<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>Highlights in Jalview Version 2.4</strong></p>
-<ul>
- DNA and protein product highlighting<br>
- URL links generated with regular expressions<br>
- URL links for sequence database cross references<br>
- New sequence fetcher dialog and DAS Sequence Fetching<br>
- JPred Service upgraded to Jpred3<br>
- Memory monitor<br>
- PFAM full alignment retrieval<br>
- Generalised sequence database reference validation<br>
- DNA Protein Product sequence db traversal (Experimental)<br>
- VAMSAS Interoperation Client (Experimental)<br>
- export annotation rows as CSV for spreadsheet import<br>
- New application command line args and optional Groovy suport<br>
- New Applet API methods and parameters<br>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
-<ul>
- Aligned cDNA translation to aligned peptide works correctly<br>
- selected region output includes visible annotations (for
- certain formats)<br>
- edit label/displaychar contains existing label/char for
- editing<br>
- Newick tree support improved for clustalW trees and preserving NHX style comments<br>
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'<br>
- Fixed exception when parsing GFF files containing global
- sequence features<br>
- Reference counting for alignment datasets<br>
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.<br>
- Save works when Jalview project is default format<br>
- Histidine should be midblue (not pink!) in Zappo<br>
- Undo recovers dataset sequence metadata when sequence
- regions are cut<br>
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly<br>
- Stockholm annotation parsing fixed and improved (PFAM records)<br>
- Re-instated Full AMSA support and .amsa file association (MyHits)<br>
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file<br>
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet<br>
- Applet Menus are always embedded in applet window on Macs.</br>
- Newly shown features appear at top of stack (in Applet)</br>
- Secondary structure lines are drawn starting from first
- column of alignment<br>
- Uniprot XML import updated for new schema release in July 2008<br>
- Sequence feature to sequence ID match for Features file is case-insensitive<br>
- Sequence features read from Features file appended to all sequences with matching IDs<br>
- PDB structure coloured correctly for associated views containing a sub-sequence<br>
- Display name and local features preserved in results retrieved from web service<br>
- Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
- Updated Application to use DAS 1.53e version of dasobert DAS client
-</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 2.10.3b1 ?</strong>
+ </p>
+ <p>
+ This is the January 2018 patch release, which addresses critical bugs in Version 2.10.3 (released November 2017).
+ The bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>.
+ </p>
+ <p>The highlights for Jalview 2.10.3 include:
+ </p>
+ <ul>
+ <li>Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features</li>
+ <li>Improved usability with <a
+ href="features/pdbsequencefetcher.html">PDB</a> and <a
+ href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+ </li>
+ <li>Short names assigned to sequences retrieved from UniProt</li>
+ <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ Remember, please enable the <em>Experimental Features</em> option in
+ the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
+ if you want to try out features below:
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff