JAL-913; Extending documentation; VARNA help;

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2f8a2fd..5371ad4 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -35,7 +35,11 @@
        <tocitem text="Multiple Views" target="multipleviews"/>
        <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
        <tocitem text="Fetching Sequences" target="seqfetch"/>
-       <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false"></tocitem>
+       <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+               <tocitem text="Viewing RNA structure" target="varna" />
+               <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+               <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+       </tocitem>
        <tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -89,16 +93,17 @@
                <tocitem text="Remove Redundancy" target="redundancy"/>
        </tocitem>
        <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
-          <tocitem text="RNA Structure Conservation" target="calcs.alstrconserv"/>
+          <tocitem text="Conservation" target="calcs.alconserv"/>          
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
+          <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
        <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
          <tocitem text="Jmol Viewer" target="pdbjmol"/>
          <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
        </tocitem>
+       <tocitem text="Viewing RNA structures" target="varna" expand="false">   </tocitem>
        <tocitem text="VAMSAS Data Exchange" target="vamsas">
                <!-- what can Jalview share with other apps -->
                <!-- what other apps exist -->