Jalview patch release now available: Version 2.11.1.1

jalviewcrowdadmin · 17 September 2020 17:50

Dear Jalview Developers !

We are pleased to announce that Jalview 2.11.1.1, the first patch release in the 2.11.1 series, is now available as an over the air update. You can also download standalone jars and the source for the new release via https://www.jalview.org/download

This patch release includes fixes for critical bugs, and also brings some new features suggested by the Jalview community.

Shift+arrow keys navigate to next gap or residue in cursor mode (enable with F2)
Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
Improved recognition of GZipped files from local disk or retrieved via the web
EMBL and EMBL CDS database records retrieved from the European Nucleotide Archive’s Data API as ‘EMBL Flatfile’ records
Improved Java Console and logging to help track down problems
Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)

Critical bug fixes include

Jalview runs correctly when launched with Turkish language settings
Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig (such as viral genomes)
Errors encountered when processing variants from VCF files yield “Error processing VCF: Format specifier ‘%s’” on the console
Count of features not shown can be wrong when there are both DNA and Protein features mapped to the position under the cursor
Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
Find doesn’t report matches that span hidden gapped columns
Jalview ignores file format parameter specifying output format when exporting an alignment via the command line

See the full release notes at:
https://www.jalview.org/development/release-history/Jalview-21111

Happy Jalviewing!

Jim, Ben, Mungo, Suzanne and Geoff.

···

-- 
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)

j_procter · 17 September 2020 17:52

Oops - apologies for the duplicate mail… I was so happy about this I sent it twice !

Hope all is well with you…
Jim.

···

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Jim Procter jprocter@compbio.dundee.ac.uk
Sent: 17 September 2020 18:50
To: jalview-dev@jalview.org jalview-dev@jalview.org
Subject: [Jalview-dev] Jalview patch release now available: Version 2.11.1.1