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
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.
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
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
Jim Procter [Mon, 13 Sep 2021 16:04:22 +0000 (17:04 +0100)]
JAL-3829 ensure unmock the FTS PDB and TDB clients after mocking for a test
Ben Soares [Mon, 13 Sep 2021 15:46:31 +0000 (16:46 +0100)]
JAL-2422 Added linux rpm and deb install locations. Changed macOS to also look for version numbers in Chimera/X (e.g. '/Applications/ChimeraX-1.2.5.app') as this is default macOS installation. Changed macOS preferences to check endswith '.app' and look for '....app/Contents/MacOS/ChimeraX' so user can select the .app folder
Jim Procter [Mon, 13 Sep 2021 15:02:25 +0000 (16:02 +0100)]
JAL-3829 minimal test of additional TDB filters - not at all robust
Jim Procter [Mon, 13 Sep 2021 15:02:02 +0000 (16:02 +0100)]
JAL-3829 select single best TDB structure and select structures from particular provider (this code is horrific !)
Jim Procter [Sun, 12 Sep 2021 14:53:39 +0000 (15:53 +0100)]
JAL-3829 JalviewJS workarounds/patches
Jim Procter [Sun, 12 Sep 2021 14:53:06 +0000 (15:53 +0100)]
JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to 14.31.54 and SwingJS to 3.3.1
Jim Procter [Sat, 11 Sep 2021 11:10:40 +0000 (12:10 +0100)]
JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response
Jim Procter [Sat, 11 Sep 2021 10:53:05 +0000 (11:53 +0100)]
JAL-3829 patch failing tests and todo for future
Jim Procter [Fri, 10 Sep 2021 14:06:56 +0000 (15:06 +0100)]
JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box
Jim Procter [Fri, 10 Sep 2021 12:45:07 +0000 (13:45 +0100)]
JAL-3829 insert title for structures from PDBe
Jim Procter [Fri, 10 Sep 2021 12:44:30 +0000 (13:44 +0100)]
JAL-3829 update for v1.0 3d-beacons api spec
Jim Procter [Fri, 10 Sep 2021 12:42:57 +0000 (13:42 +0100)]
JAL-3829 point at production 3d-beacons url
Jim Procter [Wed, 8 Sep 2021 15:58:22 +0000 (16:58 +0100)]
JAL-3829 refactor and JAL-3391 JAL-2935 first stab at coverage based selection of models for a sequence
Jim Procter [Wed, 8 Sep 2021 12:33:20 +0000 (13:33 +0100)]
JAL-3829 allow client-side selection of structures for a sequence by passing in discovered structures
Jim Procter [Wed, 8 Sep 2021 12:31:05 +0000 (13:31 +0100)]
JAL-3829 JAL-3868 TODO
Jim Procter [Wed, 8 Sep 2021 11:37:00 +0000 (12:37 +0100)]
JAL-3829 formatting
Jim Procter [Wed, 8 Sep 2021 11:34:47 +0000 (12:34 +0100)]
JAL-3829 integration test verifying mock response is valid for a live server
Jim Procter [Mon, 6 Sep 2021 13:48:46 +0000 (14:48 +0100)]
JAL-3829 work in progress - look up additional metadata from PDBe for structures discovered via TDBFTS
Jim Procter [Mon, 6 Sep 2021 13:47:41 +0000 (14:47 +0100)]
JAL-3829 look up column in FTS data
Jim Procter [Mon, 6 Sep 2021 13:47:03 +0000 (14:47 +0100)]
JAL-3829 mocking for PDBFTS for related query to UniprotFTS mock.
Jim Procter [Mon, 6 Sep 2021 09:52:49 +0000 (10:52 +0100)]
JAL-3829 pull out structure chooser query source tests to new class
Jim Procter [Fri, 3 Sep 2021 17:47:53 +0000 (18:47 +0100)]
JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
Jim Procter [Fri, 3 Sep 2021 17:42:42 +0000 (18:42 +0100)]
JAL-3829 use sequence dependent constructor for structure chooser query engine testing
Jim Procter [Fri, 3 Sep 2021 17:41:32 +0000 (18:41 +0100)]
JAL-3829 mocking for testing 3D-Beacons FTS endpoint
Jim Procter [Fri, 3 Sep 2021 17:39:14 +0000 (18:39 +0100)]
JAL-3863 promote non-canonical version of dbref to a canonical one
Jim Procter [Fri, 3 Sep 2021 16:01:43 +0000 (17:01 +0100)]
JAL-3829 comments on the 3D structure chooser’s initialisation process
Jim Procter [Fri, 3 Sep 2021 16:01:04 +0000 (17:01 +0100)]
JAL-3865 isolate PDB and TDB clients and last query records in their query objects
Jim Procter [Fri, 3 Sep 2021 15:45:16 +0000 (16:45 +0100)]
JAL-3863 passing test to verify a uniprot accession with canonical flag set is transferred via the DBRefFetcher (and the SequenceI.transferAnnotation method it calls)
Jim Procter [Fri, 3 Sep 2021 14:37:29 +0000 (15:37 +0100)]
JAL-3829 JAL-3865 StructureChooserQuerySource implementation now dependent on the type of sequences and whether they have uniprot sequence IDs
Jim Procter [Fri, 3 Sep 2021 14:36:05 +0000 (15:36 +0100)]
JAL-3855 don’t need to query Alphafold2 repository directly from PDBe FTS client since 3db client will do that
Jim Procter [Fri, 3 Sep 2021 14:33:49 +0000 (15:33 +0100)]
JAL-3829 refactored FilterOption provider to the StructureChooserQuerySource implementation - implementation now is completely independent of GUI code.
Jim Procter [Thu, 2 Sep 2021 14:53:01 +0000 (15:53 +0100)]
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons
Jim Procter [Thu, 2 Sep 2021 14:34:48 +0000 (15:34 +0100)]
Merge branch 'cherry-pick/r2_11_2_JAL-3509' into develop
gmungoc [Thu, 6 Feb 2020 16:58:11 +0000 (16:58 +0000)]
JAL-1842 unit test updated for EnsemblGene feature settings changes
gmungoc [Thu, 6 Feb 2020 16:24:46 +0000 (16:24 +0000)]
JAL-1842 adjust code to match changed semantics of FeatureSettingsModelI
gmungoc [Thu, 6 Feb 2020 16:20:13 +0000 (16:20 +0000)]
JAL-3509 JAL-1842 minor tidying of code
gmungoc [Thu, 6 Feb 2020 15:32:36 +0000 (15:32 +0000)]
JAL-1842 remove redundant call to FeatureRenderer.featuresAdded()
gmungoc [Thu, 6 Feb 2020 15:21:30 +0000 (15:21 +0000)]
JAL-3509 better placement of call to notifyFeaturesChanged()
gmungoc [Thu, 6 Feb 2020 14:44:38 +0000 (14:44 +0000)]
JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB - resolved conflicts for 2.11.2