<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>What's new ?</title>
</head>
<body>
-<p><strong>What's new ?</strong></p>
-<p><strong>Jalview Version 2.4</strong></p>
-<ul>
- VAMSAS Interoperation Client<br>
- DAS Sequence Fetching<br>
- PFAM full alignment retrieval<br>
- DNA/Protein Product traversal (Experimental)</br>
- .. (more to come)
-</ul>
-<p><strong>Issues Resolved</strong></p>
-<ul>
- .. (more to come)
-</ul>
-
-<--<p><strong>Jalview Version 2.3</strong></p>
-<ul>
- Jmol 11.0.2 integration<br>
- PDB views stored in Jalview XML files<br>
- Slide sequences<br>
- Edit sequence in place<br>
- EMBL CDS features<br>
- DAS Feature mapping<br>
- Feature ordering<br>
- Alignment Properties<br>
- Annotation Scores<br>
- Sort by scores<br>
- Feature/annotation editing in applet<br>
-</ul>
-<p><strong>Issues Resolved</strong></p>
-<ul>
- Headless state operation in 2.2.1 <br>
- Incorrect and unstable DNA pairwise alignment <br>
- Cut and paste of sequences with annotation <br>
- Feature group display state in XML<br>
- Feature ordering in XML<br>
- 2.2.1 applet had no feature transparency<br>
- Number pad keys can be used in cursor mode<br>
- Structure Viewer mirror image resolved</p>
- </ul>-->
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+ <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, and RNA secondary structure
+ annotation.</p>
+ <ul>
+ <li>Jalview's default memory limit increased to 1G. 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 now 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 improvement 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 do this !
+ </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 'Save As' dialog for Jalview's Groovy Console
+ remains affected: the workaround is to create a new file outside
+ of Jalview and then select it when saving your groovy script. We
+ hope to address this in the next major release.</li>
+ <li>OSX: Jalview only displays old news feed items</li>
+ <li>OSX: Users may have to manually configure a web browser
+ helper application ('/usr/bin/open' can be used in the Connections
+ Preferences panel to open URLs with your default browser).</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff