jalview.git
6 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

6 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

6 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

6 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 !

6 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

6 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.

6 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

6 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

6 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

6 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

6 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

7 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/...

7 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

7 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

7 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

7 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)

7 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

7 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

7 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

7 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

7 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.

7 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

7 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

7 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

7 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

7 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

7 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

7 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

7 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

7 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

7 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

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

7 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

7 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

8 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

8 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

8 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

8 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

8 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

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

8 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

8 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

8 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

8 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.

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 31 Mar 2022 22:11:44 +0000 (23:11 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3983 release note for JAL-3985
Jim Procter [Thu, 31 Mar 2022 19:44:49 +0000 (20:44 +0100)]
JAL-3983 release note for JAL-3985

8 months agoMerge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop
Jim Procter [Thu, 31 Mar 2022 19:42:53 +0000 (20:42 +0100)]
Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

8 months agoMerge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL...
Ben Soares [Thu, 31 Mar 2022 17:52:55 +0000 (18:52 +0100)]
Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

8 months agoMerge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_arch...
Ben Soares [Thu, 31 Mar 2022 17:18:40 +0000 (18:18 +0100)]
Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir

8 months agoJAL-3085 update tests and mock responses, new P0dtd1 testcase
Jim Procter [Thu, 31 Mar 2022 14:17:46 +0000 (15:17 +0100)]
JAL-3085 update tests and mock responses, new P0dtd1 testcase

8 months agoJAL-3985 formatting
Jim Procter [Thu, 31 Mar 2022 13:06:28 +0000 (14:06 +0100)]
JAL-3985 formatting

8 months agoJAL-3985 split PDB id queries into multiple queries so server doesn’t 414
Jim Procter [Thu, 31 Mar 2022 13:06:04 +0000 (14:06 +0100)]
JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

8 months agoMerge branch 'patch/JAL-3976_3dbeaconsnull' into develop
Jim Procter [Wed, 30 Mar 2022 17:35:07 +0000 (18:35 +0100)]
Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

8 months agoJAL-3976 fix mock PDBFTS query & responses patch/JAL-3976_3dbeaconsnull
Jim Procter [Wed, 30 Mar 2022 16:32:19 +0000 (17:32 +0100)]
JAL-3976 fix mock PDBFTS query & responses

8 months agoJAL-3983 known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:56:41 +0000 (16:56 +0100)]
JAL-3983 known issue note for JAL-3984

8 months agoJAL-3983 release notes for JAL-3975 and known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:54:33 +0000 (16:54 +0100)]
JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

8 months agoMerge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop
Jim Procter [Wed, 30 Mar 2022 15:52:27 +0000 (16:52 +0100)]
Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

8 months agoJAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but...
Jim Procter [Wed, 30 Mar 2022 15:51:44 +0000 (16:51 +0100)]
JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

8 months agoJAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent...
Ben Soares [Tue, 15 Mar 2022 17:13:01 +0000 (17:13 +0000)]
JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after JvOptionPane action.

8 months agoJAL-3983 update release notes for JAL-3973
Jim Procter [Wed, 30 Mar 2022 15:15:43 +0000 (16:15 +0100)]
JAL-3983 update release notes for JAL-3973

8 months agoJAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate...
Jim Procter [Wed, 30 Mar 2022 15:12:51 +0000 (16:12 +0100)]
JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball

8 months agoMerge branch 'bug/JAL-3973_source_tarball_not_building' into develop
Jim Procter [Wed, 30 Mar 2022 14:49:09 +0000 (15:49 +0100)]
Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop

8 months agoJAL-3983 release 2.11.2.1 date and release notes
Jim Procter [Wed, 30 Mar 2022 14:45:01 +0000 (15:45 +0100)]
JAL-3983 release 2.11.2.1 date and release notes

8 months agoJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details
Jim Procter [Fri, 25 Mar 2022 14:31:18 +0000 (14:31 +0000)]
JAL-3980 JAL-3979 TODOs

8 months agoJAL-3980 defensive copy - inefficient but fixes bug
Jim Procter [Fri, 25 Mar 2022 14:30:17 +0000 (14:30 +0000)]
JAL-3980 defensive copy - inefficient but fixes bug

8 months agoJAL-3981 Additional line breaks - sort of helps
Jim Procter [Fri, 25 Mar 2022 14:16:21 +0000 (14:16 +0000)]
JAL-3981 Additional line breaks - sort of helps

8 months agoJAL-3981 strategic newlines to help speed up Java's html parser
Jim Procter [Thu, 24 Mar 2022 17:02:10 +0000 (17:02 +0000)]
JAL-3981 strategic newlines to help speed up Java's html parser

8 months agoJAL-3976 skip entries with null values when analyzing
Jim Procter [Wed, 23 Mar 2022 12:22:41 +0000 (12:22 +0000)]
JAL-3976 skip entries with null values when analyzing

8 months agoJAL-3976 update tests
Jim Procter [Wed, 23 Mar 2022 12:22:15 +0000 (12:22 +0000)]
JAL-3976 update tests

8 months agoJAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict...
Ben Soares [Fri, 18 Mar 2022 18:12:17 +0000 (18:12 +0000)]
JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.

8 months agoJAL-3978 Getdown add getdownappbase property to launched Jalview
Ben Soares [Fri, 18 Mar 2022 16:55:46 +0000 (16:55 +0000)]
JAL-3978 Getdown add getdownappbase property to launched Jalview

8 months agoJAL-3978 New tasks to build archive 'old' dir with appropriate getdown resources...
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

8 months agoJAL-3978 task stub and getdown splash screens
Ben Soares [Wed, 16 Mar 2022 17:29:56 +0000 (17:29 +0000)]
JAL-3978 task stub and getdown splash screens

8 months agoAppend git.hash and git.branch to RELEASE file stored in tarball. When compiling...
Ben Soares [Sun, 13 Mar 2022 21:00:24 +0000 (21:00 +0000)]
Append git.hash and git.branch to RELEASE file stored in tarball. When compiling, if not in git repo use git.branch and git.hash from RELEASE file.

8 months agoJAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)
Ben Soares [Fri, 11 Mar 2022 09:31:57 +0000 (09:31 +0000)]
JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)

8 months agoMerge branch 'master' into releases/Release_2_11_2_Branch
Jalview Development Admin [Thu, 10 Mar 2022 17:40:40 +0000 (17:40 +0000)]
Merge branch 'master' into releases/Release_2_11_2_Branch

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch Release_2_11_2_0
Jalview Development Admin [Thu, 10 Mar 2022 01:34:08 +0000 (01:34 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3746 bump release date to 10th March - after UoD network maintenance
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

8 months agoJAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(
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 :(

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 17:31:53 +0000 (17:31 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert
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

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 10:12:18 +0000 (10:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3746 JAL-3841 fix README typo
Jim Procter [Wed, 9 Mar 2022 10:11:56 +0000 (10:11 +0000)]
JAL-3746 JAL-3841 fix README typo

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 08:14:14 +0000 (08:14 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3746 more docs tweaking and release notes
Jim Procter [Wed, 9 Mar 2022 08:09:45 +0000 (08:09 +0000)]
JAL-3746 more docs tweaking and release notes

8 months agoMerge branch 'spike/try_spotless_JAL-3438' into develop
Jim Procter [Wed, 9 Mar 2022 07:59:03 +0000 (07:59 +0000)]
Merge branch 'spike/try_spotless_JAL-3438' into develop

8 months agoJAL-3746 apply copyright to tests spike/try_spotless_JAL-3438
Jim Procter [Tue, 8 Mar 2022 21:58:37 +0000 (21:58 +0000)]
JAL-3746 apply copyright to tests

8 months agoJAL-3746 apply copyright to source
Jim Procter [Tue, 8 Mar 2022 21:56:25 +0000 (21:56 +0000)]
JAL-3746 apply copyright to source

8 months agoJAL-3438 spotless for 2.11.2.0
Jim Procter [Tue, 8 Mar 2022 21:30:05 +0000 (21:30 +0000)]
JAL-3438 spotless for 2.11.2.0

8 months agoMerge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 8 Mar 2022 20:40:15 +0000 (20:40 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch

8 months agoJAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes
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

8 months agoJAL-3108 updated Ensembl client and model species names
Jim Procter [Tue, 8 Mar 2022 18:53:09 +0000 (18:53 +0000)]
JAL-3108 updated Ensembl client and model species names

8 months agoJAL-3746 new release date for 2.11.2
Jim Procter [Tue, 8 Mar 2022 18:18:56 +0000 (18:18 +0000)]
JAL-3746 new release date for 2.11.2

8 months agoJAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes
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

8 months agoMerge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop
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

8 months agoJAL-3103 updated help doc to remove default browser choice
Ben Soares [Tue, 8 Mar 2022 12:26:28 +0000 (12:26 +0000)]
JAL-3103 updated help doc to remove default browser choice

8 months agoJAL-3103 Removed code and unused widgets for defaultBrowser
Ben Soares [Tue, 8 Mar 2022 12:14:45 +0000 (12:14 +0000)]
JAL-3103 Removed code and unused widgets for defaultBrowser

8 months agoJAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods
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

8 months agoJAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS
Ben Soares [Tue, 8 Mar 2022 00:39:04 +0000 (00:39 +0000)]
JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS

8 months agoJAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-neede...
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