X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=8402add5377a70e2ff7d1c7692572a0a20f836d1;hb=1f705a7597d9558cbb6962826bfdc2f0ac2c6a50;hp=ca759ee844a4fe4fe824707d3791cab7daf7771a;hpb=b5224b96766a131efd6c4b738058aaf1d0b3ecad;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index ca759ee..8402add 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,15 +3,24 @@
 <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>
-	<tocitem text="Input /Output" target="io"/>
-	<tocitem text="Editing Alignment" target ="edit"/>
+                <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">
 		<tocitem text="Clustal Alignment" target="clustal"/>
+                <tocitem text="Muscle Alignment" target="muscle"/>
+          	<tocitem text="JNet Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
@@ -30,19 +39,30 @@
 		<tocitem text="By conservation" target="colours.conservation"/>
 	</tocitem>
 	<tocitem text="Calculations" target="calculations" expand="false">
-		<tocitem text="Calculating trees" target="trees"/>
+		<tocitem text="Sorting alignments" target="sorting"/>
+                <tocitem text="Calculating trees" target="trees"/>
 		<tocitem text="Principal Component Analysis" target="pca"/>
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
-	<tocitem text="Menus" target="menus" expand="false">
-		<tocitem text="Desktop Menu" target="desktopMenu"/>
-		<tocitem text="Alignment Menu" target="alMenu"/>
+	<tocitem text="Window Menus" target="menus" expand="false">
+		<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="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"/>
 </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>