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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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* This file is part of Jalview.
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* Jalview is free software: you can redistribute it and/or
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+ * 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.
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- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+ * 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 2.6 introduces new web services, and includes an updated
-version of the Jmol molecular graphics visualization system. See the <a
- href="releases.html#Jalview2.6">release history</a> for the full
-details.</p>
-<p><strong>Highlights in Jalview Version 2.6</strong></p>
-<ul>
- <li><a href="webServices/JABAWS.html">JABA Web Services</a> for
- multiple alignment using:
- <ul>
- <li>ClustalW</li>
- <li>MAFFT</li>
- <li>Muscle</li>
- <li>ProbCons</li>
- <li>T-COFFEE</li>
- </ul>
- </li>
- <li>User modifiable alignment service parameters</li>
- <li>Visualization of superposed structures associated with protein
- or nucleotide sequence alignments.</li>
- <li>Export coordinates and projection as CSV from PCA viewer</li>
-</ul>
+ <p>
+ <strong>What's new in Jalview 2.10.1 ?</strong>
+ </p>
+ <p>
+ Jalview 2.10.1 was released on 29th November 2016. Full details are
+ in the <a href="releases.html#Jalview.2.10.1">Jalview 2.10.1
+ Release Notes</a>, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
+ </p>
+ <ul>
+ <li><strong>More memory efficient</strong><br />We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.</li>
+ <li><strong>Select highlighted region</strong><br />Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a Find
+ operation.</li>
+ <li><strong>New custom link mechanism for opening URLs
+ for database cross references.</strong><br /> If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the <a href="#warning"> warning dialog (see below).</a></li>
+ <li><strong>New command line export option for BioJS
+ MSAviewer</strong><br />A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.</li>
+ <li><strong>Small but significant changes to the
+ physicochemical properties and consensus calculations</strong><br />Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.</li>
+ <li><strong>Correct display of disulphide bond
+ features</strong><br /> In linked structure views, Jalview would
+ highlight all residues between in addition to the two linked
+ cysteines. The 'select columns by feature' function in the feature
+ settings would also select all intermediate columns.
+ </ul>
-<p><strong>Issues Resolved (a select list - see release history for details)</strong></p>
-<ul>
- <li>clustalx colourscheme colours Ds preferentially when both D+E
- are present in over 50% of the column</li>
- <li>Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources</li>
- <li>InstallAnywhere builds fail to launch on OS X java 10.5 update
- 4 (due to apple Java 1.6 update)</li>
-</ul>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+ <p>
+ <strong><a name="warning">Warning dialog about updating
+ your configured URL links</a></strong><br /> In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that <em>exactly</em>
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff