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
Ben Soares [Tue, 18 Aug 2020 23:38:12 +0000 (00:38 +0100)]
JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.
gmungoc [Tue, 18 Aug 2020 13:59:12 +0000 (14:59 +0100)]
JAL-3692 parse multiline CDS location correctly
Ben Soares [Tue, 18 Aug 2020 07:40:33 +0000 (08:40 +0100)]
JAL-3676 Start of documentation in help pages logging.html
git://source.jalview.org / jalview.git / log