X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=5e69a230c5c86fd93b5b14d51de8709674be17d9;hb=935e15fa16def9e538c8befaf061441b52f269ed;hp=2b8f8b95b35e8f64357c9f13bc72815da3093bbf;hpb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2b8f8b9..5e69a23 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,13 +3,18 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-		<tocitem text="Search" target="search"/>
-		<tocitem text="Wrap Alignment" target="wrap"/>
-		<tocitem text="Overview Window" target ="overview"/>
-		<tocitem text="Sequence Features" target ="seqfeatures"/>
-      		<tocitem text="Alignment Annotations" target ="alannotation"/>
-	</tocitem>
-	<tocitem text="Input /Output" target="io"/>
+                <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>
+                <tocitem text="New Output Format Controls" target="preferences"/>
+                <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>
+                <tocitem text="Sequence Feature Styles" target="seqfeatures"/>
+        </tocitem>
+	<tocitem text="Release History" target="release"/>
+      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+          <tocitem text="Conservation" target="calcs.alconserv"/>
+          <tocitem text="Quality" target="calcs.alquality"/>
+        </tocitem>
+	<tocitem text="Input / Output" target="io"/>
+	<tocitem text="Key Strokes" target="keys"/>
   	<tocitem text="Making figures" target="export"/>
 	<tocitem text="Editing Alignments" target ="edit"/>
 	<tocitem text="Web Services" target="webservice" expand="false">
@@ -44,17 +49,22 @@
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
                 <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>  
+                <tocitem text="Edit Menu" target="alwEdit"/> 
+                <tocitem text="View Menu" target="alwView"/> 
                 <tocitem text="Colour Menu" target="alwColour"/>
                 <tocitem text="Calculation Menu" target="alwCalc"/>
+				<tocitem text="Web Service Menu" target="wsMenu"/>
 		<tocitem text="Annotation Menus" target="annotMenus"/>
 		<tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
-
 	</tocitem>
+	<tocitem text="Memory Settings" target="memory" expand="false">
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
+          </tocitem>
 </tocitem>
-<tocitem text="Useful information" expand="false">
+<tocitem text="Useful information" expand="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
+	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
 </tocitem>
 </toc>