James Procter [Wed, 22 Feb 2023 22:14:15 +0000 (22:14 +0000)]
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
James Procter [Wed, 22 Feb 2023 22:02:20 +0000 (22:02 +0000)]
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
James Procter [Wed, 22 Feb 2023 14:24:04 +0000 (14:24 +0000)]
JAL-1551 source formatting
James Procter [Wed, 22 Feb 2023 14:23:56 +0000 (14:23 +0000)]
JAL-3858 simple test for PAE matrix recovery
James Procter [Wed, 22 Feb 2023 14:23:15 +0000 (14:23 +0000)]
JAL-3858 construct a PAE direct from float array
James Procter [Wed, 22 Feb 2023 13:34:54 +0000 (13:34 +0000)]
JAL-629 make sure we show GUI when not driven programmatically
James Procter [Wed, 22 Feb 2023 12:43:25 +0000 (12:43 +0000)]
JAL-4095 slightly better threshold setting and todos for improvement
James Procter [Wed, 22 Feb 2023 12:42:58 +0000 (12:42 +0000)]
JAL-4095 magic fill behaviour is PAE specific
James Procter [Wed, 22 Feb 2023 12:38:00 +0000 (12:38 +0000)]
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
James Procter [Wed, 22 Feb 2023 12:05:22 +0000 (12:05 +0000)]
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
James Procter [Thu, 16 Feb 2023 13:14:11 +0000 (13:14 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts:
src/jalview/bin/Jalview.java
James Procter [Thu, 16 Feb 2023 12:25:41 +0000 (12:25 +0000)]
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
James Procter [Wed, 15 Feb 2023 15:25:53 +0000 (15:25 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Wed, 15 Feb 2023 14:43:32 +0000 (14:43 +0000)]
Passing test for JAL-4127 failing on the JAL-1713 branch
James Procter [Wed, 15 Feb 2023 13:59:29 +0000 (13:59 +0000)]
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
James Procter [Mon, 13 Feb 2023 17:28:45 +0000 (17:28 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Fri, 10 Feb 2023 17:05:30 +0000 (17:05 +0000)]
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
James Procter [Fri, 10 Feb 2023 16:26:37 +0000 (16:26 +0000)]
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
James Procter [Fri, 10 Feb 2023 16:23:53 +0000 (16:23 +0000)]
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
James Procter [Fri, 10 Feb 2023 16:03:32 +0000 (16:03 +0000)]
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
Ben Soares [Fri, 3 Feb 2023 21:10:51 +0000 (21:10 +0000)]
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
Ben Soares [Fri, 3 Feb 2023 20:57:43 +0000 (20:57 +0000)]
JAL-629 "updated" json-simple
James Procter [Fri, 3 Feb 2023 14:18:44 +0000 (14:18 +0000)]
JAL-1551 remove temp file in src
James Procter [Fri, 3 Feb 2023 14:14:49 +0000 (14:14 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
James Procter [Tue, 31 Jan 2023 16:17:49 +0000 (16:17 +0000)]
JAL-1713 update from Jalview 2.11.3 develop
Merge branch 'develop' into feature/JAL-1713_overviewInProject
regenerated jaxb classes to resolve conflicts
Ben Soares [Thu, 26 Jan 2023 17:06:40 +0000 (17:06 +0000)]
JAL-4118 remove unnecessary sleep from QuitHandlerTest
Ben Soares [Thu, 26 Jan 2023 16:44:51 +0000 (16:44 +0000)]
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
Ben Soares [Thu, 26 Jan 2023 11:49:36 +0000 (11:49 +0000)]
JAL-1988 Add a sleep to file save test to give time for file to save
Ben Soares [Thu, 26 Jan 2023 11:10:37 +0000 (11:10 +0000)]
JAL-629 example files from nf-core
Ben Soares [Thu, 26 Jan 2023 11:10:04 +0000 (11:10 +0000)]
JAL-629 helper eclipse CLI run
Ben Soares [Thu, 26 Jan 2023 11:09:47 +0000 (11:09 +0000)]
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
James Procter [Wed, 25 Jan 2023 15:28:48 +0000 (15:28 +0000)]
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
James Procter [Wed, 25 Jan 2023 13:05:54 +0000 (13:05 +0000)]
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
James Procter [Tue, 24 Jan 2023 18:20:55 +0000 (18:20 +0000)]
JAL-4090 Release 2.11.3.0 release notes and version bump
James Procter [Tue, 24 Jan 2023 17:41:02 +0000 (17:41 +0000)]
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
James Procter [Tue, 24 Jan 2023 08:18:39 +0000 (08:18 +0000)]
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
James Procter [Tue, 24 Jan 2023 07:51:00 +0000 (07:51 +0000)]
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
James Procter [Tue, 24 Jan 2023 07:49:39 +0000 (07:49 +0000)]
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
James Procter [Tue, 24 Jan 2023 07:48:54 +0000 (07:48 +0000)]
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
James Procter [Tue, 24 Jan 2023 07:48:07 +0000 (07:48 +0000)]
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
James Procter [Tue, 24 Jan 2023 07:46:53 +0000 (07:46 +0000)]
JAL-629 don’t complain for Unary args
James Procter [Tue, 24 Jan 2023 07:46:34 +0000 (07:46 +0000)]
JAL-629 labelled breaks are frowned upon by everyone
James Procter [Tue, 24 Jan 2023 06:27:46 +0000 (06:27 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
James Procter [Tue, 24 Jan 2023 06:26:15 +0000 (06:26 +0000)]
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Ben Soares [Mon, 23 Jan 2023 23:57:06 +0000 (23:57 +0000)]
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
James Procter [Mon, 23 Jan 2023 20:17:42 +0000 (20:17 +0000)]
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
Jim Procter [Mon, 23 Jan 2023 09:32:43 +0000 (09:32 +0000)]
JAL-4102 whatsNew for 2.11.2.6
Jim Procter [Fri, 20 Jan 2023 23:40:08 +0000 (23:40 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 23:39:28 +0000 (23:39 +0000)]
JAL-4114 model_page_url not required in v2.0 response
Jim Procter [Fri, 20 Jan 2023 23:03:12 +0000 (23:03 +0000)]
JAL-4102 update date and release notes for 2.11.2.6
Jim Procter [Fri, 20 Jan 2023 22:53:26 +0000 (22:53 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 22:52:55 +0000 (22:52 +0000)]
Merge branch 'patch/Release_2_11_2_6_Branch' into develop
Jim Procter [Fri, 20 Jan 2023 20:48:43 +0000 (20:48 +0000)]
JAL-2353 primary ref candidates that should be promoted should preserve original version string
Jim Procter [Fri, 20 Jan 2023 20:44:47 +0000 (20:44 +0000)]
JAL-4114 missing mock server response
Jim Procter [Fri, 20 Jan 2023 17:53:48 +0000 (17:53 +0000)]
JAL-4114 only rank model qualities that are computed with the same method, and uprank models with pLDDT over other types of models in the same model type category
Jim Procter [Fri, 20 Jan 2023 17:52:52 +0000 (17:52 +0000)]
JAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories
Jim Procter [Fri, 20 Jan 2023 17:50:53 +0000 (17:50 +0000)]
JAL-4114 additional warnings when PDBe doesn’t return as many responses as queries made to it when adding in additional metadata
Jim Procter [Fri, 20 Jan 2023 17:49:38 +0000 (17:49 +0000)]
JAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API
Jim Procter [Fri, 20 Jan 2023 17:49:16 +0000 (17:49 +0000)]
JAL-4114 formatting
Jim Procter [Fri, 20 Jan 2023 17:48:04 +0000 (17:48 +0000)]
JAL-4114 updated mock tests and responses for v2.0 api
Ben Soares [Wed, 18 Jan 2023 15:52:10 +0000 (15:52 +0000)]
JAL-629 make sequence id key 'seqid'
Ben Soares [Wed, 11 Jan 2023 11:55:53 +0000 (11:55 +0000)]
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
Ben Soares [Wed, 11 Jan 2023 11:55:14 +0000 (11:55 +0000)]
JAL-629 refactoring TFType. Remove i18n identification of annotation.
Ben Soares [Fri, 6 Jan 2023 17:36:42 +0000 (17:36 +0000)]
JAL-3416 More explicit setting of FlatLaf macOS theme
Ben Soares [Fri, 6 Jan 2023 17:09:11 +0000 (17:09 +0000)]
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
Ben Soares [Fri, 6 Jan 2023 16:50:24 +0000 (16:50 +0000)]
JAL-3416 remove a missed panel titlebar icon in TreePanel
Ben Soares [Fri, 6 Jan 2023 16:16:02 +0000 (16:16 +0000)]
JAL-3416 Fix file permissions on bundled macOS JREs
Ben Soares [Mon, 19 Dec 2022 18:18:40 +0000 (18:18 +0000)]
JAL-629 Add image output and quit
Ben Soares [Thu, 15 Dec 2022 14:25:40 +0000 (14:25 +0000)]
JAL-629 move SubId to more logical place. Attempt removal of annotations in a better way (commented out).
Ben Soares [Wed, 14 Dec 2022 10:45:27 +0000 (10:45 +0000)]
JAL-629 Open Structure Viewer from cmdline
Ben Soares [Fri, 9 Dec 2022 13:05:10 +0000 (13:05 +0000)]
JAL-629 null check, fixed tests!
Ben Soares [Thu, 8 Dec 2022 17:29:38 +0000 (17:29 +0000)]
JAL-629 fix opening files
Ben Soares [Thu, 8 Dec 2022 17:08:49 +0000 (17:08 +0000)]
JAL-629 stray code deleted
Ben Soares [Thu, 8 Dec 2022 14:19:23 +0000 (14:19 +0000)]
JAL-629 Allow attachment of pAE file to a particular sequence
Ben Soares [Mon, 5 Dec 2022 09:32:24 +0000 (09:32 +0000)]
JAL-629 implementation of --tempfac options
Jim Procter [Wed, 30 Nov 2022 11:51:02 +0000 (11:51 +0000)]
JAL-4102 bump version number
Jim Procter [Wed, 30 Nov 2022 11:34:45 +0000 (11:34 +0000)]
JAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL-2353
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Jim Procter [Sun, 30 Oct 2022 23:19:57 +0000 (23:19 +0000)]
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Ben Soares [Wed, 23 Nov 2022 17:19:43 +0000 (17:19 +0000)]
JAL-629 Doing things with the command line arguments
Ben Soares [Thu, 17 Nov 2022 09:39:38 +0000 (09:39 +0000)]
JAL-4019 Clarification of position on 'X' in help text
Ben Soares [Wed, 16 Nov 2022 11:52:30 +0000 (11:52 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 16 Nov 2022 11:23:00 +0000 (11:23 +0000)]
JAL-3416 make flatlaf default for linux
Ben Soares [Wed, 16 Nov 2022 09:27:49 +0000 (09:27 +0000)]
JAL-4019 finalised a boolean option and tidied some comments
Ben Soares [Mon, 14 Nov 2022 20:38:04 +0000 (20:38 +0000)]
JAL-4019 Put original test back
Ben Soares [Mon, 14 Nov 2022 09:07:32 +0000 (09:07 +0000)]
JAL-4019 Make diagnostic message debug level
Ben Soares [Sun, 13 Nov 2022 20:35:13 +0000 (20:35 +0000)]
JAL-4019 small colour fix for X in the documentation
Ben Soares [Sun, 13 Nov 2022 20:31:51 +0000 (20:31 +0000)]
JAL-4019 attribution to Suzanne
Ben Soares [Sun, 13 Nov 2022 10:51:22 +0000 (10:51 +0000)]
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme
Ben Soares [Sun, 13 Nov 2022 10:50:57 +0000 (10:50 +0000)]
JAL-4019 small but important corrections to array order, and X colour
Ben Soares [Sun, 13 Nov 2022 00:54:09 +0000 (00:54 +0000)]
JAL-4019 Added tests for new Nucleotide sequence detection
Ben Soares [Sun, 13 Nov 2022 00:53:27 +0000 (00:53 +0000)]
JAL-4019 improvement to short sequence nucleotide detection, and some tidying of unused parameters
Ben Soares [Thu, 10 Nov 2022 15:21:08 +0000 (15:21 +0000)]
JAL-4019 Nucleotide Ambiguity Colour Scheme added. Test for nucleotide sequence adapted to recognise nucleotide sequences with (more than 15%) ambiguity codes. Two tests fixed.
Ben Soares [Wed, 9 Nov 2022 18:11:42 +0000 (18:11 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 18:10:20 +0000 (18:10 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 18:10:10 +0000 (18:10 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 17:47:59 +0000 (17:47 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
git://source.jalview.org / jalview.git / log