Feature Settings

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9265599..5dec601 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,9 +3,11 @@
 <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="MAFFT Alignment" target="mafft"/>\r
                <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
-               <tocitem text="Hide Regions" target="hiddenRegions"/>            \r
+               <tocitem text="Hide Regions" target="hiddenRegions"/>\r
+               <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
+               <tocitem text="MAFFT Alignment" target="mafft"/>\r
         </tocitem>\r
         <tocitem text="Release History" target="release"/>\r
         <tocitem text="Editing Alignments" target ="edit"/>    \r
@@ -19,13 +21,15 @@
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
           <tocitem text="Sequence Features File" target="features.fileformat"/>\r
           <tocitem text="User Defined Sequence Features" target="search"/>\r
-          <tocitem text="DAS Features Settings" target="das.settings"/>\r
+          <tocitem text="DAS Features Settings" target="das.viewing"/>\r
         </tocitem>\r
        <tocitem text="Web Services" target="webservice" expand="false">\r
+          <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
                <tocitem text="Clustal Alignment" target="clustal"/>\r
                 <tocitem text="Muscle Alignment" target="muscle"/>\r
                 <tocitem text="MAFFT Alignment" target="mafft"/>\r
-               <tocitem text="JNet Prediction" target="jnet"/>\r
+            </tocitem>\r
+          <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
        </tocitem>\r
        <tocitem text="Colour Schemes" target="colours" expand="false">\r
                <tocitem text="ClustalX" target="colours.clustal"/>\r