lots of tidying in doco.

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index e441033..c2221ac 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -9,9 +9,12 @@
                <tocitem text="Sequence Features" target ="seqfeatures"/>\r
        </tocitem>\r
        <tocitem text="Input /Output" target="io"/>\r
+       <tocitem text="Making figures" target="export"/>\r
        <tocitem text="Editing Alignment" target ="edit"/>\r
        <tocitem text="Web Services" target="webservice" expand="false">\r
                <tocitem text="Clustal Alignment" target="clustal"/>\r
+                <tocitem text="Muscle Alignment" target="muscle"/>\r
+               <tocitem text="JNet Prediction" target="jnet"/>\r
        </tocitem>\r
        <tocitem text="Colour Schemes" target="colours" expand="false">\r
                <tocitem text="ClustalX" target="colours.clustal"/>\r
@@ -38,7 +41,12 @@
        </tocitem>\r
        <tocitem text="Window Menus" target="menus" expand="false">\r
                <tocitem text="Desktop Window" target="desktopMenu"/>\r
-               <tocitem text="Alignment Window" target="alMenu"/>\r
+               <tocitem text="Alignment Window" target="alMenu">\r
+                <tocitem text="File Menu" target="alwFile"/>\r
+                <tocitem text="Edit Menu" target="alwEdit"/>  \r
+                <tocitem text="Colour Menu" target="alwColour"/>\r
+                <tocitem text="Calculation Menu" target="alwCalc"/>\r
+                </tocitem>\r
                <tocitem text="Popup Menu" target="popMenu"/>\r
        </tocitem>\r
 </tocitem>\r