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