</head>
<body>
<p><strong>What's new ?</strong></p>
-
-<p><strong>Jalview Version 2.3</strong></p>
-<ul>Jmol 11 integration<br>
-PDB views in Jalview XML<br>
-Slide sequences<br>
-Edit sequence in place<br>
-EMBL CDS features<br>
-DAS Feature mapping<br>
-Feature ordering<br>
-Alignment Properties<br>
-Annotation Scores<br>
-Sort by scores<br>
-Feature/annotation editing in applet<br>
+<p><strong>Highlights in Jalview Version 2.4</strong></p>
+<ul>
+ DNA and protein product highlighting<br>
+ URL links generated with regular expressions<br>
+ URL links for sequence database cross references<br>
+ New sequence fetcher dialog and DAS Sequence Fetching<br>
+ JPred Service upgraded to Jpred3<br>
+ Memory monitor<br>
+ PFAM full alignment retrieval<br>
+ Generalised sequence database reference validation<br>
+ DNA Protein Product sequence db traversal (Experimental)<br>
+ VAMSAS Interoperation Client (Experimental)<br>
+ export annotation rows as CSV for spreadsheet import<br>
+ New application command line args and optional Groovy suport<br>
+ New Applet API methods and parameters<br>
</ul>
-<p> </p>
-<p><strong>Issues Resolved</strong></p>
-<p><br>
-Headless state operation in 2.2.1
-<br>Incorrect and unstable DNA pairwise alignment
-<br>
-Cut and paste of sequences with annotation
-<br>
-Feature group display state in XML<br>
-Feature ordering in XML<br>
-2.2.1 applet had no feature transparency<br>
-</p>
+<p><strong>Issues Resolved (a select list)</strong></p>
+<ul>
+ Aligned cDNA translation to aligned peptide works correctly<br>
+ selected region output includes visible annotations (for
+ certain formats)<br>
+ edit label/displaychar contains existing label/char for
+ editing<br>
+ Newick tree support improved for clustalW trees and preserving NHX style comments<br>
+ Pathological filechooser bug avoided by not allowing
+ filenames containing a ':'<br>
+ Fixed exception when parsing GFF files containing global
+ sequence features<br>
+ Reference counting for alignment datasets<br>
+ better reporting of non-fatal warnings and error messages to user when file
+ parsing fails.<br>
+ Save works when Jalview project is default format<br>
+ Histidine should be midblue (not pink!) in Zappo<br>
+ Undo recovers dataset sequence metadata when sequence
+ regions are cut<br>
+ PDB files without pdb ID HEADER lines (like those
+ generated by MODELLER) are read in properly<br>
+ Stockholm annotation parsing fixed and improved (PFAM records)<br>
+ Re-instated Full AMSA support and .amsa file association (MyHits)<br>
+ annotation consisting of sequence associated scores can be
+ read and written correctly to annotation file<br>
+ Fixed display of hidden sequence markers and non-italic font
+ for representatives in Applet<br>
+ Applet Menus are always embedded in applet window on Macs.</br>
+ Newly shown features appear at top of stack (in Applet)</br>
+ Secondary structure lines are drawn starting from first
+ column of alignment<br>
+ Uniprot XML import updated for new schema release in July 2008<br>
+ Sequence feature to sequence ID match for Features file is case-insensitive<br>
+ Sequence features read from Features file appended to all sequences with matching IDs<br>
+ PDB structure coloured correctly for associated views containing a sub-sequence<br>
+ Display name and local features preserved in results retrieved from web service<br>
+ Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
+ Updated Application to use DAS 1.53e version of dasobert DAS client
+</ul>
+
<p> </p>
<p>See the <a href="releases.html">Release History</a> page for
details of all new features and resolved issues.</p>