X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=9ad08fa4d21ea54be810b9199d5fde7272ae11d5;hb=36f06cf52feeabc8cfde2e3207a2bc3871ded57d;hp=7d9e595a720c2a959041bc6d69ea5e12144da1b1;hpb=67594472bd8920efa45169478981b700b79ae683;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 7d9e595..9ad08fa 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,16 +2,20 @@
 <!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="Editing Alignments" target ="edit"/>	
-        <tocitem text="Cursor Mode" target="cursor"/>
+	<tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Release History" target="release"/>
+		<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="Viewing PDB Files" target="viewingpdbs"/>
 	<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"/>
@@ -28,6 +32,8 @@
                 <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"/>
@@ -55,12 +61,20 @@
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
-      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+  	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
+	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+	  <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">
@@ -82,6 +96,7 @@
           </tocitem>
         <tocitem text="Command Line" target="commandline" expand="false">
           <tocitem text="Command Line Arguments" target="clarguments"/>
+	      <tocitem text="Groovy Shell" target="groovy"/>
         </tocitem>
 </tocitem>
 <tocitem text="Useful information" expa nd="true">