Jim Procter [Tue, 21 Sep 2021 20:59:51 +0000 (21:59 +0100)]
JAL-3746 release notes and what’s new for 2.11.2 - in progress
Jim Procter [Tue, 21 Sep 2021 15:24:15 +0000 (16:24 +0100)]
Merge branch 'doc/JAL-3746_Release_2_11_2' into develop
Jim Procter [Tue, 21 Sep 2021 13:24:24 +0000 (14:24 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Tue, 21 Sep 2021 12:54:23 +0000 (13:54 +0100)]
JAL-3829 - callback finessing - leave DBRefFetcher to do progress updates itself
Jim Procter [Tue, 21 Sep 2021 10:41:18 +0000 (11:41 +0100)]
JAL-3829 prefix PDBe filters with PDBe to make clear what they search
Jim Procter [Tue, 21 Sep 2021 10:36:27 +0000 (11:36 +0100)]
JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched
Jim Procter [Tue, 21 Sep 2021 07:30:03 +0000 (08:30 +0100)]
JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry
Ben Soares [Tue, 21 Sep 2021 08:57:00 +0000 (09:57 +0100)]
JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.
Ben Soares [Mon, 20 Sep 2021 16:48:27 +0000 (17:48 +0100)]
JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle
Jim Procter [Mon, 20 Sep 2021 13:56:34 +0000 (14:56 +0100)]
JAL-3829 updated response for P01308
Jim Procter [Mon, 20 Sep 2021 13:56:15 +0000 (14:56 +0100)]
JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality
Jim Procter [Mon, 20 Sep 2021 13:55:27 +0000 (14:55 +0100)]
JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession
Jim Procter [Mon, 20 Sep 2021 13:54:50 +0000 (14:54 +0100)]
JAL-3829 throw the exception even if it has no message
Jim Procter [Mon, 20 Sep 2021 13:54:14 +0000 (14:54 +0100)]
JAL-3829 ensure nulls are not wildcards when retrieving annotation by calcId/label/description
Ben Soares [Mon, 20 Sep 2021 13:25:48 +0000 (14:25 +0100)]
JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem
Ben Soares [Mon, 20 Sep 2021 12:11:55 +0000 (13:11 +0100)]
JAL-3521 not quite working minimal build.gradle for debian and 2.11.2
Jim Procter [Mon, 20 Sep 2021 10:19:35 +0000 (11:19 +0100)]
JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view
Jim Procter [Mon, 20 Sep 2021 10:16:44 +0000 (11:16 +0100)]
JAL-3829 make sure structure data type reflects actual format identified
Jim Procter [Mon, 20 Sep 2021 10:14:41 +0000 (11:14 +0100)]
JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc
Jim Procter [Mon, 20 Sep 2021 10:13:12 +0000 (11:13 +0100)]
JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file
Ben Soares [Fri, 17 Sep 2021 17:16:57 +0000 (18:16 +0100)]
Merge branch 'merge/develop_JAL-1260' into develop
Ben Soares [Fri, 17 Sep 2021 17:11:05 +0000 (18:11 +0100)]
JAL-1260 rudimentary parsing of LOCUS line to at least get accession id
Jim Procter [Fri, 17 Sep 2021 16:42:17 +0000 (17:42 +0100)]
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons
Jim Procter [Fri, 17 Sep 2021 16:39:42 +0000 (17:39 +0100)]
JAL-3079 JAL-3055 remember to reset font transform after rendering logo
gmungoc [Tue, 18 Aug 2020 14:32:00 +0000 (15:32 +0100)]
JAL-1260 refactored multi-line qualifier separators
gmungoc [Tue, 18 Aug 2020 13:39:25 +0000 (14:39 +0100)]
JAL-1260 unit test for FileFormats updated for GenBank/ENA
gmungoc [Tue, 18 Aug 2020 13:22:56 +0000 (14:22 +0100)]
JAL-1260 file formats and IdentifyFile updates for GenBank and ENA
gmungoc [Tue, 18 Aug 2020 12:05:24 +0000 (13:05 +0100)]
JAL-1260 refactored GenBank (and EMBL) flat file parser
Jim Procter [Mon, 3 Aug 2020 13:07:03 +0000 (14:07 +0100)]
JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routine for this format
Jim Procter [Fri, 17 Sep 2021 12:13:35 +0000 (13:13 +0100)]
JAL-2226 transfer chain annotation when calcId, label and description are distinct - so annotations from multiple chains and structures are all shown.
Jim Procter [Fri, 17 Sep 2021 12:12:34 +0000 (13:12 +0100)]
JAL-2226 new method to search for annotation matching particular description as well as calcId and label
Jim Procter [Fri, 17 Sep 2021 10:45:37 +0000 (11:45 +0100)]
JAL-3829 belt and braces check to make sure there is a pdbe response available to join records from
Ben Soares [Thu, 16 Sep 2021 17:07:09 +0000 (18:07 +0100)]
JAL-3779 Added to documentation
gmungoc [Fri, 20 Nov 2020 13:04:11 +0000 (13:04 +0000)]
JAL-3779 apply properties to all groups with given name, not just first
Ben Soares [Thu, 16 Sep 2021 12:53:55 +0000 (13:53 +0100)]
JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.
Jim Procter [Thu, 16 Sep 2021 12:47:35 +0000 (13:47 +0100)]
Merge branch 'develop' into doc/JAL-3746_Release_2_11_2
Ben Soares [Thu, 16 Sep 2021 11:07:52 +0000 (12:07 +0100)]
JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText
Jim Procter [Fri, 8 Jan 2021 16:06:59 +0000 (16:06 +0000)]
JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine
Jim Procter [Fri, 8 Jan 2021 16:05:39 +0000 (16:05 +0000)]
JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).
Ben Soares [Thu, 16 Sep 2021 09:24:10 +0000 (10:24 +0100)]
JAL-3761 listToArray became rangeListToArray
gmungoc [Sat, 26 Dec 2020 08:51:37 +0000 (08:51 +0000)]
JAL-3761 more consistent parameter naming
gmungoc [Wed, 2 Dec 2020 19:59:33 +0000 (19:59 +0000)]
JAL-3761 helper method reinstated to avoid code duplication
gmungoc [Thu, 26 Nov 2020 14:17:41 +0000 (14:17 +0000)]
JAL-3761 locateInFrom/To revised with tests; unused methods removed
gmungoc [Fri, 20 Nov 2020 11:59:09 +0000 (11:59 +0000)]
JAL-3761 extra check that VCF feature is fully mappable to sequence
gmungoc [Fri, 20 Nov 2020 11:58:42 +0000 (11:58 +0000)]
JAL-3761 debugged and working (but not tidied) locateInFrom2/To2
Ben Soares [Thu, 16 Sep 2021 09:17:51 +0000 (10:17 +0100)]
JAL-3761 listToArray became rangeListToArray
gmungoc [Thu, 12 Nov 2020 10:03:02 +0000 (10:03 +0000)]
JAL-3761 locateInFrom2 work in progress commit
gmungoc [Thu, 29 Oct 2020 15:50:58 +0000 (15:50 +0000)]
JAL-3761 unit test for MapList.countPos()
gmungoc [Thu, 8 Oct 2020 07:40:18 +0000 (08:40 +0100)]
JAL-3761 failing test, formatting, method renamed
gmungoc [Thu, 1 Oct 2020 11:42:32 +0000 (12:42 +0100)]
JAL-3761 failing tests for locateInFrom/To with overlapping ranges
gmungoc [Thu, 24 Sep 2020 10:55:20 +0000 (11:55 +0100)]
JAL-3751 only merge strictly contiguous ranges of mappings
gmungoc [Tue, 29 Dec 2020 16:38:35 +0000 (16:38 +0000)]
JAL-3788 synchronize concurrent findColour() and alignmentChanged()
Ben Soares [Wed, 15 Sep 2021 19:00:48 +0000 (20:00 +0100)]
JAL-3818 formatting
gmungoc [Thu, 11 Feb 2021 11:30:20 +0000 (11:30 +0000)]
JAL-3818 process Jmol callbacks in AWT thread
Ben Soares [Wed, 15 Sep 2021 16:19:15 +0000 (17:19 +0100)]
Merge branch 'develop' into merge/develop_ben2
Ben Soares [Wed, 15 Sep 2021 16:16:25 +0000 (17:16 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Wed, 15 Sep 2021 16:16:17 +0000 (17:16 +0100)]
JAL-3829 Fixed Jmol jar -- duplicates of other classes were causing problem with shadow jar
Jim Procter [Wed, 15 Sep 2021 16:06:02 +0000 (17:06 +0100)]
Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop
Jim Procter [Wed, 15 Sep 2021 15:28:29 +0000 (16:28 +0100)]
JAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick
Jim Procter [Wed, 15 Sep 2021 15:19:08 +0000 (16:19 +0100)]
JAL-3842 fix automatic what's new link for custom version builds
Jim Procter [Wed, 15 Sep 2021 15:17:11 +0000 (16:17 +0100)]
JAL-3842 2.11.1.5 what’s new, release notes, and version bump
Conflicts:
RELEASE
Jim Procter [Wed, 15 Sep 2021 15:16:15 +0000 (16:16 +0100)]
JAL-3816 bump version number and cut release notes
Conflicts:
RELEASE
doc/building.html
Jim Procter [Wed, 15 Sep 2021 15:11:33 +0000 (16:11 +0100)]
JAL-3766 cut new patch release
Conflicts:
RELEASE
Jim Procter [Wed, 15 Sep 2021 15:10:52 +0000 (16:10 +0100)]
JAL-3758 2.11.1.2 patch release notes and version bump
Conflicts:
RELEASE
Jim Procter [Wed, 15 Sep 2021 15:09:52 +0000 (16:09 +0100)]
JAL-3741 http to https (and jar to jvp for exampleFile defaults!)
Conflicts:
src/jalview/bin/Jalview.java
src/jalview/gui/Desktop.java
Jim Procter [Wed, 15 Sep 2021 15:00:20 +0000 (16:00 +0100)]
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax
Jim Procter [Wed, 15 Sep 2021 14:56:47 +0000 (15:56 +0100)]
JAL-3675 version update and documentation for JAL-3493 JAL-3680 JAL-3638
Conflicts:
RELEASE
Jim Procter [Wed, 15 Sep 2021 14:55:46 +0000 (15:55 +0100)]
JAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in cursor mode.
help/help/html/keys.html
Ben Soares [Wed, 15 Sep 2021 14:51:01 +0000 (15:51 +0100)]
Merge branch 'develop' into merge/develop_ben2
Jim Procter [Wed, 15 Sep 2021 06:34:28 +0000 (07:34 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Sun, 7 Feb 2021 16:05:24 +0000 (16:05 +0000)]
JAL-3815 default /etc/jalview_properties under utils/debian
Jim Procter [Tue, 14 Sep 2021 18:10:15 +0000 (19:10 +0100)]
JAL-3829 parallel not welcome here
Jim Procter [Tue, 14 Sep 2021 17:59:44 +0000 (18:59 +0100)]
JAL-3829 test flakiness and human flakiness
Jim Procter [Tue, 14 Sep 2021 17:55:40 +0000 (18:55 +0100)]
JAL-3829 more info on test fail - seems to be flaky
Ben Soares [Tue, 14 Sep 2021 17:27:55 +0000 (18:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
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
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
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
Jim Procter [Tue, 14 Sep 2021 16:24:39 +0000 (17:24 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Tue, 14 Sep 2021 16:15:23 +0000 (17:15 +0100)]
JAL-3551 - doc tweak
Jim Procter [Tue, 14 Sep 2021 16:14:23 +0000 (17:14 +0100)]
JAL-3855 JAL-3829 better checks on PDB or mmCIF file based on URL path (though should really determine when processing via jmolData now we have mechanism) - ChimeraX in particular cares about file endings
Jim Procter [Tue, 14 Sep 2021 16:11:53 +0000 (17:11 +0100)]
JAL-3829 JAL-3855 moved routing for retrieving structures prior to opening a Jmol view to AppJmolBinding - this could be refactored further
Jim Procter [Tue, 14 Sep 2021 16:01:57 +0000 (17:01 +0100)]
JAL-3829 JAL-3855 ignore case when detecting alphafold ID
Jim Procter [Tue, 14 Sep 2021 14:51:39 +0000 (15:51 +0100)]
JAL-3855 detect an alphafold model and import its temperature factor as reliability
Jim Procter [Tue, 14 Sep 2021 13:38:02 +0000 (14:38 +0100)]
JAL-3829 move mock query and responses to files
Ben Soares [Tue, 14 Sep 2021 12:36:11 +0000 (13:36 +0100)]
JAL-2422 Also look in ~/Applications for ChimeraX on macOS
Jim Procter [Tue, 14 Sep 2021 11:58:51 +0000 (12:58 +0100)]
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons
Jim Procter [Tue, 14 Sep 2021 11:58:21 +0000 (12:58 +0100)]
Merge branch 'feature/JAL-2422ChimeraX' into develop
Jim Procter [Tue, 14 Sep 2021 11:36:17 +0000 (12:36 +0100)]
JAL-3829 3d-beacons doesn’t work as a sequence source just now
Jim Procter [Tue, 14 Sep 2021 11:36:01 +0000 (12:36 +0100)]
JAL-3829 avoid sending rubbish to PDBe search api
Jim Procter [Tue, 14 Sep 2021 11:35:20 +0000 (12:35 +0100)]
JAL-3829 some providers don’t provide model quality, some experimental methods don’t provide a resolution - try to leave these in their natural order
Jim Procter [Tue, 14 Sep 2021 11:34:10 +0000 (12:34 +0100)]
JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks
Ben Soares [Tue, 14 Sep 2021 09:52:42 +0000 (10:52 +0100)]
JAL-2422 More helpful highlighting/user guidance of missing structure viewer path
Ben Soares [Tue, 14 Sep 2021 08:26:46 +0000 (09:26 +0100)]
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon). Better UTF-8 Name call.
Ben Soares [Mon, 13 Sep 2021 19:58:38 +0000 (20:58 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Mon, 13 Sep 2021 19:58:28 +0000 (20:58 +0100)]
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon)
Ben Soares [Mon, 13 Sep 2021 17:05:44 +0000 (18:05 +0100)]
Merge branch 'develop' into feature/JAL-2422ChimeraX
Jim Procter [Mon, 13 Sep 2021 16:22:20 +0000 (17:22 +0100)]
Merge branch 'releases/Release_2_11_2_Branch' into develop
Jim Procter [Mon, 13 Sep 2021 16:22:10 +0000 (17:22 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Mon, 13 Sep 2021 16:19:18 +0000 (17:19 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into releases/Release_2_11_2_Branch