3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>What's new in Jalview 2.10.4b1 ?</strong>
29 <p>This is the first patch release for Jalview 2.10.4. It includes
30 the following new patches:</p>
32 <li>HGVS nomenclature used for variant annotation retrieved
34 <li>Uniprot import fails for some sequences (Cannot import
35 features with multiple variant elements)</li>
36 <li>Clustal files with sequence positions in right-hand column
37 are now parsed correctly</li>
38 <li>Wrap view - export to SVG - IDs shown but not alignment
39 area in exported graphic</li>
40 <li>F2/Keyboard mode edits work when Overview window has input
42 <li>Windows specific fixes:
44 <li>Annotation panel set too high when annotation added to
46 <li>Updated search paths for Chimera default installation</li>
47 <li>Windows File Shortcuts can be dragged onto the Jalview
49 <li>Drag URL from Chrome, Firefox, IE to Jalview desktop on
50 Windows doesn't open file:<br /> Dragging the currently open
51 URL and links from a page viewed in Firefox or Chrome on
52 Windows is now fully supported.<br />
53 <strong>If you are using Edge</strong>, only links in the page
55 <strong>With Internet Explorer</strong>, only the currently open
56 URL in the browser can be dropped onto Jalview.
61 <p>Highlights in the 2.10.4 series include:</p>
63 <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
64 <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
65 <li>Critical patches for running Jalview on OSX with Java 10</li>
66 <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
67 <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
68 <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
69 <li>New buttons on the Structure Chooser for adding structures
70 to an existing view, and disabling automatic superposition
71 according to linked alignments</li>
72 <li>Annotation transfer between Chimera and Jalview <em>(formerly only
73 available in 'Experimental' mode)</em></li>
76 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