MorellThomas [Sat, 22 Jul 2023 13:29:51 +0000 (15:29 +0200)]
Implement MSA, scoring and counting the connections
MorellThomas [Sun, 9 Jul 2023 16:41:58 +0000 (18:41 +0200)]
Copied PCA files to PaSiMap analogues and changed all names
MorellThomas [Sat, 8 Jul 2023 16:17:55 +0000 (18:17 +0200)]
Includes the PaSiMap button in the CalculationChooser
MorellThomas [Sun, 2 Jul 2023 08:39:42 +0000 (10:39 +0200)]
Fixed build.gradle, provide diff
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
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, 26 Oct 2022 08:13:24 +0000 (09:13 +0100)]
JAL-3416 (and others) increasing number of STDERR lines used for jalview.bin.CommandLineOperations tests for increased robustness
Ben Soares [Tue, 25 Oct 2022 12:07:19 +0000 (13:07 +0100)]
JAL-3416 Making FlatLaF default for macs due to a problem with VAqua not starting on macs
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 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 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
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
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
Ben Soares [Mon, 1 Aug 2022 10:32:43 +0000 (11:32 +0100)]
JAL-4056 fixed tl;dr section of doc/building.md
Ben Soares [Tue, 26 Jul 2022 17:01:48 +0000 (18:01 +0100)]
JAL-4036 Fixed the virus_host_id query field
Ben Soares [Tue, 26 Jul 2022 17:01:27 +0000 (18:01 +0100)]
JAL-4036 Added text to help about different number and date range acceptable formats
Ben Soares [Mon, 25 Jul 2022 16:09:43 +0000 (17:09 +0100)]
JAL-4036 updated help about new UniProt API
Ben Soares [Mon, 25 Jul 2022 10:00:52 +0000 (11:00 +0100)]
JAL-4036 moved a comment block
Ben Soares [Mon, 25 Jul 2022 09:57:51 +0000 (10:57 +0100)]
JAL-4034 button looks better also on other OSes with the 0 vertical insets
Ben Soares [Sun, 24 Jul 2022 16:37:59 +0000 (17:37 +0100)]
JAL-4034 add round corners to 3DB confirmation button with icon on a mac
Ben Soares [Fri, 22 Jul 2022 17:17:34 +0000 (18:17 +0100)]
JAL-4036 Changes made from code review CR-JAL-265
Ben Soares [Fri, 22 Jul 2022 10:55:16 +0000 (11:55 +0100)]
JAL-4036 Add getDbName to the GFTSPanelI and add an index code message to the index dropdown tooltip as appropriate
Ben Soares [Fri, 22 Jul 2022 10:06:24 +0000 (11:06 +0100)]
JAL-4036 removing the query field code from the dropdown indexes
Ben Soares [Thu, 21 Jul 2022 20:00:49 +0000 (21:00 +0100)]
JAL-4036 Don't autosearch changing index when autosearch is de-selected
Ben Soares [Thu, 21 Jul 2022 20:00:15 +0000 (21:00 +0100)]
JAL-4036 add search fieldname to dropdown list
Ben Soares [Thu, 21 Jul 2022 19:59:22 +0000 (20:59 +0100)]
JAL-4036 removed often duplicated pluralisation in message
Ben Soares [Thu, 21 Jul 2022 19:58:06 +0000 (20:58 +0100)]
JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API
Jim Procter [Wed, 20 Jul 2022 14:51:51 +0000 (15:51 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 20 Jul 2022 14:51:16 +0000 (15:51 +0100)]
JAL-4046 started release notes for 2.11.2.4 patch release
Jim Procter [Wed, 20 Jul 2022 14:44:03 +0000 (15:44 +0100)]
JAL-4045 - don't apply distribution dependent scale factor to the axis lines!
Ben Soares [Fri, 15 Jul 2022 17:38:33 +0000 (18:38 +0100)]
JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance
Ben Soares [Fri, 15 Jul 2022 17:37:04 +0000 (18:37 +0100)]
JAL-4034 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (similar to JalviewJS)
Ben Soares [Tue, 12 Jul 2022 11:13:28 +0000 (12:13 +0100)]
JAL-4034 change to jalview property name
Ben Soares [Tue, 12 Jul 2022 10:58:35 +0000 (11:58 +0100)]
JAL-4034 showConfirmDialog works for both desktop and jalviewjs
Ben Soares [Mon, 11 Jul 2022 16:14:56 +0000 (17:14 +0100)]
JAL-4034 Non-blocking 3D Beacons query after warning dialog
Ben Soares [Mon, 11 Jul 2022 15:25:17 +0000 (16:25 +0100)]
JAL-4034 allow a jalview_property to set the threshold level
git://source.jalview.org / jalview.git / log