Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5a92936..a65cafe 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 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,23 +20,14 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-       <tocitem text="What's new" target="new" expand="true">
-    <tocitem text="Protein Disorder Prediction" target="disorder"/>
-    <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-               <tocitem text="Viewing RNA structure" target="varna" />
-               <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
-               <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
-               <tocitem text="HTML annotation report" target="io.seqreport"/>
-               <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
-               <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
-         <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
-         <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
-         <tocitem text="DNA or Protein PCA calculation" target="pca"/>
-         <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
-       </tocitem>
-    <tocitem text="Editing Alignments" target ="edit"/>        
-    <tocitem text="Cursor Mode" target="cursor"/>
-       <tocitem text="Key Strokes" target="keys"/>
+ <tocitem text="What's new" target="new" expand="true">
+    <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+    <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+    <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
+  </tocitem>
+  <tocitem text="Editing Alignments" target ="edit"/>  
+  <tocitem text="Cursor Mode" target="cursor"/>
+  <tocitem text="Key Strokes" target="keys"/>
        <tocitem text="Input / Output" target="io"/>
        <tocitem text="Making Figures" target="export"/>
        <tocitem text="Hidden Regions" target="hiddenRegions"/>
@@ -66,6 +57,7 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+          <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
           <tocitem text="Protein Disorder Prediction" target="disorder"/>
           <tocitem text="Alignment Conservation Analysis" target="aacon"/>
           <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>