Jim Procter [Fri, 21 Oct 2022 15:08:23 +0000 (16:08 +0100)]
JAL-2349 JAL-3855 experiment masking hidden columns in contact matrix
Jim Procter [Fri, 21 Oct 2022 15:04:44 +0000 (16:04 +0100)]
JAL-4033 - heuristic threshold for pAE matrix - mark any column where pAE values for column+8.. lie outside threshold - definitely better to do a watershed or other type of clustering
Jim Procter [Thu, 20 Oct 2022 20:00:49 +0000 (21:00 +0100)]
JAL-2349 formatting/pick correct exception
Jim Procter [Thu, 20 Oct 2022 16:14:24 +0000 (17:14 +0100)]
JAL-2349 JAL-3855 off by one and daft return
Jim Procter [Thu, 20 Oct 2022 15:45:16 +0000 (16:45 +0100)]
JAL-2349 avoid div-by-zero when annotation height is zero (though poss better to simply avoid rendering contact at all)
Jim Procter [Thu, 20 Oct 2022 15:29:03 +0000 (16:29 +0100)]
JAL-2349 JAL-3855 adapt renderer for AlignmentI.getContactList(..) mapping to sequence associated reference frame
Jim Procter [Thu, 20 Oct 2022 15:28:00 +0000 (16:28 +0100)]
JAL-2349 JAL-3855 ContactListI.getPosition() to recover original position passed to ContactMatrixI.getContactListFor(..)
Jim Procter [Thu, 20 Oct 2022 14:45:51 +0000 (15:45 +0100)]
JAL-2349 JAL-3855 experimenting with filtering columns based on mean of contact map range
Jim Procter [Thu, 20 Oct 2022 14:14:31 +0000 (15:14 +0100)]
JAL-3855 JAL-2349 AlignmentI.getContactList takes care of mapping columns to sequence positions for sequence associated contact matrices. Need to map selected positions back for drag selects
Jim Procter [Thu, 20 Oct 2022 13:00:49 +0000 (14:00 +0100)]
JAL-4033 fix drag selections and distinguish row/columnwise highlights from intersections on matrix
Jim Procter [Thu, 20 Oct 2022 10:23:36 +0000 (11:23 +0100)]
JAL-2349 (still buggy) interactive selection - time to write tests!
Jim Procter [Thu, 20 Oct 2022 09:50:49 +0000 (10:50 +0100)]
JAL-2349 tooltip reports value from contact range
Jim Procter [Thu, 20 Oct 2022 09:50:42 +0000 (10:50 +0100)]
JAL-2349 adjusted range calculation to be inclusive rather than inclusive, exclusive of bounds
Jim Procter [Thu, 20 Oct 2022 09:49:21 +0000 (10:49 +0100)]
JAL-2349 debugged click/drag and added yellow rubber banding (like Alphafold)
Jim Procter [Thu, 20 Oct 2022 09:08:39 +0000 (10:08 +0100)]
JAL-2349 JAL-3855 - interactive point-wise row/column selection, and first attempt at alt-drag for region selections (not yet working!)
Jim Procter [Thu, 20 Oct 2022 09:07:57 +0000 (10:07 +0100)]
JAL-3855 RGB colours from the alphafold paE scale.
Jim Procter [Wed, 19 Oct 2022 12:10:58 +0000 (13:10 +0100)]
JAL-2349 JAL-4033 refactored contact matrix geom calc to allow reporting of mapped positions in tooltip
Jim Procter [Mon, 17 Oct 2022 16:56:51 +0000 (17:56 +0100)]
JAL-2349 JAL-3855 column selection highlighting
Jim Procter [Mon, 17 Oct 2022 11:49:02 +0000 (12:49 +0100)]
JAL-3855 bump AF version to 3 - keep contact renderer happy by filling out maxcols and maxrows attribute in PAE
Jim Procter [Mon, 17 Oct 2022 11:19:34 +0000 (12:19 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 17 Oct 2022 11:19:24 +0000 (12:19 +0100)]
JAL-2349 JAL-3855 tests that probably should be part of Functional..
Jim Procter [Mon, 17 Oct 2022 11:18:44 +0000 (12:18 +0100)]
JAL-3855 report download errors as errors!
Jim Procter [Mon, 17 Oct 2022 11:18:22 +0000 (12:18 +0100)]
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred as reference annotation
Jim Procter [Sat, 15 Oct 2022 12:00:00 +0000 (13:00 +0100)]
JAL-2349 reusable contact map holder for SequenceI and AnnotatedCollectionI
Jim Procter [Sat, 15 Oct 2022 11:40:17 +0000 (12:40 +0100)]
JAL-3855 2349 TODO
Jim Procter [Sat, 15 Oct 2022 10:11:34 +0000 (11:11 +0100)]
JAL-3855 import pAE when StructureSelectionManager parses an alphaFold structure. Works but AlignmentI holding the contact matrices prevents transfer.
Jim Procter [Sat, 15 Oct 2022 10:09:52 +0000 (11:09 +0100)]
JAL-3855 pAE v2 import
Jim Procter [Fri, 14 Oct 2022 16:05:06 +0000 (17:05 +0100)]
JAL-3855 refactor the pAE retrieval code so it can be called via structureselectionmanager
Jim Procter [Fri, 14 Oct 2022 15:40:16 +0000 (16:40 +0100)]
Merge branch 'features/JAL-3895_alphafoldcolours' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Jim Procter [Fri, 14 Oct 2022 15:38:56 +0000 (16:38 +0100)]
Merge branch 'develop' into features/JAL-3895_alphafoldcolours
Jim Procter [Tue, 11 Oct 2022 15:54:16 +0000 (16:54 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:53:25 +0000 (16:53 +0100)]
JAL-4065 final fix for 2.11.2.5 - 5pm BST release
Jim Procter [Tue, 11 Oct 2022 15:16:37 +0000 (16:16 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:16:01 +0000 (16:16 +0100)]
JAL-4065 revised to avoid a visit from the apostrophe police
Jim Procter [Tue, 11 Oct 2022 14:44:01 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:43:36 +0000 (15:43 +0100)]
JAL-4073 update tests
Jim Procter [Tue, 11 Oct 2022 14:28:03 +0000 (15:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:26:59 +0000 (15:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 11 Oct 2022 14:24:32 +0000 (15:24 +0100)]
JAL-4073 fix PEBCAK failure
Ben Soares [Tue, 11 Oct 2022 13:43:10 +0000 (14:43 +0100)]
JAL-4014 Changed gecos display names to match labels in help
Jim Procter [Tue, 11 Oct 2022 12:10:56 +0000 (13:10 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 12:10:29 +0000 (13:10 +0100)]
JAL-4065 revised whatsNew to make sense !
Jim Procter [Tue, 11 Oct 2022 10:32:29 +0000 (11:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 10:32:05 +0000 (11:32 +0100)]
JAL-4065 release 2.11.2.5 date is 11th Oct
Jim Procter [Fri, 7 Oct 2022 15:32:43 +0000 (16:32 +0100)]
Fix for JAL-4075 - don’t write a label in secondary structure annotation element
Jim Procter [Fri, 7 Oct 2022 14:53:01 +0000 (15:53 +0100)]
JAL-4065 update citations for Pfam and Rfam and added the Interpro citation
Jim Procter [Fri, 7 Oct 2022 14:19:54 +0000 (15:19 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:19:21 +0000 (15:19 +0100)]
JAL-4065 2.11.2.5 release version bump
Jim Procter [Fri, 7 Oct 2022 14:14:42 +0000 (15:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:14:08 +0000 (15:14 +0100)]
JAL-4065 release notes and updated release date for 2.11.2.5
Jim Procter [Thu, 6 Oct 2022 17:14:19 +0000 (18:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 17:13:09 +0000 (18:13 +0100)]
stable url for PFAM retrieval via interpro api :) JAL-4073
Jim Procter [Thu, 6 Oct 2022 17:08:26 +0000 (18:08 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 16:25:53 +0000 (17:25 +0100)]
JAL-3895 alphafold colours via pluggable annotation row builder. Also ensures min/max set correctly
Jim Procter [Thu, 6 Oct 2022 11:36:33 +0000 (12:36 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 11:31:14 +0000 (12:31 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 11:22:09 +0000 (12:22 +0100)]
JAL-4065 release notes for JAL-4073 JAL-4074
Jim Procter [Thu, 6 Oct 2022 11:21:28 +0000 (12:21 +0100)]
JAL-4073 Pfam retrieval now works via a template including $PFAMID$ and $ALTYPE$ (full, seed, etc). Also changed name of PFAM_BASEURL_KEY to PFAM_INTERPRO_URL_TEMPLATE to avoid misconfiguration
Jim Procter [Thu, 6 Oct 2022 11:19:13 +0000 (12:19 +0100)]
Patch for JAL-4074 - any content ending in ‘gzip’ recognised as a gzipped stream to decompress
Ben Soares [Thu, 29 Sep 2022 14:55:25 +0000 (15:55 +0100)]
Merge branch 'develop' into bug/JAL-1988_JAL-3772_improved_quit_handling
Ben Soares [Mon, 26 Sep 2022 19:17:14 +0000 (20:17 +0100)]
JAL-1988 JAL-3772 linked undostack to saved changes flags. No confirmation if all viewports have been saved individually
Ben Soares [Mon, 26 Sep 2022 19:16:23 +0000 (20:16 +0100)]
JAL-1988 better wording for quit dialog
Ben Soares [Fri, 23 Sep 2022 17:34:12 +0000 (18:34 +0100)]
JAL-1988 JAL-3772 Quit confirmation dialog boxes with saving files check and wait
Ben Soares [Fri, 23 Sep 2022 17:33:36 +0000 (18:33 +0100)]
JAL-3676 extra information about jalview_properties file being used in Java Console
Ben Soares [Fri, 23 Sep 2022 17:28:14 +0000 (18:28 +0100)]
JAL-1988 property based fake delay whilst saving project file
Jim Procter [Fri, 16 Sep 2022 13:24:20 +0000 (14:24 +0100)]
JAL-4065 release notes for JAL-4061 JAL-4062
Jim Procter [Fri, 16 Sep 2022 13:23:21 +0000 (14:23 +0100)]
JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke
Jim Procter [Thu, 15 Sep 2022 17:57:20 +0000 (18:57 +0100)]
JAL-4061 JAL-4062 documentation and button labels.. will need revising !
Jim Procter [Thu, 15 Sep 2022 17:56:41 +0000 (18:56 +0100)]
JAL-4061 use alignment panel’s feature renderer to limit search to just the visible features
Jim Procter [Thu, 15 Sep 2022 17:19:35 +0000 (18:19 +0100)]
JAL-4061 support incremental search of features
Jim Procter [Thu, 15 Sep 2022 16:05:03 +0000 (17:05 +0100)]
JAL-4061 tests, bugfixes and TODOs for matching feature(s) and descriptions incrementally
Jim Procter [Thu, 15 Sep 2022 15:18:30 +0000 (16:18 +0100)]
JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequences() to clipboard
Jim Procter [Thu, 15 Sep 2022 11:23:42 +0000 (12:23 +0100)]
Merge branch 'develop' into features/JAL-4061_and_JAL-4062_findselectfeatures
Jim Procter [Thu, 15 Sep 2022 11:21:51 +0000 (12:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 15 Sep 2022 11:21:03 +0000 (12:21 +0100)]
JAL-4065 release notes for JAL-4014 and JAL-4063 in 2.11.2.5
Jim Procter [Thu, 15 Sep 2022 11:17:59 +0000 (12:17 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 15 Sep 2022 11:17:10 +0000 (12:17 +0100)]
JAL-4065 - new release notes featuring JAL-3612 fix
Jim Procter [Wed, 14 Sep 2022 11:19:13 +0000 (12:19 +0100)]
Merge branch 'bug/JAL-3612_overviewFeatureOrdering' into develop
Jim Procter [Wed, 14 Sep 2022 10:05:32 +0000 (11:05 +0100)]
JAL-4061 JAL-4062 button in Find dialog to copy highlighted regions to clipboard
Jim Procter [Wed, 14 Sep 2022 10:04:50 +0000 (11:04 +0100)]
JAL-4061 JAL-4062 Find can now search features
Ben Soares [Fri, 2 Sep 2022 16:26:06 +0000 (17:26 +0100)]
JAL-1988 Added a saves in progress check for quit
Ben Soares [Wed, 31 Aug 2022 16:19:03 +0000 (17:19 +0100)]
JAL-1988 added a saveInProgress stack to BackupFiles
Ben Soares [Tue, 23 Aug 2022 10:29:18 +0000 (11:29 +0100)]
JAL-4014 JAL-4063 Added gecos colourScheme names (INFO message) and fixed Clustal colourScheme name
Jim Procter [Mon, 8 Aug 2022 17:49:08 +0000 (18:49 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 17:48:01 +0000 (18:48 +0100)]
JAL-4046 release on 9th August 2022
Jim Procter [Mon, 8 Aug 2022 17:28:28 +0000 (18:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 17:28:15 +0000 (18:28 +0100)]
JAL-4046 JAL-3993 imports reformatting
Jim Procter [Mon, 8 Aug 2022 17:27:29 +0000 (18:27 +0100)]
JAL-4046 JAL-3993 patch for 2.11.2.4 release
Jim Procter [Mon, 8 Aug 2022 17:09:54 +0000 (18:09 +0100)]
JAL-4046 release notes for JAL-3991
Jim Procter [Mon, 8 Aug 2022 17:01:19 +0000 (18:01 +0100)]
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop
Jim Procter [Mon, 8 Aug 2022 16:54:11 +0000 (17:54 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 16:50:39 +0000 (17:50 +0100)]
JAL-4046 release notes for JAL-4014 - gecos colourschemes
Jim Procter [Mon, 8 Aug 2022 16:16:14 +0000 (17:16 +0100)]
Merge branch 'improvement/JAL-4014_gecos_colour_schemes' into develop
Jim Procter [Mon, 8 Aug 2022 16:07:42 +0000 (17:07 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 16:06:24 +0000 (17:06 +0100)]
JAL-4056 documented in release notes for JAL-4043
Jim Procter [Mon, 8 Aug 2022 15:46:04 +0000 (16:46 +0100)]
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop
Jim Procter [Mon, 8 Aug 2022 15:42:51 +0000 (16:42 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 15:42:21 +0000 (16:42 +0100)]
JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)
Jim Procter [Mon, 8 Aug 2022 15:17:49 +0000 (16:17 +0100)]
JAL-4034 show the loading spinner when switching between tabs
Jim Procter [Mon, 8 Aug 2022 13:47:31 +0000 (14:47 +0100)]
Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop
git://source.jalview.org / jalview.git / log