Jim Procter [Mon, 7 Feb 2022 17:13:49 +0000 (17:13 +0000)]
Merge branch 'feature/JAL-1713_overviewInProject' into bug/JAL-3785autoOverviewTitle
Jim Procter [Mon, 7 Feb 2022 17:04:01 +0000 (17:04 +0000)]
JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop
regenerated jaxb bindings for updated schemas on develop & feature branch
Conflicts:
src/jalview/gui/Preferences.java
src/jalview/xml/binding/jalview/JalviewModel.java
src/jalview/xml/binding/jalview/ObjectFactory.java
src/jalview/xml/binding/jalview/package-info.java
Jim Procter [Mon, 7 Feb 2022 16:07:33 +0000 (16:07 +0000)]
JAL-3186 remove ‘Variable Colour’ from the sequence feature settings popup menu
Jim Procter [Fri, 4 Feb 2022 14:34:20 +0000 (14:34 +0000)]
Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop
Combines patches for JAL-3806 prior to redaction of shared CDS dataset sequences with patches for JAL-3673
Conflicts:
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/util/MappingUtils.java
test/jalview/util/MappingUtilsTest.java
Jim Procter [Fri, 4 Feb 2022 13:19:48 +0000 (13:19 +0000)]
JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon
Jim Procter [Fri, 4 Feb 2022 13:13:02 +0000 (13:13 +0000)]
JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS
Ben Soares [Thu, 3 Feb 2022 19:38:32 +0000 (19:38 +0000)]
JAL-3949 upgraded log4j to 2.17.1 (no actual known vulnerabilities\!), though this doesn't fix the issue
Jim Procter [Thu, 3 Feb 2022 14:59:31 +0000 (14:59 +0000)]
JAL-3806 use the covers() test for each selected sequence and the complementary alignment’s sequence as a filter for direct CDS-Protein mappings (ensures overlapping CDS coding for distinct proteins do not all get selected)
Jim Procter [Thu, 3 Feb 2022 14:20:11 +0000 (14:20 +0000)]
JAL-3806 use same logic as for mouse over highlighting to work out extent of selected region in complement alignment
Jim Procter [Thu, 3 Feb 2022 13:41:25 +0000 (13:41 +0000)]
JAL-3806 todo - problem seems to be Protein:Many CDS are not selected
Jim Procter [Thu, 3 Feb 2022 13:18:44 +0000 (13:18 +0000)]
JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test data needs to be revised for assumptions made by CrossRef about sequences retrieved from dbsources
Ben Soares [Fri, 28 Jan 2022 18:22:54 +0000 (18:22 +0000)]
Merge branch 'develop' into improvement/JAL-3420_match_jvl_icon_with_new_website_jvl_icon
Ben Soares [Fri, 28 Jan 2022 18:22:27 +0000 (18:22 +0000)]
new jvl_file svg, png, ico and icns files, and changed references to Jalview-Launch to jvl_file
Jim Procter [Fri, 28 Jan 2022 17:24:15 +0000 (17:24 +0000)]
JAL-3137 tests are for linux only
Jim Procter [Fri, 28 Jan 2022 17:08:35 +0000 (17:08 +0000)]
Merge branch 'merge/develop_JAL-3725' into develop
Conflicts:
src/jalview/gui/PopupMenu.java
Jim Procter [Thu, 27 Jan 2022 14:21:39 +0000 (14:21 +0000)]
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop
Conflicts:
src/jalview/bin/MemorySetting.java
Jim Procter [Wed, 26 Jan 2022 23:41:08 +0000 (23:41 +0000)]
JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)
Jim Procter [Wed, 26 Jan 2022 23:32:26 +0000 (23:32 +0000)]
JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763 release notes
Jim Procter [Wed, 26 Jan 2022 23:26:04 +0000 (23:26 +0000)]
Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds' into develop
Jim Procter [Wed, 26 Jan 2022 19:54:17 +0000 (19:54 +0000)]
JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)
Jim Procter [Wed, 26 Jan 2022 19:36:23 +0000 (19:36 +0000)]
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds
Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/util/MapList.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
gmungoc [Thu, 28 Jan 2021 16:56:55 +0000 (16:56 +0000)]
JAL-3806 (2.11.2 version) more lax allowance (3 positions) for stop codon
Jim Procter [Thu, 6 Jan 2022 12:29:01 +0000 (12:29 +0000)]
JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser
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 [Tue, 18 Jan 2022 12:24:23 +0000 (12:24 +0000)]
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)
Jim Procter [Mon, 17 Jan 2022 12:36:40 +0000 (12:36 +0000)]
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release
Jim Procter [Mon, 17 Jan 2022 11:54:32 +0000 (11:54 +0000)]
JAL-3746 possible release date 1st Feb 2022
Jim Procter [Mon, 17 Jan 2022 11:54:16 +0000 (11:54 +0000)]
JAL-3746 Release notes for patch JAL-3702 JAL-3915
Jim Procter [Mon, 17 Jan 2022 11:45:47 +0000 (11:45 +0000)]
Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop
Ben Soares [Wed, 12 Jan 2022 12:32:06 +0000 (12:32 +0000)]
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished
Ben Soares [Tue, 11 Jan 2022 20:13:57 +0000 (20:13 +0000)]
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data
Ben Soares [Tue, 11 Jan 2022 16:04:49 +0000 (16:04 +0000)]
close filehandles straight after parse, without setting an error
Ben Soares [Mon, 10 Jan 2022 20:31:29 +0000 (20:31 +0000)]
JAL-3937 enable AIA download of intermediate certificates when needed
Jim Procter [Thu, 6 Jan 2022 09:58:49 +0000 (09:58 +0000)]
JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases
Jim Procter [Thu, 6 Jan 2022 09:47:28 +0000 (09:47 +0000)]
Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop
Ben Soares [Wed, 22 Dec 2021 11:17:41 +0000 (11:17 +0000)]
Merge branch 'develop' into critical/JAL-3933_log4j_update_for_develop_branch
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, 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)
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
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 17:49:19 +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 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 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]
Jim Procter [Fri, 19 Nov 2021 15:43:44 +0000 (15:43 +0000)]
JAL-3926 disable autosearch by default
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 18:13:37 +0000 (18:13 +0000)]
JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks
Jim Procter [Fri, 5 Nov 2021 16:51:37 +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 12:12:34 +0000 (12:12 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 2 Nov 2021 12:10:08 +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 [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 14:27:40 +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
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 16:36:35 +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
git://source.jalview.org / jalview.git / log