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<p>
- <strong>Jalview 2.11 - major and minor new features</strong>
+ <strong>Jalview 2.11.1.3</strong>
</p>
- <p>Jalview 2.11 introduces support for loading VCF files, and new
- filters and shading models for sequence features. Under the hood,
- we've addressed many bugs, and also made some important changes in
- the way the Jalview desktop is installed and launched.</p>
+ <p>Jalview 2.11.1.3 is the third 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.</p>
<ul>
- <li><em>VCF Support</em>. 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><em>The Jalview Launcher and Update System</em><br />
- 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 Install4J who provided us with a free license for their
- installation system, and Jalview's over the air update system is
- based on Three Rings' Getdown system.</li>
- <li><em>Backup files</em><br />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.</li>
- <li><em>PCA plots stored in Jalview Projects</em><br />The PCA
- viewer has also been enhanced and the user interface revised.</li>
- <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>
</ul>
<p>
- The full list of bugs fixed in this release can be found in the <a
- href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
+ For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
+ Jalview 2.11.1.1 release notes</a>.
</p>
<p>
- <strong>Jalview and Java 11, 13, and onwards</strong>
+ <strong>Known Issues</strong>
</p>
- <p>The Jalview application comes bundled with its own independent
- Java installation which will be updated automatically from
- www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
- runtime, but installations will be migrated to the latest Java
- release once remaining issues have been addressed.</p>
+ <ul>
+ <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>
+ </ul>
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git://source.jalview.org / jalview.git / blobdiff