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
Jim Procter [Mon, 17 Aug 2020 15:56:52 +0000 (16:56 +0100)]
JAL-3675 release notes for JAL-3691
Jim Procter [Mon, 17 Aug 2020 15:53:31 +0000 (16:53 +0100)]
Merge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 15:49:16 +0000 (16:49 +0100)]
JAL-3675 JAL-3561 documented in release notes
Jim Procter [Mon, 17 Aug 2020 15:38:49 +0000 (16:38 +0100)]
JAL-3675 report JAL-3702 as known defect
Jim Procter [Mon, 17 Aug 2020 15:25:07 +0000 (16:25 +0100)]
Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 15:09:26 +0000 (16:09 +0100)]
JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.
Jim Procter [Mon, 17 Aug 2020 11:13:03 +0000 (12:13 +0100)]
JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1
Jim Procter [Mon, 17 Aug 2020 10:03:57 +0000 (11:03 +0100)]
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 09:51:05 +0000 (10:51 +0100)]
JAL-3675 JAL-3597 release notes
Jim Procter [Mon, 17 Aug 2020 09:03:47 +0000 (10:03 +0100)]
Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Ben Soares [Fri, 14 Aug 2020 12:01:06 +0000 (13:01 +0100)]
JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.
Ben Soares [Thu, 13 Aug 2020 22:05:00 +0000 (23:05 +0100)]
JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size
gmungoc [Mon, 20 Jul 2020 08:17:29 +0000 (09:17 +0100)]
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB
gmungoc [Tue, 14 Jul 2020 08:43:50 +0000 (09:43 +0100)]
JAL-3597 additional references nulled, bug in test corrected
Jim Procter [Thu, 13 Aug 2020 16:51:44 +0000 (17:51 +0100)]
JAL-3675 brought forward patch to build.gradle for changed main class variable in build.properties
Jim Procter [Thu, 13 Aug 2020 14:53:53 +0000 (15:53 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' of source.jalview.org/git/jalview into releases/Release_2_11_1_Branch
Ben Soares [Wed, 12 Aug 2020 12:48:57 +0000 (13:48 +0100)]
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.
Jim Procter [Wed, 12 Aug 2020 12:29:23 +0000 (13:29 +0100)]
JAL-3675 added JAL-3576 as known defect (colocated features appear in different order when exported/reimported)
Ben Soares [Tue, 7 Jul 2020 23:47:55 +0000 (00:47 +0100)]
JAL-3608 Changes from code review CR-JAL-236
Conflicts:
src/jalview/bin/Jalview.java
Jim Procter [Tue, 11 Aug 2020 15:24:26 +0000 (16:24 +0100)]
JAL-3675 fix issue attribution for JAL-3667 release note line
Jim Procter [Tue, 11 Aug 2020 14:54:24 +0000 (15:54 +0100)]
JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for JAL-2983
Jim Procter [Fri, 26 Jun 2020 16:24:16 +0000 (17:24 +0100)]
JAL-3673 make sure font metrics are updated if dealing with reference sequence font !
Jim Procter [Tue, 11 Aug 2020 14:01:10 +0000 (15:01 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
gmungoc [Tue, 11 Aug 2020 09:35:32 +0000 (10:35 +0100)]
JAL-3371 more fine-grained slider; set Param slider to initial default
gmungoc [Thu, 6 Aug 2020 08:49:23 +0000 (09:49 +0100)]
JAL-3490 match count independent of contiguous matches count
Jim Procter [Mon, 10 Aug 2020 14:10:35 +0000 (15:10 +0100)]
JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations
Jim Procter [Mon, 10 Aug 2020 14:02:53 +0000 (15:02 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into patch/JAL-3691_No_score_models_available
Jim Procter [Mon, 10 Aug 2020 14:01:23 +0000 (15:01 +0100)]
JAL-3628 JAL-3708 call Cache.initLogger() before using Cache.log in static methods with no class-level guarantee logs are initialised
Ben Soares [Wed, 5 Aug 2020 21:57:13 +0000 (22:57 +0100)]
JAL-3691 Changed .toUppoerCase().startsWith(...) to .regionMatches(true,...) as upper-cased 'i' in Turkish is not 'I'.
Jim Procter [Wed, 5 Aug 2020 16:41:36 +0000 (17:41 +0100)]
JAL-3628 init log after loading testProps for each backupfile test
Jim Procter [Wed, 5 Aug 2020 16:29:19 +0000 (17:29 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
gmungoc [Wed, 5 Aug 2020 16:01:37 +0000 (17:01 +0100)]
JAL-3692 unit test updated for ?gzip download endpoint URL
gmungoc [Wed, 5 Aug 2020 15:53:17 +0000 (16:53 +0100)]
JAL-3692 parse multiline feature qualifiers and escaped quotes
Jim Procter [Wed, 5 Aug 2020 15:41:48 +0000 (16:41 +0100)]
JAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL-3677 and bumped release date for 2.11.1.1 to next Tuesday(ish)
Jim Procter [Wed, 5 Aug 2020 14:47:31 +0000 (15:47 +0100)]
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Ben Soares [Tue, 4 Aug 2020 18:30:47 +0000 (19:30 +0100)]
JAL-3477 Improved command line arguments description in memory.html
Ben Soares [Tue, 4 Aug 2020 17:13:02 +0000 (18:13 +0100)]
JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html
Ben Soares [Mon, 3 Aug 2020 10:20:05 +0000 (11:20 +0100)]
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax
Jim Procter [Mon, 3 Aug 2020 13:38:19 +0000 (14:38 +0100)]
JAL-3675 report JAL-3701 as known defect
Jim Procter [Mon, 3 Aug 2020 13:10:41 +0000 (14:10 +0100)]
JAL-3675 release notes for JAL-3692
Jim Procter [Mon, 3 Aug 2020 12:45:49 +0000 (13:45 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 3 Aug 2020 11:06:42 +0000 (12:06 +0100)]
JAL-3692 fix up test for 2.11.1 series datamodel API
gmungoc [Mon, 27 Jul 2020 15:34:04 +0000 (16:34 +0100)]
JAL-3692 set CDS /product as EMBLCDSPROTEIN description
gmungoc [Mon, 27 Jul 2020 15:26:08 +0000 (16:26 +0100)]
JAL-3692 refactor/complete parsing, more unit test coverage
gmungoc [Fri, 24 Jul 2020 08:38:45 +0000 (09:38 +0100)]
JAL-3692 parse DE for description, and other refactoring...
gmungoc [Thu, 23 Jul 2020 10:43:32 +0000 (11:43 +0100)]
JAL-3692 URL tests updated
gmungoc [Wed, 22 Jul 2020 09:55:43 +0000 (10:55 +0100)]
JAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings
gmungoc [Tue, 21 Jul 2020 11:22:18 +0000 (12:22 +0100)]
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)
Conflicts:
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/ebi/EBIFetchClient.java
Ben Soares [Fri, 31 Jul 2020 16:29:34 +0000 (17:29 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum
Jim Procter [Wed, 29 Jul 2020 17:48:52 +0000 (18:48 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 29 Jul 2020 17:47:40 +0000 (18:47 +0100)]
JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel
Jim Procter [Wed, 29 Jul 2020 16:46:33 +0000 (17:46 +0100)]
JAL-3675 mention -open argument in the command line arguments table
Jim Procter [Wed, 29 Jul 2020 16:46:17 +0000 (17:46 +0100)]
JAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs
Jim Procter [Tue, 28 Jul 2020 12:43:48 +0000 (13:43 +0100)]
JAL-3675 update release note for JAL-2656
Jim Procter [Tue, 28 Jul 2020 10:32:46 +0000 (11:32 +0100)]
JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header
Jim Procter [Tue, 28 Jul 2020 10:29:20 +0000 (11:29 +0100)]
JAL-2656 recognise Gzipped file input streams by their content, not their filename
Jim Procter [Tue, 28 Jul 2020 10:18:56 +0000 (11:18 +0100)]
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints
Jim Procter [Mon, 27 Jul 2020 18:15:16 +0000 (19:15 +0100)]
JAL-3675 release notes for JAL-3615 and JAL-2656
gmungoc [Thu, 2 Jul 2020 16:24:28 +0000 (17:24 +0100)]
JAL-2656 JAL-3615 check response headers to test for gzipped url reply
gmungoc [Thu, 2 Jul 2020 14:28:36 +0000 (15:28 +0100)]
JAL-3615 used gzip endpoints for Pfam and Rfam
redact parent commits related to JalviewJS for 2.11.1.1 patch
Jim Procter [Mon, 27 Jul 2020 15:46:47 +0000 (16:46 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Conflict in way transparency slider was inited - followed HEAD's pattern here.
Jim Procter [Mon, 27 Jul 2020 15:16:34 +0000 (16:16 +0100)]
JAL-3675 release notes for JAL-3621
git://source.jalview.org / jalview.git / log