X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c34a573b58041e178800ee72eb638f446ef72bae;hb=f3018be7da2a80e635bfc78b8f8f3e58877cce29;hp=1762e22eb49ae2a73fba5efb2c37274442581464;hpb=80ef6283ac0c84f0f82cf8cd5599bfe6b14ee907;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 1762e22..c34a573 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,12 +1,30 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
+<!--
+  Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+  
+  This program 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 2
+  of the License, or (at your option) any later version.
+  
+  This program 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 this program; if not, write to the Free Software
+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+-->
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="true">
       <tocitem text="Release History" target="release"/>
-	  <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
-	  <tocitem text="Mapping between Sequences" target="seqmappings"/>
-    </tocitem>
+		<tocitem text="Sequence Retrieval" target="seqfetch"/>
+		<tocitem text="VAMSAS Interoperation" target="vamsas"/>
+	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
 	<tocitem text="Key Strokes" target="keys"/>
@@ -71,6 +89,10 @@
 	  <tocitem text="Jmol Viewer" target="pdbjmol"/>
 	  <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
 	</tocitem>
+	<tocitem text="VAMSAS Data Exchange" target="vamsas">
+		<!-- what can Jalview share with other apps -->
+		<!-- what other apps exist -->
+		</tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
@@ -94,6 +116,7 @@
           <tocitem text="Command Line Arguments" target="clarguments"/>
 	      <tocitem text="Groovy Shell" target="groovy"/>
         </tocitem>
+       	<tocitem text="Privacy" target="privacy"/>
 </tocitem>
 <tocitem text="Useful information" expa nd="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>