-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.07 </p>\r
-<p><a href="features/seqfetch.html">Sequence Fetcher</a> has been added to quickly \r
- retrieve sequences with known ids from several databases.</p>\r
-<p><a href="features/seqfeatures.html">Sequence Features enhanced</a> to allow \r
- the user to display all features of a Uniprot file on the alignment and subsequently \r
- colour, hide or show overlapping features. </p>\r
-<p><a href="io/fileformats.html">Choose to omit /start-end from sequences when \r
- saving files.</a> This is important for saving files to be used by some programs \r
- which cannot read the original Jalview sequence output with the appended /start-end.</p>\r
-<p><a href="features/pdbviewer.html">PDB structure viewer enhanced</a>. Mapping \r
- between sequence and structure has been enhanced, colours on the alignment are \r
- reflected in the structure viewer.</p>\r
-<p><a href="http://www.jalview.org/examples/applet.html">Jalview Applet can read \r
- in feature files, PDB files be used as input to HTML form</a> See the website \r
- to find out the new parameters available for the Applet Version of Jalview.</p>\r
-<p> </p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<p>Group Editing is possible with Control and mouse click. Alt key and mouse press \r
- does not work as this translates as the middle mouse button, which since 2.04 \r
- is now used to scroll the alignment and change the font size. </p>\r
-<p>HTML export now writes groups and features which were previously missing.</p>\r
-<p> </p>\r
-<p>See the <a href="releases.html">Release History</a> page for details of all \r
- new features and resolved issues. </p>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+<p><strong>What's new ?</strong></p>
+<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><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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff