Jim Procter [Mon, 17 Jan 2022 12:20:08 +0000 (12:20 +0000)]
JAL-3940 update release notes for JAL-3702,JAL-3935 in 2.11.1.7 release
Ben Soares [Wed, 12 Jan 2022 12:32:06 +0000 (12:32 +0000)]
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished
Ben Soares [Tue, 11 Jan 2022 20:13:57 +0000 (20:13 +0000)]
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data
Ben Soares [Tue, 11 Jan 2022 16:04:49 +0000 (16:04 +0000)]
close filehandles straight after parse, without setting an error
Conflicts:
src/jalview/project/Jalview2XML.java
(locale aware PDBID string compare)
Ben Soares [Tue, 11 Jan 2022 14:45:42 +0000 (14:45 +0000)]
JAL-3937 update releases.html
Ben Soares [Mon, 10 Jan 2022 20:58:04 +0000 (20:58 +0000)]
JAL-3937 enable AIA download of intermediate certificates when needed
Jim Procter [Thu, 6 Jan 2022 09:56:11 +0000 (09:56 +0000)]
JAL-3934 update whats new
Jim Procter [Thu, 6 Jan 2022 09:45:17 +0000 (09:45 +0000)]
Merge branch 'task/JAL-3934_update_log4j_again' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 6 Jan 2022 09:42:47 +0000 (09:42 +0000)]
JAL-3934 trigger patch release for log4j version bump
Ben Soares [Wed, 22 Dec 2021 11:12:37 +0000 (11:12 +0000)]
JAL-3934 updated log4j from 2.16.0 to 2.17.0
Jim Procter [Mon, 20 Dec 2021 14:03:35 +0000 (14:03 +0000)]
JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch
Jim Procter [Mon, 20 Dec 2021 09:50:51 +0000 (09:50 +0000)]
JAL-3842 patch what’s new text
Jim Procter [Mon, 20 Dec 2021 08:04:21 +0000 (08:04 +0000)]
JAL-3842 release 2.11.1.5 release notes
Jim Procter [Mon, 20 Dec 2021 07:45:38 +0000 (07:45 +0000)]
Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch
Ben Soares [Wed, 15 Dec 2021 13:23:16 +0000 (13:23 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Ben Soares [Wed, 15 Dec 2021 13:16:11 +0000 (13:16 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Jim Procter [Wed, 15 Dec 2021 10:38:22 +0000 (10:38 +0000)]
JAL-3933 remove obsolete Castor logging configuration
Jim Procter [Wed, 15 Dec 2021 10:36:18 +0000 (10:36 +0000)]
JAL-3933 configure root logger console appender to stderr
Ben Soares [Tue, 14 Dec 2021 20:31:44 +0000 (20:31 +0000)]
JAL-3933 updated slf4j to 1.7.32
Ben Soares [Tue, 14 Dec 2021 20:00:40 +0000 (20:00 +0000)]
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped log4j classes from jabaws-min-client jar. Updated sl4j jars in j8lib
Jim Procter [Tue, 13 Jul 2021 10:45:25 +0000 (11:45 +0100)]
JAL-3842 fix automatic what's new link for custom version builds
Jim Procter [Wed, 30 Jun 2021 10:31:37 +0000 (11:31 +0100)]
JAL-3842 JAL-3746 (need to cherry pick to develop) - automatically generate link to latest release notes in what's new
Jim Procter [Wed, 9 Jun 2021 17:06:37 +0000 (18:06 +0100)]
JAL-3842 2.11.1.5 what’s new, release notes, and version bump
Jim Procter [Wed, 9 Jun 2021 16:38:46 +0000 (17:38 +0100)]
Merge branch 'patch/JAL-3840_2_11_1_4' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 9 Jun 2021 15:53:09 +0000 (16:53 +0100)]
JAL-3840 don’t update the modal residue count for gaps
Jim Procter [Wed, 9 Jun 2021 15:40:42 +0000 (16:40 +0100)]
fixes JAL-3840
Jim Procter [Wed, 9 Jun 2021 15:35:11 +0000 (16:35 +0100)]
JAL-3840 failing test - show that addGaps overflows
Ben Soares [Mon, 26 Apr 2021 17:27:28 +0000 (18:27 +0100)]
JAL-3248 Archived old README. Added new README to point user to doc/building.md
Ben Soares [Mon, 26 Apr 2021 16:56:19 +0000 (17:56 +0100)]
JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6
Ben Soares [Mon, 19 Apr 2021 15:37:24 +0000 (16:37 +0100)]
JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values
Jim Procter [Tue, 9 Mar 2021 13:03:09 +0000 (13:03 +0000)]
JAL-3816 release date updated to 9th March
Jim Procter [Fri, 5 Mar 2021 18:19:55 +0000 (18:19 +0000)]
JAL-3816 release date set for 8th March and updated what's new
Jim Procter [Fri, 5 Mar 2021 17:44:19 +0000 (17:44 +0000)]
JAL-3816 new known defects JAL-3705 and JAL-3806
Jim Procter [Thu, 4 Mar 2021 11:44:06 +0000 (11:44 +0000)]
Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"
This reverts commit
cb628aab46f9027e71b71203b322f96710e09990, reversing
changes made to
a40669b2eeb34a6c760b63c172a31a194b456f24.
Jim Procter [Thu, 4 Mar 2021 11:39:02 +0000 (11:39 +0000)]
Revert "JAL-3816 release notes for JAL-3806"
This reverts commit
ead40d75a04715c80c61e34e277bb995cb2bef90.
Jim Procter [Fri, 26 Feb 2021 15:02:55 +0000 (15:02 +0000)]
JAL-3816 release notes for JAL-3806
Jim Procter [Fri, 26 Feb 2021 14:02:27 +0000 (14:02 +0000)]
Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch
Jim Procter [Fri, 26 Feb 2021 13:55:59 +0000 (13:55 +0000)]
JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release
Jim Procter [Wed, 24 Feb 2021 16:49:05 +0000 (16:49 +0000)]
Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 24 Feb 2021 16:48:48 +0000 (16:48 +0000)]
Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch
Ben Soares [Fri, 12 Feb 2021 18:24:50 +0000 (18:24 +0000)]
JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references
gmungoc [Thu, 11 Feb 2021 11:30:20 +0000 (11:30 +0000)]
JAL-3818 process Jmol callbacks in AWT thread
Ben Soares [Wed, 10 Feb 2021 00:19:36 +0000 (00:19 +0000)]
JAL-3521 Change grouped Jalview windows on linux taskbar to have name Jalview
Ben Soares [Wed, 10 Feb 2021 00:12:16 +0000 (00:12 +0000)]
JAL-3521 Changed wording of INSTALLATION in source tarball build_properties
Ben Soares [Mon, 8 Feb 2021 19:00:18 +0000 (19:00 +0000)]
JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...
Ben Soares [Mon, 8 Feb 2021 11:57:20 +0000 (11:57 +0000)]
JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg
Jim Procter [Sun, 7 Feb 2021 16:06:47 +0000 (16:06 +0000)]
JAL-3816 bump version number and cut release notes
Jim Procter [Sun, 7 Feb 2021 16:05:24 +0000 (16:05 +0000)]
JAL-3815 default /etc/jalview_properties under utils/debian
Ben Soares [Sat, 6 Feb 2021 18:19:17 +0000 (18:19 +0000)]
JAL-3251 debian build using maven, simplified build.gradle not needed
Ben Soares [Sat, 6 Feb 2021 01:51:09 +0000 (01:51 +0000)]
JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian
Jim Procter [Fri, 5 Feb 2021 17:25:21 +0000 (17:25 +0000)]
Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches
Jim Procter [Fri, 5 Feb 2021 17:24:58 +0000 (17:24 +0000)]
Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_down_build.gradle_for_debian
Jim Procter [Fri, 5 Feb 2021 17:07:54 +0000 (17:07 +0000)]
JAL-3814 don’t automatically launch the news browser when the desktop is first opened
Jim Procter [Fri, 5 Feb 2021 17:07:18 +0000 (17:07 +0000)]
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 17:05:03 +0000 (17:05 +0000)]
JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository
Jim Procter [Fri, 5 Feb 2021 17:03:12 +0000 (17:03 +0000)]
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 17:01:09 +0000 (17:01 +0000)]
JAL-3814 NONEWS property
gmungoc [Thu, 4 Feb 2021 15:09:15 +0000 (15:09 +0000)]
JAL-3806 fix and test for one-to-many sequence mapping case
gmungoc [Thu, 28 Jan 2021 16:56:55 +0000 (16:56 +0000)]
JAL-3806 more lax allowance (3 positions) for stop codon
Ben Soares [Tue, 26 Jan 2021 15:27:19 +0000 (15:27 +0000)]
JAL-3521 Updating file opening marker to %u
Ben Soares [Tue, 26 Jan 2021 13:59:13 +0000 (13:59 +0000)]
JAL-3521 Debian mime-type and desktop helper files, and script to create them
Ben Soares [Thu, 19 Nov 2020 17:58:36 +0000 (17:58 +0000)]
JAL-3521 removed unnecessary parts of the ext project in build.gradle
Ben Soares [Thu, 19 Nov 2020 16:17:39 +0000 (16:17 +0000)]
JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar
Jim Procter [Thu, 29 Oct 2020 20:01:45 +0000 (20:01 +0000)]
JAL-3766 what’s new and release notes for 2.11.1.3
Jim Procter [Thu, 29 Oct 2020 15:35:08 +0000 (15:35 +0000)]
JAL-3759 fix compilation error for test
Jim Procter [Thu, 29 Oct 2020 15:20:38 +0000 (15:20 +0000)]
JAL-3766 release notes for JAL-3759
Jim Procter [Thu, 29 Oct 2020 15:17:37 +0000 (15:17 +0000)]
JAL-3759 exclude hidden columns when processing column selection
Jim Procter [Thu, 29 Oct 2020 15:13:16 +0000 (15:13 +0000)]
Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 29 Oct 2020 15:10:54 +0000 (15:10 +0000)]
JAL-3766 release notes for JAL-3765 JAL-3763 JAL-3760 JAL-3751 JAL-3748 JAL-3725 JAL-3700 JAL-3611
Jim Procter [Thu, 29 Oct 2020 14:24:24 +0000 (14:24 +0000)]
Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_11_1_Branch
Ben Soares [Thu, 29 Oct 2020 14:19:51 +0000 (14:19 +0000)]
JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename
gmungoc [Thu, 29 Oct 2020 11:30:56 +0000 (11:30 +0000)]
JAL-3700 mapped sequence group includes short (or all gapped) sequences
Jim Procter [Wed, 28 Oct 2020 23:24:47 +0000 (23:24 +0000)]
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon
Jim Procter [Wed, 28 Oct 2020 22:56:38 +0000 (22:56 +0000)]
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)
gmungoc [Thu, 27 Aug 2020 15:02:06 +0000 (16:02 +0100)]
JAL-3725 restrict mapped virtual feature location to mapped region
Conflicts:
src/jalview/gui/PopupMenu.java
gmungoc [Thu, 27 Aug 2020 14:44:45 +0000 (15:44 +0100)]
JAL-3725 helper methods for computing mapped feature range overlap
gmungoc [Thu, 27 Aug 2020 14:40:22 +0000 (15:40 +0100)]
JAL-3725 exclude stop codon from CDS-to-protein mapping
Jim Procter [Wed, 28 Oct 2020 16:40:00 +0000 (16:40 +0000)]
Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch
Ben Soares [Wed, 28 Oct 2020 12:18:59 +0000 (12:18 +0000)]
JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+
Jim Procter [Tue, 27 Oct 2020 11:02:36 +0000 (11:02 +0000)]
JAL-3768 noticed failure of test when run as part of suite via gradle - whilst patching JAL-3700 JAL-3748 JAL-3763 for 2.11.1.3
Jim Procter [Tue, 27 Oct 2020 10:54:58 +0000 (10:54 +0000)]
JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.
Jim Procter [Tue, 27 Oct 2020 12:58:26 +0000 (12:58 +0000)]
update test for JAL-3763 redact shared DS sequences for contiguous CDS
gmungoc [Thu, 22 Oct 2020 13:48:25 +0000 (14:48 +0100)]
JAL-3763 Javadoc, check for null, additional tests
gmungoc [Thu, 24 Sep 2020 10:55:20 +0000 (11:55 +0100)]
JAL-3751 only merge strictly contiguous ranges of mappings
gmungoc [Thu, 22 Oct 2020 09:40:58 +0000 (10:40 +0100)]
JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion
gmungoc [Thu, 8 Oct 2020 14:30:22 +0000 (15:30 +0100)]
JAL-3700 JAL-3763 create datasets for test sequences
gmungoc [Thu, 8 Oct 2020 14:29:24 +0000 (15:29 +0100)]
JAL-3763 failsafe check for null
gmungoc [Thu, 8 Oct 2020 14:06:57 +0000 (15:06 +0100)]
JAL-3763 refactored getCoveringMapping for virtual feature discovery
gmungoc [Thu, 8 Oct 2020 14:05:32 +0000 (15:05 +0100)]
JAL-3763 always make a new dataset sequence for CDS sequence
gmungoc [Thu, 17 Sep 2020 10:19:24 +0000 (11:19 +0100)]
JAL-3700 additions and corrections to unit tests
(trivial) Conflicts:
test/jalview/util/MappingUtilsTest.java
Jim Procter [Wed, 21 Oct 2020 15:24:46 +0000 (16:24 +0100)]
JAL-3766 release notes for JAL-3611 JAL-3765
Jim Procter [Wed, 21 Oct 2020 15:21:28 +0000 (16:21 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' of source.jalview.org/git/jalview into releases/Release_2_11_1_Branch
Jim Procter [Wed, 21 Oct 2020 15:20:59 +0000 (16:20 +0100)]
Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 21 Oct 2020 15:20:46 +0000 (16:20 +0100)]
JAL-3766 cut new patch release
Jim Procter [Tue, 20 Oct 2020 16:23:30 +0000 (17:23 +0100)]
JAL-3765 fix test
Jim Procter [Tue, 20 Oct 2020 16:13:33 +0000 (17:13 +0100)]
fix for JAL-3765
Jim Procter [Mon, 19 Oct 2020 17:07:29 +0000 (18:07 +0100)]
JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence
Ben Soares [Wed, 29 Apr 2020 14:55:58 +0000 (15:55 +0100)]
JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar
Jim Procter [Tue, 29 Sep 2020 15:41:39 +0000 (16:41 +0100)]
JAL-3760 fix tests for changed behaviour
Jim Procter [Tue, 29 Sep 2020 14:26:34 +0000 (15:26 +0100)]
JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like
git://source.jalview.org / jalview.git / log