X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0f476a5bc7ed27d702f94431d11e2a293e1c176a;hb=246746e55bd02c66746d5cd872f49890cbae206a;hp=af9a16aa0d981a789ad3b55b246702e0aed0234c;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index af9a16a..0f476a5 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,17 +2,21 @@
 <!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="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 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 +33,26 @@
 		<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="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">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>