<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
<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>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ The Jalview 2.7 release features new web services, and important
+ improvements to the way in which Jalview handles alignments and
+ associated PDB structures, as well as numerous minor improvements and
+ bug fixes. Version 2.7 of the JalviewLite applet also features a
+ significantly enhanced Javascript API enabling it to be more easily
+ integrated with javascript based web applications. <br /> For full
+ details see the <a href="releases.html#Jalview2.7">Jalview 2.7
+ release history</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Desktop Version 2.7</strong>
+ </p>
+ <ul>
+ <li>New <a href="features/viewingpdbs.html">structure viewer
+ options</a>:
+ <ul>
+ <li>Colour and superimpose 3D structures of complexes and
+ multi-domain chains using several different alignments</li>
+ <li>Drag and drop to associate PDB files with sequences that
+ have the same name</li>
+ <li>Open and superimpose all associated structures for the
+ current selection</li>
+ </ul>
+ <li>New web services for <a href="webServices/shmr.html">alignment
+ analysis</a></li>
+ <li>Improved graphical user interface for <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
+ </li>
+ <li>Sort associated alignment views option in tree viewer</li>
+ <li>Default colours for <a
+ href="colourSchemes/annotationColouring.html">shading alignment
+ by quantitative annotation</a>.
+ </li>
+ <li><a href="webServices/newsreader.html">Jalview Desktop RSS
+ reader</a> - following important updates at <a
+ href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
+ </ul>
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+ <p>
+ <strong>Issues Resolved (a select list - see the <a
+ href="releases.html#Jalview2.7">release history</a> for full details)
+ </strong>
+ </p>
+ <p>
+ <strong>Issues in the Jalview Desktop</strong>
+ <ul>
+ <li>Problems viewing associated structures for sequences
+ retrieved from UNIPROT</li>
+ <li>Problems viewing Jalview projects from older versions in
+ version 2.6</li>
+ <li>Preservation of hidden annotation rows and tree bootstrap
+ values in projects</li>
+ <li>Newly added JABAWS servers not always visible in web services
+ menu</li>
+ </ul>
+ <strong>Issues specific to the JalviewLite Applet</strong>
+ <ul>
+ <li>Layout problems when lots of annotation rows are displayed</li>
+ <li><= shown as = in annotation row tooltip</li>
+ <li>export features raises exception when no features exist</li>
+ <li>relative URLs not handled properly when used in parameters
+ and annotation files</li>
+ </ul>
+ <strong>Issues affecting both applet and application</strong>
+ <ul>
+ <li>sequence numbering not preserved in MSF alignment output</li>
+ <li>sequence associated secondary structure not correctly parsed
+ in interleaved stockholm</li>
+ <li>sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ <li>Jalview PDB file reader does not extract sequence from deoxy
+ nucleotide chains correctly</li>
+ <li>Sequence length given in alignment properties window is off
+ by 1</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff