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
Ben Soares [Fri, 25 Sep 2020 08:39:02 +0000 (09:39 +0100)]
JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle
Jim Procter [Fri, 25 Sep 2020 07:16:18 +0000 (08:16 +0100)]
JAL-3758 tweak what’s new for 2.11.1.2!
Jim Procter [Fri, 25 Sep 2020 07:05:03 +0000 (08:05 +0100)]
JAL-3758 release Fri 25th Sep
Jim Procter [Fri, 25 Sep 2020 06:45:13 +0000 (07:45 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' of source.jalview.org/git/jalview into releases/Release_2_11_1_Branch
Ben Soares [Thu, 24 Sep 2020 17:16:17 +0000 (18:16 +0100)]
JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...
Jim Procter [Thu, 24 Sep 2020 13:38:44 +0000 (14:38 +0100)]
JAL-3758 2.11.1.2 patch release notes and version bump
Jim Procter [Thu, 24 Sep 2020 13:36:17 +0000 (14:36 +0100)]
JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)
Ben Soares [Wed, 23 Sep 2020 22:41:36 +0000 (23:41 +0100)]
JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as
Ben Soares [Wed, 8 Jul 2020 16:01:32 +0000 (17:01 +0100)]
JAL-3633 ensure check both or https:// for urls
Jim Procter [Wed, 23 Sep 2020 16:34:32 +0000 (17:34 +0100)]
JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows testAlignProteinAsDna_incompleteStartCodon to pass
Jim Procter [Wed, 23 Sep 2020 16:17:10 +0000 (17:17 +0100)]
JAL-3748 fix compilation error
Jim Procter [Wed, 23 Sep 2020 16:11:39 +0000 (17:11 +0100)]
JAL-3748 maximal test for JAL-3748 using covid19 CDS/Protein
Jim Procter [Wed, 23 Sep 2020 15:39:51 +0000 (16:39 +0100)]
JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region
Jim Procter [Wed, 23 Sep 2020 15:38:50 +0000 (16:38 +0100)]
JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch
Jim Procter [Wed, 23 Sep 2020 15:35:18 +0000 (16:35 +0100)]
JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.
Jim Procter [Tue, 22 Sep 2020 14:30:18 +0000 (15:30 +0100)]
JAL-3748 test data for SplitFrameTest
Jim Procter [Tue, 22 Sep 2020 14:09:51 +0000 (15:09 +0100)]
JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash
Jim Procter [Tue, 22 Sep 2020 13:45:11 +0000 (14:45 +0100)]
JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences
Jim Procter [Tue, 22 Sep 2020 13:30:23 +0000 (14:30 +0100)]
JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar
Jim Procter [Thu, 17 Sep 2020 12:38:15 +0000 (13:38 +0100)]
JAL-3675 release notes for JAL-3750 JAL-3751
Jim Procter [Thu, 17 Sep 2020 11:28:03 +0000 (12:28 +0100)]
Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 17 Sep 2020 11:19:40 +0000 (12:19 +0100)]
JAL-3741 http to https (and jar to jvp for exampleFile defaults!)
Jim Procter [Thu, 17 Sep 2020 11:09:42 +0000 (12:09 +0100)]
JAL-3750 parse protocol before checking if argument to -open can be opened as a file
Jim Procter [Thu, 17 Sep 2020 10:35:46 +0000 (11:35 +0100)]
JAL-3675 patch release date 17th September 2020
Jim Procter [Wed, 16 Sep 2020 16:46:36 +0000 (17:46 +0100)]
JAL-3748 preserve sequence IDs from original alignment view when alignment returned by web service or analysis method.
Jim Procter [Wed, 16 Sep 2020 16:45:12 +0000 (17:45 +0100)]
JAL-3748 recover complement alignment from complement alignmentView rather than let ‘alignAs’ to do the work
Jim Procter [Wed, 16 Sep 2020 16:43:18 +0000 (17:43 +0100)]
JAL-3748 make findAlignedSequence require mapped from/to to properly contain the given CDS or protein sequence
Jim Procter [Wed, 16 Sep 2020 16:39:22 +0000 (17:39 +0100)]
JAL-3748 pass a list to findAlignedSequence to return mapping that relates CDS and the returned Peptide sequence to avoid searching twice
Jim Procter [Wed, 16 Sep 2020 16:37:15 +0000 (17:37 +0100)]
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence
Jim Procter [Wed, 16 Sep 2020 16:33:26 +0000 (17:33 +0100)]
JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true) to verify mapping matches seq’s dataset sequence start/end rather than seq
Jim Procter [Wed, 16 Sep 2020 09:06:46 +0000 (10:06 +0100)]
Merge branch 'failingTest/JAL-3748_reconstructCDSafterProteinMSA' into cherry-pick/JAL-3700mapSequenceSelection
gmungoc [Wed, 5 Aug 2020 08:13:33 +0000 (09:13 +0100)]
JAL-3700 fix for propagation of sort commands
gmungoc [Mon, 3 Aug 2020 15:28:15 +0000 (16:28 +0100)]
JAL-3700 check for 'covering' mapping when matching CDS to peptides
Jim Procter [Wed, 16 Sep 2020 06:02:04 +0000 (07:02 +0100)]
JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView so it can be recovered after a web service operation
Jim Procter [Tue, 15 Sep 2020 17:05:24 +0000 (18:05 +0100)]
JAL-3675 logged JAL-3748 as known defect
Jim Procter [Tue, 15 Sep 2020 15:48:48 +0000 (16:48 +0100)]
JAL-3765 JAL-3718 release notes
git://source.jalview.org / jalview.git / log