patch name, reference and URL for Multi-Harmony : JAL-724

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index d416dfa..926a710 100755 (executable)
--- 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,12 @@
 <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="Multi-Harmony Alignment 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="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"/>        
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -48,13 +49,11 @@
        <tocitem text="JABAWS" target="jabaws"/>
        <tocitem text="Web Service Preferences" target="wsprefs"/>
        <tocitem text="Web Service Parameters" target="wsparams"/>
-          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
-               <tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
+       <tocitem text="Sequence Alignment" target="msaservice" expand="false">
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+          <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"/>