JAL-913; Documentation of RNA Structure Conservation

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 95aa62a..2f8a2fd 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -20,9 +20,10 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
        <tocitem text="What's new" target="new" expand="true">
-      <tocitem text="Graduated Feature Colours" target="features.featureschemes"/>
-      <tocitem text="Sort by Features" target="seqfeatures.settings"/>
-      <tocitem text="Envision2 Service" target="webservice"/>
+      <tocitem text="Jaba Web Services" target="jabaws"/>
+      <tocitem text="Superpositions with Jmol 12" target="pdbjmol"/>
+      <tocitem text="Web Service Parameters" target="wsparams"/>
+      <tocitem text="Web Service Preferences" target="wsprefs"/>
       <tocitem text="Release History" target="release"/>
        </tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>        
@@ -34,6 +35,7 @@
        <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="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -69,12 +71,14 @@
                <tocitem text="Turn propensity" target="colours.turn"/>
                <tocitem text="Buried index" target="colours.buried"/>
                <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+               <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
                <tocitem text="Blosum62" target="colours.blosum"/>
                <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 text="By Annotation" target="colours.annotation"/>
+               <tocitem text="By RNA Helices" target="colours.rnahelices"/>
        </tocitem>
        <tocitem text="Calculations" target="calculations" expand="false">
                <tocitem text="Sorting alignments" target="sorting"/>
@@ -86,6 +90,7 @@
        </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="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>