<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.
- *
+ *
* 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>Jalview 2.5.1 is a bug fix release for the 2.5 version of
-Jalview. See the <a href="releases.html#Jalview2.5.1">release
-history</a> for the bugs that this release resolves.</p>
-<p><strong>Highlights in Jalview Version 2.5</strong></p>
-<ul>
- Linked viewing of nucleic acid sequences and structures<br/>
- Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.<br/>
- Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
- Shading features by score or associated description<br/>
- Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
- New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
-</ul>
-<em>Jalview Desktop:</em>
-<ul>
- Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources<br/>
- Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.<br/>
- Group-associated consensus, sequence logos and conservation
- plots<br/>
- Symbol distributions for each column can be exported and
- visualized as sequence logos<br/>
- Jalview Java Console<br/>
- New webservice for submitting sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
- Improved VAMSAS synchronization and sharing of selections.<br/>
-</ul>
-<em>JalviewLite:</em>
-<ul>
- Middle button resizes annotation row height<br/>
- New Parameters - including default tree display settings.<br/>
- Non-positional features displayed in ID tooltip<br/>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
-<ul>
- <ul>
- Source field in GFF files parsed as feature source rather
- than description<br/>
- Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).<br/>
- URL links generated for all feature links (bugfix)<br/>
- Codons containing ambiguous nucleotides translated as 'X' in
- peptide product<br/>
- Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.<br/>
- Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)<br/>
- Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.<br/>
- </ul>
- <em>Desktop Issues</em>
- <ul>
- Better handling of exceptions during sequence retrieval<br/>
- PDB files retrieved from URLs are cached properly<br/>
- Sequence description lines properly shared via VAMSAS<br/>
- Sequence fetcher fetches multiple records for all data
- sources<br/>
- Ensured that command line das feature retrieval completes
- before alignment figures are generated.<br/>
- Reduced time taken when opening file browser for first time.<br/>
- User defined group colours properly recovered from Jalview projects.<br/>
- </ul>
-</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 ?</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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff