- <li><strong>The Jalview Launcher and Update System</strong>.
- Jalview's new installation model means you'll only need to
- download and install Jalview once. After installation, Jalview
- will automatically keep itself up to date. The launcher also sets
- Jalview's memory automatically, so you'll never again have to
- manually configure Java's memory settings.<br />We are grateful
- to ej Technologies for providing a free open source project
- license for <a
- href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
- and also to <a
- href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
- Rings Design</a> for Jalview's new over the air update system: <a
- href="https://github.com/threerings/getdown">Getdown</a>.</li>
- <li><strong>VCF Support</strong>. Proteins and genomic contigs with
- chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants <a
- href="features/importvcf.html">imported from a local VCF file</a>.</li>
- <li><strong>Feature filters and attribute colourschemes</strong>. A new
- <a href="features/featureschemes.html">Feature Display
- Settings</a> dialog allows filters and feature attribute based
- colourschemes to be constructed, and a new <em>filters</em> column
- added to the <a href="features/featuresettings.html">Feature
- Settings</a> dialog. Jalview's sequence feature datamodel has also
- been further optimised, and is now maintained as a separate
- library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
- <li><strong>Alternative tables for CDS translation</strong>. The <a
- href="menus/alwcalculate.html">Translate as cDNA</a> option now
- offers alternative amino acid coding schemes.</li>
- <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
- href="calculations/pca.html">PCA viewer</a> user interface has
- also been improved.</li>
- <li><strong>Backup files</strong>. Jalview will automatically
- create backups when overwriting existing files, and - unlike with
- earlier versions - should Jalview crash during a save, the original
- file will be unaffected. The <a
- href="features/preferences.html#backups">Backups tab</a> in
- Jalview's preferences dialog allows the number and format of
- backup filenames to be configured.</li>
+ <li>Shift+arrow keys navigate to next gap or residue in cursor
+ mode (enable with F2)</li>
+ <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+ 2.23</li>
+ <li>Improved recognition of GZipped files from local disk or
+ retrieved via the web</li>
+ <li>EMBL and EMBL CDS database records retrieved from the
+ European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
+ <li>Improved <a href="logging.html">Java Console and
+ logging</a> to help track down problems
+ </li>
+ <li>Improved support for Hi-DPI (4K) screens when running on
+ Linux (Requires Java 11+)</li>
+ </ul>
+ <p>Critical bug fixes include</p>
+ <ul>
+ <li>Jalview runs correctly when launched with Turkish language
+ settings</li>
+ <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+ products shown for a single contig (such as viral genomes)</li>
+ <li>Errors encountered when processing variants from VCF files
+ yield "Error processing VCF: Format specifier '%s'" on the console</li>
+ <li>Count of features not shown can be wrong when there are
+ both DNA and Protein features mapped to the position under
+ the cursor</li>
+ <li>Sequence ID for reference sequence is clipped when Right
+ align Sequence IDs enabled</li>
+ <li>Find doesn't report matches that span hidden gapped columns</li>
+ <li>Jalview ignores file format parameter specifying output
+ format when exporting an alignment via the command line</li>