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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- *
+ * 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/>.
--->
+ * 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>
+ <strong>What's new ?</strong></p>
<p>
- The Jalview 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications. <br /> For full
- details see the <a href="releases.html#Jalview2.7">Jalview 2.7
- release history</a>.
+ 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>
- <strong>Highlights in Jalview Desktop Version 2.7</strong>
+ 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>
- <ul>
- <li>New <a href="features/viewingpdbs.html">structure viewer
- options</a>:
- <ul>
- <li>Colour and superimpose 3D structures of complexes and
- multi-domain chains using several different alignments</li>
- <li>Drag and drop to associate PDB files with sequences that
- have the same name</li>
- <li>Open and superimpose all associated structures for the
- current selection</li>
- </ul>
- <li>New web services for <a href="webServices/shmr.html">alignment
- analysis</a></li>
- <li>Improved graphical user interface for <a
- href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
- </li>
- <li>Sort associated alignment views option in tree viewer</li>
- <li>Default colours for <a
- href="colourSchemes/annotationColouring.html">shading alignment
- by quantitative annotation</a>.
- </li>
- <li><a href="webServices/newsreader.html">Jalview Desktop RSS
- reader</a> - following important updates at <a
- href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
- </ul>
-
+ <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
<p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.7">release history</a> for full details)
- </strong>
- </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>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>Problems viewing associated structures for sequences
- retrieved from UNIPROT</li>
- <li>Problems viewing Jalview projects from older versions in
- version 2.6</li>
- <li>Preservation of hidden annotation rows and tree bootstrap
- values in projects</li>
- <li>Newly added JABAWS servers not always visible in web services
- menu</li>
- </ul>
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- <li>Layout problems when lots of annotation rows are displayed</li>
- <li><= shown as = in annotation row tooltip</li>
- <li>export features raises exception when no features exist</li>
- <li>relative URLs not handled properly when used in parameters
- and annotation files</li>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <ul>
- <li>sequence numbering not preserved in MSF alignment output</li>
- <li>sequence associated secondary structure not correctly parsed
- in interleaved stockholm</li>
- <li>sequences containing lowercase letters are not properly
- associated with their pdb files</li>
- <li>Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly</li>
- <li>Sequence length given in alignment properties window is off
- by 1</li>
- </ul>
+ 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>
</body>
</html>