- <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>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!</li>
+ <li>Co-located features exported and re-imported are ordered
+ differently when shown on alignment and in tooltips. (Also affects
+ v2.11.1.0)</li>
+ <li>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.</li>