X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0f476a5bc7ed27d702f94431d11e2a293e1c176a;hb=27b299821e542ddd590e3191682017c093fec14d;hp=ca759ee844a4fe4fe824707d3791cab7daf7771a;hpb=b5224b96766a131efd6c4b738058aaf1d0b3ecad;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index ca759ee..0f476a5 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -7,11 +7,15 @@
 		<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="Editing Alignment" target ="edit"/>
+	<tocitem text="Input / Output" target="io"/>
+  	<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"/>
@@ -30,15 +34,24 @@
 		<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="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>
 <tocitem text="Useful information" expand="false">