No need to hava SSX as array

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index e441033..5e69a23 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,15 +3,24 @@
 <toc version="1.0">\r
 <tocitem text="Jalview Documentation" target="home" expand="true" >\r
        <tocitem text="What's new" target="new" expand="false">\r
-               <tocitem text="Search" target="search"/>\r
-               <tocitem text="Wrap Alignment" target="wrap"/>\r
-               <tocitem text="Overview Window" target ="overview"/>\r
-               <tocitem text="Sequence Features" target ="seqfeatures"/>\r
-       </tocitem>\r
-       <tocitem text="Input /Output" target="io"/>\r
-       <tocitem text="Editing Alignment" target ="edit"/>\r
+                <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>\r
+                <tocitem text="New Output Format Controls" target="preferences"/>\r
+                <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>\r
+                <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
+        </tocitem>\r
+       <tocitem text="Release History" target="release"/>\r
+       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+          <tocitem text="Conservation" target="calcs.alconserv"/>\r
+          <tocitem text="Quality" target="calcs.alquality"/>\r
+        </tocitem>\r
+       <tocitem text="Input / Output" target="io"/>\r
+       <tocitem text="Key Strokes" target="keys"/>\r
+       <tocitem text="Making figures" target="export"/>\r
+       <tocitem text="Editing Alignments" 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
@@ -38,12 +47,24 @@
        </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="View Menu" target="alwView"/> \r
+                <tocitem text="Colour Menu" target="alwColour"/>\r
+                <tocitem text="Calculation Menu" target="alwCalc"/>\r
+                               <tocitem text="Web Service Menu" target="wsMenu"/>\r
+               <tocitem text="Annotation Menus" target="annotMenus"/>\r
                <tocitem text="Popup Menu" target="popMenu"/>\r
+                </tocitem>\r
        </tocitem>\r
+       <tocitem text="Memory Settings" target="memory" expand="false">\r
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
+          </tocitem>\r
 </tocitem>\r
-<tocitem text="Useful information" expand="false">\r
+<tocitem text="Useful information" expand="true">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
+       <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
        <tocitem text="The Genetic Code" target="geneticCode"/>\r
 </tocitem>\r
 </toc>\r