Jalview 2.11.1.4

Jalview 2.11.1.4 is the fourth patch release in the 2.11.1 series. One critical bug was fixed in this release - when Jalview would occasionally hang when viewing structures in Jmol. This release also introduces a number of new configuration options for disabling web service connections used by the Jalview Debian package.

Jalview 2.11.1.1

Jalview 2.11.1.1 is the first patch release in the 2.11.1 series. It includes fixes for critical bugs, and brings a 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

Jalview failed to launch, displaying an error saying it was "unable to download the necessary files"

If you have a problem launching Jalview that results in an error message on the splash screen reading

"We were unable to download the necessary files after five attempts. You can try running the application again, but if it fails you may need to uninstall and reinstall."

(like this screenshot:

How do I set web proxy settings for Jalview's auto-updater and web services?

 

Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site.  Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings.  In this case it may pop up a window asking for proxy settings.  If this does not happen, and proxy settings are required, you can create a file called

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