X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c34a573b58041e178800ee72eb638f446ef72bae;hb=bccb0e877e424519b1d799278cdb529f974cb026;hp=2a068975c1ac5c655d7a8508c4ce4a0e282f9604;hpb=75167d6c23db7b520308891dba5376b904109143;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2a06897..c34a573 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,20 +1,39 @@
 <?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"/>
 	<tocitem text="Input / Output" target="io"/>
-  	<tocitem text="Making figures" target="export"/>
+  	<tocitem text="Making Figures" target="export"/>
 	<tocitem text="Hidden Regions" target="hiddenRegions"/>
 	<tocitem text="Multiple Views" target="multipleviews"/>
 	<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
+	<tocitem text="Fetching Sequences" target="seqfetch"/>
 	<tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -31,6 +50,8 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+		<tocitem text="Sequence Retrieval" target="seqfetch"/>
+		<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
@@ -68,6 +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">
@@ -91,6 +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"/>