- <p>
- <strong>What's new ?</strong></p>
- <p>
- Jalview 2.8.1 includes new features for group creation, RNA secondary
- structure prediction and a host bug fixes. It also includes support
- for <a href="http://www.compbio.dundee.ac.uk/JABAWS">version 2.1
- of JABA</a> and includes a Spanish translation of its user interface.<br />
- The highlights are detailed below, and the full list is given in the <a
- href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
- </p>
- <p>The Desktop and web based applet include new keystrokes for
- defining and undefining groups, and PAM250 has been added to the range
- of score models available for use by the tree and PCA calculations.
- The Jalview project file format has also been extended for handling
- RNA and protein secondary structure annotation, in anticipation for
- new structure based secondary structure support in Jalview 2.8.2.</p>
- <p><strong>Internationalisation</strong></p>
- <p>Jalview 2.8.1 is the first release to include support for
- displaying Jalview's user interface in different languages. In August
- 2013, David Roldán-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created
- Jalview's first spanish user interface translation.</p>
- <p>
- If you notice any problems, or would like to help translate Jalview's
- user interface into other languages, head over to <a
- href="http://issues.jalview.org">issues.jalview.org</a> and put in a
- feature request describing the translations you can provide to the <a
- href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>. David has also <a
- href="https://wiki.jalview.org/index.php/Development:i18n">documented
- the process of creating i18n translations</a> to help you get started.
- </p>
- <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
- <p>
- This version of Jalview includes a client to access the new services available in <a
- href="http://www.compbio.dundee.ac.uk/jabaws/">JABA v2.1</a> , which
- provides services for RNA consensus secondary structure prediction and
- two new alignment programs (<a
- href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
- href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
- <p>
- To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
- client documentation</a>.
- </p>
- <div align="center">
- <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
- summer student, Dan Barton.</em>
- </div>
+ <p>
+ <strong>What's new in Jalview 2.10.5 ?</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>
+ <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>
+ </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 !
+ </p>
+ <p>
+ <strong>Jalview and Java 10</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>
+ <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>