Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826)

[jalview.git] / help / html / whatsNew.html

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index cf96d47..3ff173b 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,80 +24,35 @@
                <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
+               The Jalview 2.7.1 release features (tbc)
+               <br /> For full
+               details see the <a href="releases.html#Jalview2.7.1">Jalview 2.7.1
                        release history</a>.
        </p>
        <p>
-               <strong>Highlights in Jalview Desktop Version 2.7</strong>
+               <strong>Highlights in Jalview Desktop Version 2.7.1</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>
+
+       <li>New Purine/Pyrimidine colour scheme</li>
+       <li>Colouring of RNA secondary structure by helices.  See <a href="na/index.html">Nucleic Acid Support</a></li>
+       <li>Embedded <a href="http://www.varna.fr/">VARNA</a> RNA secondary structure viewer.
        </ul>
 
        <p>
                <strong>Issues Resolved (a select list - see the <a
-                       href="releases.html#Jalview2.7">release history</a> for full details)
+                       href="releases.html#Jalview2.7.1">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>&lt;= 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>