X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=940629297cd56be3ed8039fe11b49fdf61085434;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2bc4187896a7dcd06e14eefa806087cd2e0e17b5;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2bc4187..9406292 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,9 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="true">
-      <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
-          <tocitem text="Jalview News Reader" target="newsreader"/>
-          <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
-      <tocitem text="Default Annotation preferences" target="colours.annotation"/>
-      <tocitem text="Jaba Web Services" target="jabaws"/>
+		<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="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -36,6 +33,11 @@
 	<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 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"/>
@@ -53,7 +55,7 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+          <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
 		<tocitem text="Sequence Retrieval" target="seqfetch"/>
 		<tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
 		<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
@@ -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"/>
@@ -85,15 +89,17 @@
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
   	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
+          <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 -->