Ben Soares [Wed, 22 Dec 2021 11:12:37 +0000 (11:12 +0000)]
JAL-3934 updated log4j from 2.16.0 to 2.17.0
Ben Soares [Wed, 22 Dec 2021 11:12:37 +0000 (11:12 +0000)]
JAL-3934 updated log4j from 2.16.0 to 2.17.0
Jim Procter [Wed, 22 Dec 2021 10:32:30 +0000 (10:32 +0000)]
Merge branch 'releases/Release_2_11_1_Branch'
Jim Procter [Mon, 20 Dec 2021 14:03:35 +0000 (14:03 +0000)]
JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch
Jim Procter [Mon, 20 Dec 2021 09:50:51 +0000 (09:50 +0000)]
JAL-3842 patch what’s new text
Jim Procter [Mon, 20 Dec 2021 08:04:21 +0000 (08:04 +0000)]
JAL-3842 release 2.11.1.5 release notes
Jim Procter [Mon, 20 Dec 2021 07:45:38 +0000 (07:45 +0000)]
Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch
Ben Soares [Wed, 15 Dec 2021 13:23:16 +0000 (13:23 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Ben Soares [Wed, 15 Dec 2021 13:16:11 +0000 (13:16 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Ben Soares [Wed, 15 Dec 2021 13:23:16 +0000 (13:23 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Ben Soares [Wed, 15 Dec 2021 13:16:11 +0000 (13:16 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Jim Procter [Wed, 15 Dec 2021 10:38:22 +0000 (10:38 +0000)]
JAL-3933 remove obsolete Castor logging configuration
Jim Procter [Wed, 15 Dec 2021 10:36:18 +0000 (10:36 +0000)]
JAL-3933 configure root logger console appender to stderr (2.11.2 version)
Jim Procter [Wed, 15 Dec 2021 10:38:22 +0000 (10:38 +0000)]
JAL-3933 remove obsolete Castor logging configuration
Jim Procter [Wed, 15 Dec 2021 10:36:18 +0000 (10:36 +0000)]
JAL-3933 configure root logger console appender to stderr
Ben Soares [Tue, 14 Dec 2021 23:23:08 +0000 (23:23 +0000)]
JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars
Ben Soares [Tue, 14 Dec 2021 20:31:44 +0000 (20:31 +0000)]
JAL-3933 updated slf4j to 1.7.32
Ben Soares [Tue, 14 Dec 2021 20:00:40 +0000 (20:00 +0000)]
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped log4j classes from jabaws-min-client jar. Updated sl4j jars in j8lib
Jim Procter [Mon, 13 Dec 2021 18:19:46 +0000 (18:19 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 13 Dec 2021 18:17:33 +0000 (18:17 +0000)]
JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons search for example project
Jim Procter [Mon, 13 Dec 2021 17:49:36 +0000 (17:49 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 13 Dec 2021 17:49:19 +0000 (17:49 +0000)]
JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it
Jim Procter [Mon, 13 Dec 2021 16:26:22 +0000 (16:26 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 13 Dec 2021 14:15:06 +0000 (14:15 +0000)]
JAL-3929 preserve lowercase pdbid in group name for transferred features
Jim Procter [Wed, 8 Dec 2021 18:58:42 +0000 (18:58 +0000)]
Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelAPI_autoshowview' into develop
Jim Procter [Wed, 8 Dec 2021 18:53:57 +0000 (18:53 +0000)]
JAL-3551 pymol docs - work in progress
Jim Procter [Wed, 8 Dec 2021 18:52:45 +0000 (18:52 +0000)]
JAL-3929 don’t use the url encoded pdbId in feature group when transferring features from associated structure to a sequence
Jim Procter [Wed, 8 Dec 2021 15:59:38 +0000 (15:59 +0000)]
JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol
Jim Procter [Wed, 8 Dec 2021 15:48:37 +0000 (15:48 +0000)]
JAL-3551 JAL-3931 view pymol commands/responses in Log.trace
Jim Procter [Wed, 8 Dec 2021 15:45:51 +0000 (15:45 +0000)]
JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file
Jim Procter [Wed, 8 Dec 2021 15:44:04 +0000 (15:44 +0000)]
JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded ID to the features transferred from the structure file
Ben Soares [Tue, 7 Dec 2021 13:22:26 +0000 (13:22 +0000)]
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview
Ben Soares [Tue, 7 Dec 2021 12:39:06 +0000 (12:39 +0000)]
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview
Jim Procter [Thu, 2 Dec 2021 11:23:25 +0000 (11:23 +0000)]
JAL-3904 use new AlignPanel API method
Jim Procter [Thu, 2 Dec 2021 11:22:54 +0000 (11:22 +0000)]
JAL-3904 simple method to make an alignPanel the currently viewed one in the alignframe
Ben Soares [Mon, 29 Nov 2021 20:00:21 +0000 (20:00 +0000)]
JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]
Ben Soares [Thu, 25 Nov 2021 11:08:15 +0000 (11:08 +0000)]
JAL-3553 added filesize to json
Jim Procter [Fri, 19 Nov 2021 15:43:44 +0000 (15:43 +0000)]
JAL-3926 disable autosearch by default
Ben Soares [Fri, 19 Nov 2021 14:55:31 +0000 (14:55 +0000)]
JAL-3553 now creating a json file for use on website. It's easier to parse all the info here than on the website!
Ben Soares [Tue, 16 Nov 2021 18:02:11 +0000 (18:02 +0000)]
JAL-3553 copy sha256sums to a versioned filename too when created
Ben Soares [Tue, 16 Nov 2021 17:01:34 +0000 (17:01 +0000)]
JAL-3553 added customized labels for install4j output.txt
Ben Soares [Tue, 16 Nov 2021 16:55:29 +0000 (16:55 +0000)]
JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt
Jim Procter [Mon, 8 Nov 2021 18:47:33 +0000 (18:47 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Nov 2021 18:24:06 +0000 (18:24 +0000)]
JAL-3855 verify pdb suffix is preserved when locally loaded file is saved in project and imported
Jim Procter [Mon, 8 Nov 2021 18:22:35 +0000 (18:22 +0000)]
JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFile(PDBEntry) method in JmolBinding - avoid code duplication for retrieval and import of 3d data
Jim Procter [Mon, 8 Nov 2021 18:18:28 +0000 (18:18 +0000)]
JAL-3855 try harder to ignore DNA/RNA only structures when deciding whether to download from SIFTS
Jim Procter [Mon, 8 Nov 2021 18:15:33 +0000 (18:15 +0000)]
JAL-3921 wait around until session file has been written
Jim Procter [Fri, 5 Nov 2021 18:14:37 +0000 (18:14 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 5 Nov 2021 18:13:37 +0000 (18:13 +0000)]
JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks
Jim Procter [Fri, 5 Nov 2021 16:56:31 +0000 (16:56 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 5 Nov 2021 16:51:37 +0000 (16:51 +0000)]
JAL-3829 format and tidy up unused code
Jim Procter [Fri, 5 Nov 2021 16:38:15 +0000 (16:38 +0000)]
JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers
Jim Procter [Fri, 5 Nov 2021 12:45:13 +0000 (12:45 +0000)]
JAL-3875 fully reset filter combo-box when fetch 3d-beacons button is pressed, and ensure first 3d-beacons option selected when structures are discovered even when cached structures are present.
Ben Soares [Fri, 5 Nov 2021 10:14:12 +0000 (10:14 +0000)]
JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text.
Jim Procter [Wed, 3 Nov 2021 11:49:36 +0000 (11:49 +0000)]
JAL-3915 JAL-3746 documentation for removed rnaview options
Jim Procter [Wed, 3 Nov 2021 11:48:53 +0000 (11:48 +0000)]
JAL-3916 TODO for improved selection of covering structures
Jim Procter [Wed, 3 Nov 2021 11:35:23 +0000 (11:35 +0000)]
JAL-3916 TODO for improved selection of covering structures
Jim Procter [Wed, 3 Nov 2021 11:33:14 +0000 (11:33 +0000)]
JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service
Jim Procter [Tue, 2 Nov 2021 12:13:09 +0000 (12:13 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 2 Nov 2021 12:12:34 +0000 (12:12 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 2 Nov 2021 12:12:05 +0000 (12:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 2 Nov 2021 12:10:08 +0000 (12:10 +0000)]
JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions
Ben Soares [Mon, 1 Nov 2021 17:45:12 +0000 (17:45 +0000)]
JAL-3907 changed two commented out lines to reflect location of future upgraded JRE zipfiles.
Ben Soares [Mon, 1 Nov 2021 17:31:34 +0000 (17:31 +0000)]
JAL-3907 added creation of symbolic links to workaround an install4j9 problem with parsing packed jre filenames with hyphens.
Ben Soares [Thu, 28 Oct 2021 19:13:04 +0000 (20:13 +0100)]
JAL-3830 forgot to uncheck this
Ben Soares [Thu, 28 Oct 2021 17:35:33 +0000 (18:35 +0100)]
JAL-3830 polished setup app for macos
Ben Soares [Wed, 27 Oct 2021 19:32:25 +0000 (20:32 +0100)]
JAL-3830 quick fix to installer text
Ben Soares [Wed, 27 Oct 2021 19:24:45 +0000 (20:24 +0100)]
JAL-3830 install4j9 tries to parse and can't cope with the hyphens and filename format of the jre-VERSION-OS-ARCH.tar.gz JRE tar files, so using underscores in symbolic links
Ben Soares [Tue, 26 Oct 2021 17:16:12 +0000 (18:16 +0100)]
JAL-3830 Added steps for install4j9 to create macOS symbolic link to wrapper script (link) at /Applications/Jalview.app/Contents/MacOS/jalview and to add icon to Dock
Ben Soares [Tue, 26 Oct 2021 17:06:31 +0000 (18:06 +0100)]
JAL-3907 adjusted download_jdks.sh and download_jres.sh scripts to use adoptium and added Java 17 download. Added JAVA_VERSION=17 as a gradle build property option.
Jim Procter [Mon, 18 Oct 2021 14:27:55 +0000 (15:27 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 18 Oct 2021 14:27:40 +0000 (15:27 +0100)]
Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop
Jim Procter [Mon, 18 Oct 2021 14:04:52 +0000 (15:04 +0100)]
JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution
Jim Procter [Mon, 18 Oct 2021 12:18:59 +0000 (13:18 +0100)]
JAL-3904 override buildActionMenu to add in additional menu actions after rebuild
Jim Procter [Mon, 18 Oct 2021 11:39:40 +0000 (12:39 +0100)]
JAL-3904 failing test
Ben Soares [Tue, 5 Oct 2021 17:53:16 +0000 (18:53 +0100)]
JAL-3416 make flat default laf for linux
Ben Soares [Mon, 4 Oct 2021 19:13:00 +0000 (20:13 +0100)]
JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties
Ben Soares [Mon, 4 Oct 2021 16:46:03 +0000 (17:46 +0100)]
Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux
gmungoc [Thu, 27 Aug 2020 15:02:06 +0000 (16:02 +0100)]
JAL-3725 restrict mapped virtual feature location to mapped region
gmungoc [Thu, 27 Aug 2020 14:44:45 +0000 (15:44 +0100)]
JAL-3725 helper methods for computing mapped feature range overlap
gmungoc [Thu, 27 Aug 2020 14:40:22 +0000 (15:40 +0100)]
JAL-3725 exclude stop codon from CDS-to-protein mapping
Jim Procter [Fri, 1 Oct 2021 16:38:22 +0000 (17:38 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 1 Oct 2021 16:36:35 +0000 (17:36 +0100)]
JAL-3616 show name of structure viewer in ‘new view’ button
Jim Procter [Fri, 1 Oct 2021 16:32:20 +0000 (17:32 +0100)]
JAL-3616 explicit configure external viewer config
Jim Procter [Fri, 1 Oct 2021 13:04:03 +0000 (14:04 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 1 Oct 2021 13:03:44 +0000 (14:03 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Fri, 1 Oct 2021 13:02:24 +0000 (14:02 +0100)]
JAL-3829 3d beacons logo - misi varadi gave permission to re-use but most likely it is CC-0
Ben Soares [Fri, 1 Oct 2021 11:35:22 +0000 (12:35 +0100)]
Merge branch 'improvement/JAL-3594_logos_for_jalview_test' into develop
Jim Procter [Fri, 1 Oct 2021 11:32:06 +0000 (12:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 1 Oct 2021 11:31:45 +0000 (12:31 +0100)]
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop
Jim Procter [Fri, 1 Oct 2021 11:28:09 +0000 (12:28 +0100)]
JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.
Ben Soares [Fri, 1 Oct 2021 11:10:37 +0000 (12:10 +0100)]
Merge branch 'develop' into improvement/JAL-3594_logos_for_jalview_test
Ben Soares [Fri, 1 Oct 2021 11:08:16 +0000 (12:08 +0100)]
JAL-3594 New Jalview Test logos and .icns/.ico creation helper script
Jim Procter [Fri, 1 Oct 2021 09:35:08 +0000 (10:35 +0100)]
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons
Ben Soares [Thu, 30 Sep 2021 23:16:09 +0000 (00:16 +0100)]
JAL-3594 Changed logo for Jalview Test
Ben Soares [Thu, 30 Sep 2021 23:08:41 +0000 (00:08 +0100)]
JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer.
gmungoc [Tue, 11 Aug 2020 09:35:32 +0000 (10:35 +0100)]
JAL-3371 more fine-grained slider; set Param slider to initial default
Jim Procter [Thu, 30 Sep 2021 10:19:41 +0000 (11:19 +0100)]
Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop
Ben Soares [Wed, 29 Sep 2021 19:51:22 +0000 (20:51 +0100)]
JAL-3885 Made the database JComboBox have StringPair entries to allow a display value, set to the single item dbname if there's a single item
Jim Procter [Wed, 29 Sep 2021 14:50:09 +0000 (15:50 +0100)]
JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record