X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c0b0adc9af83e4d4d0b63b3b84f0e4d851707547;hb=85ecbca5f81c04b841e568861718a1253fb36824;hp=38fe9da1567b7a9cfdda08dc1ce26dd370249a96;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 38fe9da..c0b0adc 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,18 +2,17 @@
 <!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="Getting Started" target="start"/>
-	<tocitem text="Whats new" target="new" expand="false">
+	<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="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
 	</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"/>
@@ -30,13 +29,18 @@
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
 	</tocitem>
-	<tocitem text="Calculations" expand="false">
-		<tocitem text="Calculating trees" target="trees"/>
-		<tocitem text="Conservation" target="conservation"/>
+	<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="Menus" target="menus" expand="false">
+		<tocitem text="Desktop Menu" target="desktopMenu"/>
+		<tocitem text="Alignment Menu" target="alMenu"/>
+		<tocitem text="Popup Menu" target="popMenu"/>
+	</tocitem>
 </tocitem>
 <tocitem text="Useful information" expand="false">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>