X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FJalviewRNASupport.html;h=161791c3fc3f32bae4ad3a6477b52ea3976e63cb;hb=b3dafcbca0f7fc90080bc670e1289758d6147252;hp=d96cca53381bf60b9474930a38b0116393dbad9d;hpb=61aa402837621b3e80ec61d56152ea0c858b319d;p=jalview.git

diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html
index d96cca5..161791c 100644
--- a/doc/JalviewRNASupport.html
+++ b/doc/JalviewRNASupport.html
@@ -1,14 +1,14 @@
 <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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
@@ -22,11 +22,10 @@
 Jalview RNA Support
 </h1>
 <p>
-Jalview RNA support has been added in part during a 
-<a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2010">Google Summer of Code Project</a>.
-More information about this project can be found at the 
-<a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Extending_Jalview_to_Support_RNA_Alignment_Annotation_and_Secondary_Structure_Visualization">
-NESCent wiki page</a> and the project <a href="http://jalview-rnasupport.blogspot.com/">blog</a>. 
+Jalview RNA support was first added during a 
+<a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2010">2010 Google Summer of Code Project</a> by  
+Lauren Lui (see her <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Extending_Jalview_to_Support_RNA_Alignment_Annotation_and_Secondary_Structure_Visualization">
+NESCent wiki page</a> and the project <a href="http://jalview-rnasupport.blogspot.com/">blog</a>).  
 </p>
 <h2>What was added</h2>
 <p>
@@ -39,6 +38,16 @@ NESCent wiki page</a> and the project <a href="http://jalview-rnasupport.blogspo
 annotation panel.</li>
 </ul>
 </p>
+<p>In 2011, Jan Engelhardt was supported by <a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2011">GSOC</a> to extend Lauren's work, with <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:_Extending_Jalview_support_for_handling_RNA">support for viewing secondary structure in VARNA and visualizing base pair contact conservation</a>.
+</p>
+<h2>What Jan added</h2>
+<p>
+<ul>
+<li>Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files</li>
+<li>Incorporated <a href="varna.lri.fr">VARNA</a> into the desktop application</li>
+<li>Added a new base pair consensus histogram and sequence logo annotation row</li> 
+</ul>  
+</p>
 <h2>TODO</h2>
 <h3>Secondary Structure Visualization/Annotation</h3>
 <ul>
@@ -47,7 +56,6 @@ annotation panel.</li>
 <li>Editing of secondary structure line</li>
 <li>Update helix colouring when secondary structure changes.</li>
 <li>Support per sequence in RNA secondary structure annotation</li>
-<li>Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files</li>
 </ul>
 
 <h3>Colour schemes</h3>
