X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c1a6812e91ed5236d93044eef404be72bbcfb0dc;hb=378126d607a06854e8752d156120462459364586;hp=0bcf3e6d493d192eb83dc243cb7328abb9f7909b;hpb=ec2ca463eac1e1573ced542b4abedcd50441badc;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 0bcf3e6..c1a6812 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -7,12 +7,16 @@
 		<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="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="Input /Output" target="io"/>
-	<tocitem text="Editing Alignment" target ="edit"/>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
 		<tocitem text="Zappo" target="colours.zappo"/>
@@ -29,13 +33,25 @@
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
 	</tocitem>
-	<tocitem text="Calculations" expand="false">
-                <tocitem text="Sorting alignments" target="sorting"/>
-		<tocitem text="Calculating trees" target="trees"/>
+	<tocitem text="Calculations" target="calculations" expand="false">
+		<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="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="Annotation Menus" target="annotMenus"/>
+		<tocitem text="Popup Menu" target="popMenu"/>
+                </tocitem>
+
+	</tocitem>
 </tocitem>
 <tocitem text="Useful information" expand="false">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>