-<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/applets.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>
+<!--
+ * 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.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+ <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>
+ <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