fri, 11 Feb 2022 12:39:51 +0000 (12:39 +0000)]
JAL-3949 read ~/.jalview_properties before initialising the logging
git://source.jalview.org / jalview.git / log