</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.5 ?</strong>
+ <strong>Jalview 2.11 - major and minor new features</strong>
</p>
- <p>Jalview 2.10.5 is a minor release that includes critical
- patches for users working with Ensembl, RNA secondary structure
- annotation, and those running Jalview on OSX with Java 10.</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>Jalview's default memory limit increased to 1G. <br/>If you have
- problems starting Jalview 2.10.5 and you have 1G or less
- physical memory on your machine, you will need to <a
- href="memory.html#memsetting">reduce the memory</a> allocated to
- Jalview.
- </li>
- <li>EPS, PNG and SVG export now includes hidden sequence
- markers, and representative sequences are marked in bold.</li>
- <li>Ensembl Client updated for Ensembl Rest API v7.<br />The
- latest Ensembl API is not backwards compatible with earlier
- versions of Jalview, so if you require Ensembl functionality you
- will need to install this release.
- </li>
- <li>Improved support for VIENNA extended dot-bracket notation
- for RNA secondary structure.</li>
- <li>Positional and selected region highlighting in VARNA
- 'trimmed sequence' view made more reliable.</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.2.10.5">2.10.5 Release Notes</a>. The
- majority of bug fixes and improvements in 2.10.5 are due to Jalview users
- contacting us via the jalview-discuss email list. Thanks to everyone
- who took the time to help make Jalview better !
+ href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
</p>
<p>
- <strong>Jalview and Java 10</strong>
+ <strong>Jalview and Java 11, 13, and onwards</strong>
</p>
- <p>This release addresses a critical bug for OSX users who are
- running Jalview with Java 10 which can prevent files being saved
- correctly through the 'Save As' dialog box.</p>
- <em>Known Issues</em>
+ <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>
+ 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 / commitdiff