3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>What's new ?</title>
24 <strong>What's new ?</strong>
27 The Jalview 2.7 release features new web services, and important
28 improvements to the way in which Jalview handles alignments and
29 associated PDB structures, as well as numerous minor improvements and
30 bug fixes. Version 2.7 of the JalviewLite applet also features a
31 significantly enhanced Javascript API enabling it to be more easily
32 integrated with javascript based web applications. <br /> For full
33 details see the <a href="releases.html#Jalview2.7">Jalview 2.7
37 <strong>Highlights in Jalview Desktop Version 2.7</strong>
40 <li>New <a href="features/viewingpdbs.html">structure viewer
43 <li>Colour and superimpose 3D structures of complexes and
44 multi-domain chains using several different alignments</li>
45 <li>Drag and drop to associate PDB files with sequences that
46 have the same name</li>
47 <li>Open and superimpose all associated structures for the
48 current selection</li>
50 <li>New web services for <a href="webServices/shmr.html">alignment
52 <li>Improved graphical user interface for <a
53 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
55 <li>Sort associated alignment views option in tree viewer</li>
56 <li>Default colours for <a
57 href="colourSchemes/annotationColouring.html">shading alignment
58 by quantitative annotation</a>.
60 <li><a href="webServices/newsreader.html">Jalview Desktop RSS
61 reader</a> - following important updates at <a
62 href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
66 <strong>Issues Resolved (a select list - see the <a
67 href="releases.html#Jalview2.7">release history</a> for full details)
71 <strong>Issues in the Jalview Desktop</strong>
73 <li>Problems viewing associated structures for sequences
74 retrieved from UNIPROT</li>
75 <li>Problems viewing Jalview projects from older versions in
77 <li>Preservation of hidden annotation rows and tree bootstrap
78 values in projects</li>
79 <li>Newly added JABAWS servers not always visible in web services
82 <strong>Issues specific to the JalviewLite Applet</strong>
84 <li>Layout problems when lots of annotation rows are displayed</li>
85 <li><= shown as = in annotation row tooltip</li>
86 <li>export features raises exception when no features exist</li>
87 <li>relative URLs not handled properly when used in parameters
88 and annotation files</li>
90 <strong>Issues affecting both applet and application</strong>
92 <li>sequence numbering not preserved in MSF alignment output</li>
93 <li>sequence associated secondary structure not correctly parsed
94 in interleaved stockholm</li>
95 <li>sequences containing lowercase letters are not properly
96 associated with their pdb files</li>
97 <li>Jalview PDB file reader does not extract sequence from deoxy
98 nucleotide chains correctly</li>
99 <li>Sequence length given in alignment properties window is off