</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.4 ?</strong>
- </p>
- <p>
- This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+ <strong>Jalview 2.11 - major and minor new features</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>
<ul>
- <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
- <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
- <li>Critical patches for running Jalview on OSX with Java 10</li>
- <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
- <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
- <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
- <li>New buttons on the Structure Chooser for adding structures
- to an existing view, and disabling automatic superposition
- according to linked alignments</li>
- <li>Annotation transfer between Chimera and Jalview <em>(formerly only
- available in 'Experimental' mode)</em></li>
+ <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 imported
+ from a local VCF file.</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
+ via Getdown.</li>
</ul>
<p>
- The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
- Release Notes</a>.
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Jalview and Java 11, 13, and onwards</strong>
</p>
+ <p>Java 11 provides improved performance and better OS
+ integration, so we now recommend users select our Java 11 Jalview
+ distribution rather than the legacy Java 8 build.</p>
+ <em>Known Issues - update for 211 </em>
+ <ul>
+ <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file
+ to load yields a FileNotFound exception.</br>The workaround is to first
+ clear the 'Untitled' filename before selecting the file you wish
+ to load.
+ </li>
+ <li>OSX: Links don't open when clicked on or via the Sequence
+ or Alignment window popup menu.</li>
+ <li>OSX (Webstart): Jalview only displays old news feed items</li>
+ </ul>
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git://source.jalview.org / jalview.git / blobdiff