From f6a7e5514230be7ea8c2d4cccb504b4ed95f80ef Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 8 Nov 2012 10:59:13 +0000
Subject: [PATCH] embed links to major features in main page

---
 help/html/whatsNew.html |   38 +++++++++++++++++---------------------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index d9b6360..39ef82f 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -36,36 +36,33 @@
   <strong>Highlights in Jalview Version 2.8</strong>
  </p>
  <ul>
-  <li>Improved JABA client and new JABAWS 2.0 Services
+  <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a> client and new JABAWS 2.0 Services</strong>
    <ul>
-    <li>AACon alignment conservation</li>
-    <li>Protein disorder - DisEMBL, RONN, GlobPlot and IUPred</li>
-    <li>Clustal Omega - huge protein alignments</li>
+    <li><a href="webServices/AACon.html">AACon alignment conservation</a></li>
+    <li><a href="webServices/proteinDisorder.html">Protein disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
+    <li>Clustal Omega for creating huge protein alignments</li>
    </ul>
   </li>
-  <li><strong>Support for RNA</strong>
+  <li><strong>Support for <a href="na/index.html">RNA</a></strong>
    <ul>
-    <li>Import sequence and alignment associated WUSS or VIENNA
-     secondary structure notation from stockholm and clustalW files or
-     as jalview annotation.</li>
+    <li>Import sequence and alignment associated WUSS or VIENNA dot-bracket
+     notation from files and the <strong>RFAM</strong> database</li>
     <li>Interactive editing of RNA secondary structure annotation</li>
     <li>Colour scheme for purine/pyrimidine and to highlight RNA
      helices</li>
-    <li>RNA canonical base pair consensus score and sequence logo</li>
-    <li>Embedded <a href="http://varna.lri.fr/">VARNA</a> RNA
+    <li>RNA canonical <a href="calculations/structureconsensus.html">base pair consensus score</a> and sequence logo</li>
+    <li>Embedded <a href="features/varna.html">VARNA</a> RNA
      secondary structure viewer in the Desktop
     </li>
-   </ul> See <a href="na/index.html">Nucleic Acid Support</a> for full
-   details.</li>
-  <li>Parse and display T-COFFEE alignment quality scores</li>
-  <li>Shade individual sequence positions according to alignment
-   annotation scores</li>
-  <li>Enhanced PCA viewer: more export options, and switch between
+   </ul></li>
+  <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE alignment quality scores</a> (thanks to Paolo Tomassi of the Notredame Group)</li>
+  <li><a href="colourSchemes/annotationColouring.html">Per sequence alignment annotation shading</a></li>
+  <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more export options, and switch between
    different PCA modes and residue score models</li>
-  <li>New Jalview Desktop database fetcher GUI</li>
-  <li>Support for DAS 1.6 and DAS 2.0 sources</li>
-  <li>Export sequence database annotation as HTML report</li>
-  <li>Normalised Sequence Logo Display</li>
+  <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database fetcher</a> GUI</li>
+  <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to new JDAS Distributed Annotation client library)</li>
+  <li>Export sequence database annotation as <a href="io/exportseqreport.html">HTML report</a></li>
+  <li>Normalised <a href="calculations/consensus.html">Sequence Logo Display</a></li>
  </ul>
  <p>
   <strong>Issues Resolved (a select list - see the <a
@@ -175,7 +172,6 @@
   </li>
  </ul>
  <strong>Issues affecting both applet and application</strong>
- <em>General</em>
  <ul>
   <li>
    <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] -         -->Redundancy
-- 
1.7.10.2