jalview.git
3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch Release_2_11_2_3
Jim Procter [Tue, 5 Jul 2022 21:53:03 +0000 (22:53 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4012 release date bump and JAL-4004 tweak to include current version in generated...
Jim Procter [Tue, 5 Jul 2022 21:52:27 +0000 (22:52 +0100)]
JAL-4012 release date bump and JAL-4004 tweak to include current version in generated whatsNew.html

3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 4 Jul 2022 14:59:58 +0000 (15:59 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4012 updated release date and whats new for 2.11.2.3
Jim Procter [Mon, 4 Jul 2022 14:58:04 +0000 (15:58 +0100)]
JAL-4012 updated release date and whats new for 2.11.2.3

3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 1 Jul 2022 13:12:45 +0000 (14:12 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4012 tweak release notes wording for legacy.uniprot
Jim Procter [Fri, 1 Jul 2022 13:08:52 +0000 (14:08 +0100)]
JAL-4012 tweak release notes wording for legacy.uniprot

3 months agoMerge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop
Jim Procter [Fri, 1 Jul 2022 12:55:20 +0000 (13:55 +0100)]
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop

3 months agoJAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and...
Jim Procter [Fri, 1 Jul 2022 12:44:40 +0000 (13:44 +0100)]
JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new

3 months agoJAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)
Jim Procter [Thu, 30 Jun 2022 16:37:02 +0000 (17:37 +0100)]
JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

3 months agoMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_optio...
Ben Soares [Tue, 28 Jun 2022 12:32:51 +0000 (13:32 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

3 months agoJAL-1988 Don't put Quit in the File menu if there's a handler for it improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
Ben Soares [Tue, 28 Jun 2022 12:31:55 +0000 (13:31 +0100)]
JAL-1988 Don't put Quit in the File menu if there's a handler for it

3 months agoMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_optio...
Ben Soares [Thu, 23 Jun 2022 15:02:46 +0000 (16:02 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

3 months agoJAL-1988 Check for setHandler capability to avoid About and Preferences menu options...
Ben Soares [Thu, 23 Jun 2022 14:28:46 +0000 (15:28 +0100)]
JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void

3 months agoJAL-3027 Avoid FlatLAF Desktop class is JalviewJS
Ben Soares [Fri, 17 Jun 2022 16:10:52 +0000 (17:10 +0100)]
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

3 months agoJAL-4012 release notes for JAL-1988,JAL-3416
Jim Procter [Wed, 15 Jun 2022 15:17:59 +0000 (16:17 +0100)]
JAL-4012 release notes for JAL-1988,JAL-3416

3 months agoJAL-1988 JAL-3416 avoid unnecessary static flag
Jim Procter [Wed, 15 Jun 2022 14:54:56 +0000 (15:54 +0100)]
JAL-1988 JAL-3416 avoid unnecessary static flag

3 months agoJAL-3418 JAL-1988 don’t need java version check anymore
Jim Procter [Wed, 15 Jun 2022 14:54:19 +0000 (15:54 +0100)]
JAL-3418 JAL-1988 don’t need java version check anymore

3 months agoMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_optio...
Jim Procter [Wed, 15 Jun 2022 14:41:53 +0000 (15:41 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

3 months agoJAL-1988 Hack to ensure Quit dialog box is moved to front
Ben Soares [Mon, 13 Jun 2022 17:32:22 +0000 (18:32 +0100)]
JAL-1988 Hack to ensure Quit dialog box is moved to front

3 months agoJAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop...
Ben Soares [Mon, 13 Jun 2022 17:14:11 +0000 (18:14 +0100)]
JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.

3 months agoMerge branch 'develop' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and...
Ben Soares [Mon, 13 Jun 2022 16:22:52 +0000 (17:22 +0100)]
Merge branch 'develop' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option

3 months agoJAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set
Ben Soares [Mon, 13 Jun 2022 15:20:12 +0000 (16:20 +0100)]
JAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set

3 months agoMerge branch 'improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler' into improvement...
Jim Procter [Mon, 13 Jun 2022 11:24:07 +0000 (12:24 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option

3 months agoMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_optio...
Jim Procter [Mon, 13 Jun 2022 11:22:31 +0000 (12:22 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler

3 months agoJAL-3416 remove flat as default for linux
Ben Soares [Mon, 13 Jun 2022 10:43:35 +0000 (11:43 +0100)]
JAL-3416 remove flat as default for linux

3 months agoJAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system... JAL-3416_different_look_and_feel_on_linux
Ben Soares [Mon, 13 Jun 2022 10:20:50 +0000 (11:20 +0100)]
JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system to set APQhandler for both J9+ and now Java 8

3 months agoJAL-3416 Added some mac specific FlatLAF settings. Note this is not the default...
Ben Soares [Mon, 13 Jun 2022 10:18:31 +0000 (11:18 +0100)]
JAL-3416 Added some mac specific FlatLAF settings.  Note this is not the default macOS LaF, this is only when -Dlaf=flat is set on a mac when running Jalview

3 months agoJAL-3416 updated FlatLAF libraries to 2.3. Added the flatlaf-extras library
Ben Soares [Mon, 13 Jun 2022 10:17:04 +0000 (11:17 +0100)]
JAL-3416 updated FlatLAF libraries to 2.3.  Added the flatlaf-extras library

3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 9 Jun 2022 13:37:56 +0000 (14:37 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
Jim Procter [Thu, 9 Jun 2022 13:25:39 +0000 (14:25 +0100)]
JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

3 months agoMerge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
Jim Procter [Thu, 9 Jun 2022 13:07:04 +0000 (14:07 +0100)]
Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop

3 months agoJAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore
Jim Procter [Thu, 9 Jun 2022 13:03:55 +0000 (14:03 +0100)]
JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore

3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 9 Jun 2022 11:37:18 +0000 (12:37 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4014 release notes for JAL-4026 patches
Jim Procter [Thu, 9 Jun 2022 11:35:26 +0000 (12:35 +0100)]
JAL-4014 release notes for JAL-4026 patches

3 months agoJAL-4026 increase timeouts for command line ops
Jim Procter [Thu, 9 Jun 2022 11:16:08 +0000 (12:16 +0100)]
JAL-4026 increase timeouts for command line ops

3 months agoJAL-4026 ignore StructureSelectionManager events if no viewer is available to act...
Jim Procter [Thu, 9 Jun 2022 10:20:22 +0000 (11:20 +0100)]
JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them

3 months agoJAL-4026 always wait 50ms before checking if the calculation worker is still running...
Jim Procter [Thu, 9 Jun 2022 09:38:44 +0000 (10:38 +0100)]
JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

3 months agoJAL-4026 update the viewport’s wrapped width after calculating it
Jim Procter [Thu, 9 Jun 2022 07:18:31 +0000 (08:18 +0100)]
JAL-4026 update the viewport’s wrapped width after calculating it

3 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 8 Jun 2022 15:32:14 +0000 (16:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

3 months agoJAL-4014 release notes for JAL-4023 and JAL-4024
Jim Procter [Wed, 8 Jun 2022 14:17:16 +0000 (15:17 +0100)]
JAL-4014 release notes for JAL-4023 and JAL-4024

3 months agoMerge branch 'improvement/JAL-4023_snotation_for_trees' into develop
Jim Procter [Wed, 8 Jun 2022 14:11:27 +0000 (15:11 +0100)]
Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop

3 months agoMerge branch 'patch/JAL-4024_jumpScrollHang' into develop
Jim Procter [Wed, 8 Jun 2022 14:11:01 +0000 (15:11 +0100)]
Merge branch 'patch/JAL-4024_jumpScrollHang' into develop

3 months agoJAL-4012 what’s new and release notes (in the new styleee!) for JAL-4004, JAL-3989...
Jim Procter [Wed, 8 Jun 2022 14:04:44 +0000 (15:04 +0100)]
JAL-4012 what’s new and release notes (in the new styleee!) for JAL-4004, JAL-3989 and JAL-3553

3 months agoJAL-4004 delete temporary file mistakenly checked in
Jim Procter [Wed, 8 Jun 2022 13:42:48 +0000 (14:42 +0100)]
JAL-4004 delete temporary file mistakenly checked in

3 months agoMerge branch 'issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop' into...
Jim Procter [Wed, 8 Jun 2022 13:01:17 +0000 (14:01 +0100)]
Merge branch 'issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop' into develop

3 months agoJAL-4024 only render partially when new view overlaps with last rendered annotation... patch/JAL-4024_jumpScrollHang
Jim Procter [Wed, 8 Jun 2022 12:10:42 +0000 (13:10 +0100)]
JAL-4024 only render partially when new view overlaps with last rendered annotation panel view

4 months agoJAL-4020 class formatting
Ben Soares [Tue, 7 Jun 2022 13:14:53 +0000 (14:14 +0100)]
JAL-4020 class formatting

4 months agoJAL-4020 added the \Scripts\pymol.exe. to the pathList
Ben Soares [Tue, 7 Jun 2022 09:13:29 +0000 (10:13 +0100)]
JAL-4020 added the \Scripts\pymol.exe. to the pathList

4 months agoJAL-4020 Added the +2 arg for PyMOLWin.exe allowing older versions of PyMOL
Ben Soares [Mon, 6 Jun 2022 18:56:53 +0000 (19:56 +0100)]
JAL-4020 Added the +2 arg for PyMOLWin.exe allowing older versions of PyMOL

4 months agoJAL-4020 updated tests
Ben Soares [Mon, 6 Jun 2022 16:00:03 +0000 (17:00 +0100)]
JAL-4020 updated tests

4 months agoJAL-4020 class reformatting
Ben Soares [Mon, 6 Jun 2022 15:35:08 +0000 (16:35 +0100)]
JAL-4020 class reformatting

4 months agoJAL-4020 Added path search for global installation path and older version installatio...
Ben Soares [Mon, 6 Jun 2022 13:54:43 +0000 (14:54 +0100)]
JAL-4020 Added path search for global installation path and older version installation paths

4 months agoJAL-4023 use %g for distances (scientific notation for very small or large values) improvement/JAL-4023_snotation_for_trees
Jim Procter [Mon, 6 Jun 2022 13:09:01 +0000 (14:09 +0100)]
JAL-4023 use %g for distances (scientific notation for very small or large values)

4 months agoJAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places...
Ben Soares [Mon, 6 Jun 2022 13:03:50 +0000 (14:03 +0100)]
JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places starting with default install dir.  Added a new version (1.3) to ChimeraX

4 months agoJAL-4023 store distances as doubles
Jim Procter [Mon, 6 Jun 2022 11:22:03 +0000 (12:22 +0100)]
JAL-4023 store distances as doubles

4 months agoMerge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_de... issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
Ben Soares [Thu, 12 May 2022 15:06:59 +0000 (16:06 +0100)]
Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_develop

Took Issues Resolved (1 issue) from releases.html 2.11.2.3 row and put
in help/markdown/releases/release-2_11_2_3.md
and regenerated releases.html with
gradle releasesTemplates

4 months agoMerge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3
Jim Procter [Wed, 11 May 2022 14:50:10 +0000 (15:50 +0100)]
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3

4 months agoJAL-4012 JAL-4008 release notes for Jalview 2.11.2.3
Jim Procter [Wed, 11 May 2022 12:44:36 +0000 (13:44 +0100)]
JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

4 months agoJAL-4008 update jabaws client to 2.2.1 - definitely no log4j references ! patch/JAL-4008_jabaws_2_2_1_patch
Jim Procter [Tue, 10 May 2022 16:56:51 +0000 (17:56 +0100)]
JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

4 months agoMerge branch 'releases/Release_2_11_2_Branch' Release_2_11_2_2
Jalview Development Admin [Tue, 10 May 2022 11:17:28 +0000 (12:17 +0100)]
Merge branch 'releases/Release_2_11_2_Branch'

4 months agoJAL-4004 cosmetic improvements for Java documentation renderer
Ben Soares [Tue, 10 May 2022 09:06:38 +0000 (10:06 +0100)]
JAL-4004 cosmetic improvements for Java documentation renderer

4 months agoJAL-4004 gradle task releasesTemplates now part of main build dependency tree. Improv...
Ben Soares [Mon, 9 May 2022 22:21:27 +0000 (23:21 +0100)]
JAL-4004 gradle task releasesTemplates now part of main build dependency tree. Improvements to releases.html.

4 months agoJAL-4004 working templates and generated whatsNew.html and releases.html file for...
Ben Soares [Mon, 9 May 2022 22:19:45 +0000 (23:19 +0100)]
JAL-4004 working templates and generated whatsNew.html and releases.html file for both browser and Doc viewer

4 months agoJAL-4004 remove stray empty h3 headers
Ben Soares [Mon, 9 May 2022 21:58:46 +0000 (22:58 +0100)]
JAL-4004 remove stray empty h3 headers

4 months agoJAL-4004 gradle releasesTemplates builds releases.html
Ben Soares [Mon, 9 May 2022 18:23:06 +0000 (19:23 +0100)]
JAL-4004 gradle releasesTemplates builds releases.html

4 months agoJAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo...
Ben Soares [Mon, 9 May 2022 11:27:27 +0000 (12:27 +0100)]
JAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo website

4 months agoJAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time...
Ben Soares [Mon, 9 May 2022 10:33:27 +0000 (11:33 +0100)]
JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time in release date header

5 months agoJAL-4004 Now generating hugo files from help/markdown/...
Ben Soares [Thu, 5 May 2022 16:02:39 +0000 (17:02 +0100)]
JAL-4004 Now generating hugo files from help/markdown/...

5 months agoJAL-4004 existing releases-VERSION.md files and releases.html template
Ben Soares [Wed, 4 May 2022 13:45:07 +0000 (14:45 +0100)]
JAL-4004 existing releases-VERSION.md files and releases.html template

5 months agoJAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version...
Ben Soares [Wed, 4 May 2022 00:18:03 +0000 (01:18 +0100)]
JAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version-VERSION/_index.md

5 months agoJAL-3989 improved parsing and formatting now using flex CSS layout for columns
Ben Soares [Tue, 3 May 2022 11:35:42 +0000 (12:35 +0100)]
JAL-3989 improved parsing and formatting now using flex CSS layout for columns

5 months agoJAL-1544 minor errors in releases.html and one missing version (2.8.2b1)
Ben Soares [Tue, 3 May 2022 11:35:04 +0000 (12:35 +0100)]
JAL-1544 minor errors in releases.html and one missing version (2.8.2b1)

5 months agoJAL-3989 small improvements to output markdown
Ben Soares [Fri, 29 Apr 2022 12:29:17 +0000 (13:29 +0100)]
JAL-3989 small improvements to output markdown

5 months agoJAL-3989 add in issue shortcodes to the archive version page changes list
Ben Soares [Thu, 28 Apr 2022 13:47:55 +0000 (14:47 +0100)]
JAL-3989 add in issue shortcodes to the archive version page changes list

5 months agoJAL-1544 version number typo, probably copy and paste
Ben Soares [Wed, 27 Apr 2022 22:41:20 +0000 (23:41 +0100)]
JAL-1544 version number typo, probably copy and paste

5 months agoJAL-3989 Populate template files for hugo build: archive version files including...
Ben Soares [Wed, 27 Apr 2022 22:39:34 +0000 (23:39 +0100)]
JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file

5 months agoJAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build...
Ben Soares [Mon, 25 Apr 2022 19:32:54 +0000 (20:32 +0100)]
JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/...  This is better in multiple ways including collating files needed for the hugo website and website docroot.

5 months agoJAL-3989 Independent creation of JSON installer sections
Ben Soares [Mon, 25 Apr 2022 16:58:56 +0000 (17:58 +0100)]
JAL-3989 Independent creation of JSON installer sections

5 months agoJAL-3978 clean up unnecessary local variables for JALVIEW_VERSION_UNDERSCORES
Ben Soares [Mon, 25 Apr 2022 14:03:49 +0000 (15:03 +0100)]
JAL-3978 clean up unnecessary local variables for JALVIEW_VERSION_UNDERSCORES

5 months agoJAL-3989 Changed to using com.google.common.hash for SHA256 sum, for gradle 7 compati...
Ben Soares [Fri, 22 Apr 2022 15:17:09 +0000 (16:17 +0100)]
JAL-3989 Changed to using com.google.common.hash for SHA256 sum, for gradle 7 compatibility

5 months agoMerge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989
Ben Soares [Thu, 21 Apr 2022 19:24:35 +0000 (20:24 +0100)]
Merge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989

5 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 19 Apr 2022 14:04:00 +0000 (15:04 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

5 months agoJAL-3992 bump version and report updates in 2.11.2.2 release notes
Jim Procter [Tue, 19 Apr 2022 14:03:23 +0000 (15:03 +0100)]
JAL-3992 bump version and report updates in 2.11.2.2 release notes

5 months agoMerge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop
Jim Procter [Tue, 19 Apr 2022 14:02:17 +0000 (15:02 +0100)]
Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop

5 months agoMerge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop
Jim Procter [Tue, 19 Apr 2022 13:57:56 +0000 (14:57 +0100)]
Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop

5 months agoJAL-3997 check for tooltip being null before checking equivalence to last tooltip... bug/JAL-3997_NPE_in_wrapped_mode
Jim Procter [Mon, 18 Apr 2022 13:49:47 +0000 (14:49 +0100)]
JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

5 months agoMerge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm bug/JAL-3365_extendedDSSP_via_stockholm
Jim Procter [Mon, 18 Apr 2022 12:27:14 +0000 (13:27 +0100)]
Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

5 months agoJAL-3992 fix path
Jim Procter [Mon, 18 Apr 2022 11:51:59 +0000 (12:51 +0100)]
JAL-3992 fix path

5 months agoJAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files
Jim Procter [Sat, 16 Apr 2022 12:36:06 +0000 (13:36 +0100)]
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

5 months agoJAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode
Jim Procter [Wed, 13 Apr 2022 15:13:40 +0000 (16:13 +0100)]
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

6 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 19:48:38 +0000 (20:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

6 months agoJAL-3990 release notes and what’s new Release_2_11_2_1
Jim Procter [Tue, 5 Apr 2022 19:44:48 +0000 (20:44 +0100)]
JAL-3990 release notes and what’s new

6 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:50:33 +0000 (18:50 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

6 months agoJAL-3981 patch tests and remove errant imports
Jim Procter [Tue, 5 Apr 2022 17:37:11 +0000 (18:37 +0100)]
JAL-3981 patch tests and remove errant imports

6 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:15:28 +0000 (18:15 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

6 months agoJAL-3990 gradle spotlessApply
Jim Procter [Tue, 5 Apr 2022 17:14:52 +0000 (18:14 +0100)]
JAL-3990 gradle spotlessApply

6 months agoJAL-3990 release notes for 2.11.2.1 patch release
Jim Procter [Tue, 5 Apr 2022 17:12:13 +0000 (18:12 +0100)]
JAL-3990 release notes for 2.11.2.1 patch release

6 months agoMerge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop
Jim Procter [Tue, 5 Apr 2022 16:57:40 +0000 (17:57 +0100)]
Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

6 months agoJAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some...
Ben Soares [Tue, 5 Apr 2022 11:25:37 +0000 (12:25 +0100)]
JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places

6 months agoJAL-3989 fix a build date once in build.gradle, not each time getDate() is called.
Ben Soares [Mon, 4 Apr 2022 11:01:22 +0000 (12:01 +0100)]
JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.