Jalview 2.11.1.2
Jalview 2.11.1.2 is the second patch release, fixing a bug
introduced in last weeks Jalview 2.11.1.1 release affecting display
of Jalview's example project for some users. Together, these
releases include fixes for a number of critical bugs, and also contains a
handful of 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
For the full release notes, see the
Jalview 2.11.1.1 release notes.
Known Issues
- We've had reports from a small number of windows 10 users
who see a warning dialog pop up when Jalview tries to save a new
version of an existing file. If you are affected by this bug and
this latest version of Jalview doesn't fix it, please let us know!
- Co-located features exported and re-imported are ordered
differently when shown on alignment and in tooltips. (Also affects
v2.11.1.0)
- Drag and drop of alignment file onto alignment window when
in a HiDPI scaled mode in Linux only works for the top left
quadrant of the alignment window