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 2.4</strong></p>
26 DNA and protein product highlighting<br>
27 URL links generated with regular expressions<br>
28 URL links for sequence database cross references<br>
29 New sequence fetcher dialog and DAS Sequence Fetching<br>
30 JPred Service upgraded to Jpred3<br>
32 PFAM full alignment retrieval<br>
33 Generalised sequence database reference validation<br>
34 DNA Protein Product sequence db traversal (Experimental)<br>
35 VAMSAS Interoperation Client (Experimental)<br>
36 export annotation rows as CSV for spreadsheet import<br>
37 New application command line args and optional Groovy suport<br>
38 New Applet API methods and parameters<br>
40 <p><strong>Issues Resolved (a select list)</strong></p>
42 Aligned cDNA translation to aligned peptide works correctly<br>
43 selected region output includes visible annotations (for
45 edit label/displaychar contains existing label/char for
47 Newick tree support improved for clustalW trees and preserving NHX style comments<br>
48 Pathological filechooser bug avoided by not allowing
49 filenames containing a ':'<br>
50 Fixed exception when parsing GFF files containing global
52 Reference counting for alignment datasets<br>
53 better reporting of non-fatal warnings and error messages to user when file
55 Save works when Jalview project is default format<br>
56 Histidine should be midblue (not pink!) in Zappo<br>
57 Undo recovers dataset sequence metadata when sequence
59 PDB files without pdb ID HEADER lines (like those
60 generated by MODELLER) are read in properly<br>
61 Stockholm annotation parsing fixed and improved (PFAM records)<br>
62 Re-instated Full AMSA support and .amsa file association (MyHits)<br>
63 annotation consisting of sequence associated scores can be
64 read and written correctly to annotation file<br>
65 Fixed display of hidden sequence markers and non-italic font
66 for representatives in Applet<br>
67 Applet Menus are always embedded in applet window on Macs.</br>
68 Newly shown features appear at top of stack (in Applet)</br>
69 Secondary structure lines are drawn starting from first
70 column of alignment<br>
71 Uniprot XML import updated for new schema release in July 2008<br>
72 Sequence feature to sequence ID match for Features file is case-insensitive<br>
73 Sequence features read from Features file appended to all sequences with matching IDs<br>
74 PDB structure coloured correctly for associated views containing a sub-sequence<br>
75 Display name and local features preserved in results retrieved from web service<br>
76 Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
77 Updated Application to use DAS 1.53e version of dasobert DAS client
81 <p>See the <a href="releases.html">Release History</a> page for
82 details of all new features and resolved issues.</p>