-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.1</p>\r
-<p>The multiple sequence alignment program <a href="webServices/mafft.html">MAFFT</a> \r
- is available from the default Web Service list.</p>\r
-<p>The sequence feature retrieval system using DBFetch from EBI has been replaced \r
- with <a href="features/dassettings.html">DAS Feature fetching</a> capabilities.</p>\r
-<p><a href="features/hiddenRegions.html">Hide sequences and columns</a></p>\r
-<p>Export Annotations and Features</p>\r
-<p>GFF file reading / writing</p>\r
-<p>Associate structures with sequences from local PDB files</p>\r
-<p>Add sequences to existing alignment</p>\r
-<p>Recently opened files / URL lists</p>\r
-<p>Applet can launch the full application</p>\r
-<p>Applet has transparency for features (Java 1.2 required)</p>\r
-<p>Applet has user defined colours parameter</p>\r
-<p> </p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<p>Redundancy Panel reinstalled in the Applet</p>\r
-<p>Monospaced font - EPS / rescaling bug fixed</p>\r
-<p>Annotation files with sequence references bug fixed</p>\r
-<p> </p>\r
-<p>See the <a href="releases.html">Release History</a> page for details of all\r
- new features and resolved issues. </p>\r
-</body>\r
-</html>\r
+<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 in Jalview 2.10.4b1 ?</strong>
+ </p>
+ <p>This is the first patch release for Jalview 2.10.4. It includes
+ the following new patches:</p>
+ <ul>
+ <li>HGVS nomenclature used for variant annotation retrieved
+ from Uniprot</li>
+ <li>Uniprot import fails for some sequences (Cannot import
+ features with multiple variant elements)</li>
+ <li>Clustal files with sequence positions in right-hand column
+ are now parsed correctly</li>
+ <li>Wrap view - export to SVG - IDs shown but not alignment
+ area in exported graphic</li>
+ <li>F2/Keyboard mode edits work when Overview window has input
+ focus</li>
+ <li>Windows specific fixes:
+ <ul>
+ <li>Annotation panel set too high when annotation added to
+ view</li>
+ <li>Updated search paths for Chimera default installation</li>
+ <li>Windows File Shortcuts can be dragged onto the Jalview
+ Desktop</li>
+ <li>Drag URL from Chrome, Firefox, IE to Jalview desktop on
+ Windows doesn't open file:<br /> Dragging the currently open
+ URL and links from a page viewed in Firefox or Chrome on
+ Windows is now fully supported.<br />
+ <strong>If you are using Edge</strong>, only links in the page
+ can be dragged.<br />
+ <strong>With Internet Explorer</strong>, only the currently open
+ URL in the browser can be dropped onto Jalview.
+ </li>
+ </ul>
+ </li>
+ </ul>
+ <p>Highlights in the 2.10.4 series include:</p>
+ <ul>
+ <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>
+ </ul>
+ <p>
+ The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>.
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff