X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c1a6812e91ed5236d93044eef404be72bbcfb0dc;hb=bacb105d85f7d068c8cd643cd337b832aeb80343;hp=c49436de681b6f1804a40b1cfadd8638afe92fc5;hpb=bfbc6adb2123ba3e4c267384c0d39849f888c794;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c49436d..c1a6812 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,12 +1,24 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!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="Menus"  expand="true" >
-	<tocitem text="File" target="home"/>
-	<tocitem text="Edit" target="home"/>
-	<tocitem text="Font" target="home"/>
-	<tocitem text="View" target="home"/>
-	<tocitem text="Colour" target="colours">
+<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 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="Colour Schemes" target="colours" expand="false">
+		<tocitem text="ClustalX" target="colours.clustal"/>
 		<tocitem text="Zappo" target="colours.zappo"/>
 		<tocitem text="Taylor" target="colours.taylor"/>
 		<tocitem text="Hydrophobicity" target="colours.hydro"/>
@@ -16,12 +28,32 @@
 		<tocitem text="Buried index" target="colours.buried"/>
 		<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
 		<tocitem text="Blosum62" target="colours.blosum"/>
-		<tocitem text="PID" target="colours.pid"/>		
+		<tocitem text="by Percentage Identity" target="colours.pid"/>	
+		<tocitem text="User Defined" target="colours.user"/>
+		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
+		<tocitem text="By conservation" target="colours.conservation"/>
+	</tocitem>
+	<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 text="Calculate" target="calculate"/>
-	<tocitem text="Align" target="home"/>
 </tocitem>
-<tocitem text="Useful information">
+<tocitem text="Useful information" expand="false">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
 </tocitem>