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
Jim Procter [Tue, 15 Sep 2020 15:34:53 +0000 (16:34 +0100)]
Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Ben Soares [Tue, 15 Sep 2020 15:17:18 +0000 (16:17 +0100)]
JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.
Ben Soares [Mon, 14 Sep 2020 22:23:11 +0000 (23:23 +0100)]
JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files
Jim Procter [Tue, 15 Sep 2020 12:52:02 +0000 (13:52 +0100)]
JAL-3675 typo in release notes :(
Jim Procter [Tue, 15 Sep 2020 11:43:35 +0000 (12:43 +0100)]
JAL-3675 update release date and release notes for JAL-3732
gmungoc [Thu, 18 Jun 2020 14:43:51 +0000 (15:43 +0100)]
JAL-3648 resize annotation panel after dragging to resize graph height
Jim Procter [Thu, 3 Sep 2020 12:43:40 +0000 (13:43 +0100)]
JAL-3675 update release date and release notes for JAL-3280
Jim Procter [Thu, 3 Sep 2020 11:20:22 +0000 (12:20 +0100)]
Merge branch 'improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 3 Sep 2020 10:42:43 +0000 (11:42 +0100)]
JAL-3675 whats new, logging and release notes tidying for 2.11.1.1.
Jim Procter [Thu, 3 Sep 2020 09:52:04 +0000 (10:52 +0100)]
JAL-3676 rework logging docs.
Jim Procter [Thu, 3 Sep 2020 08:07:42 +0000 (09:07 +0100)]
Merge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_correctly' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 3 Sep 2020 07:07:48 +0000 (08:07 +0100)]
JAL-3676 remove mention of Castor
Jim Procter [Thu, 3 Sep 2020 06:41:45 +0000 (07:41 +0100)]
JAL-3675 tweak release notes for JAL-3667, JAL-3702
Jim Procter [Thu, 3 Sep 2020 06:21:56 +0000 (07:21 +0100)]
JAL-3675 update sequence fetcher service documentation for JAL-3692 (ENA Flatfile) and refreshed links for other endpoints.
Ben Soares [Wed, 2 Sep 2020 17:25:40 +0000 (18:25 +0100)]
JAL-3280 Test for remote release build_properties file version check
Ben Soares [Tue, 1 Sep 2020 16:45:21 +0000 (17:45 +0100)]
JAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.
Ben Soares [Mon, 31 Aug 2020 17:38:15 +0000 (18:38 +0100)]
JAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults to release appbase) for build_properties VERSION insteadl of jnlp file.
Jim Procter [Mon, 31 Aug 2020 17:05:59 +0000 (18:05 +0100)]
JAL-3680 merged description of individual cursor key actions
Jim Procter [Mon, 31 Aug 2020 16:49:18 +0000 (17:49 +0100)]
JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow
JAL-3733 TODO - provide an undo for sequence/group up/down moves
Ben Soares [Fri, 28 Aug 2020 10:10:33 +0000 (11:10 +0100)]
JAL-3676 adding Axis and Castor loggging properties to the help text
Ben Soares [Thu, 27 Aug 2020 14:53:02 +0000 (15:53 +0100)]
JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
Ben Soares [Thu, 27 Aug 2020 09:09:13 +0000 (10:09 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
Jim Procter [Tue, 25 Aug 2020 16:45:53 +0000 (17:45 +0100)]
report JAL-3127 as known defect (fix targeted for 2.11.2)
Jim Procter [Fri, 26 Jun 2020 16:12:31 +0000 (17:12 +0100)]
JAL-3671 hardwire log4j.root logger to INFO to supress jetty and httpclient log output
Jim Procter [Fri, 21 Aug 2020 10:45:26 +0000 (11:45 +0100)]
JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam
git://source.jalview.org / jalview.git / log