3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 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>
23 <p><strong>What's new ?</strong></p>
24 <p><strong>Highlights in Jalview Version 2.5</strong></p>
26 Linked viewing of nucleic acid sequences and structures<br/>
27 Automatic Scrolling option in View menu to display the
28 currently highlighted region of an alignment.<br/>
29 Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
30 Shading features by score or associated description<br/>
31 Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
32 New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
34 <em>Jalview Desktop:</em>
36 Fetch DB References capabilities and UI expanded to support
37 retrieval from DAS sequence sources<br/>
38 Enable or disable non-positional feature and database
39 references in sequence ID tooltip from View menu in application.<br/>
40 Group-associated consensus, sequence logos and conservation
42 Symbol distributions for each column can be exported and
43 visualized as sequence logos<br/>
44 Jalview Java Console<br/>
45 New webservice for submitting sequences and IDs to <a
46 href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
47 Improved VAMSAS synchronization and sharing of selections.<br/>
51 Middle button resizes annotation row height<br/>
52 New Parameters - including default tree display settings.<br/>
53 Non-positional features displayed in ID tooltip<br/>
55 <p><strong>Issues Resolved (a select list)</strong></p>
58 Source field in GFF files parsed as feature source rather
60 Non-positional features are now included in sequence feature
61 and gff files (controlled via non-positional feature visibility in
63 URL links generated for all feature links (bugfix)<br/>
64 Codons containing ambiguous nucleotides translated as 'X' in
66 Match case switch in find dialog box works for both sequence
67 ID and sequence string and query strings do not have to be in upper
68 case to match case-insensitively.<br/>
69 Jalview Annotation File generation/parsing consistent with
70 documentation (e.g. Stockholm annotation can be exported and
72 Find incrementally searches ID string matches as well as
73 subsequence matches, and correctly reports total number of both.<br/>
75 <em>Desktop Issues</em>
77 Better handling of exceptions during sequence retrieval<br/>
78 PDB files retrieved from URLs are cached properly<br/>
79 Sequence description lines properly shared via VAMSAS<br/>
80 Sequence fetcher fetches multiple records for all data
82 Ensured that command line das feature retrieval completes
83 before alignment figures are generated.<br/>
84 Reduced time taken when opening file browser for first time.<br/>
85 User defined group colours properly recovered from Jalview projects.<br/>
90 <p>See the <a href="releases.html">Release History</a> page for
91 details of all new features and resolved issues.</p>