Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index e27d41a..aa10130 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,42 +1,33 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-  Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-  
-  This file is part of Jalview.
-  
-  Jalview is free software: you can redistribute it and/or
-  modify it under the terms of the GNU General Public License 
-  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-   
-  Jalview is distributed in the hope that it will be useful, but 
-  WITHOUT ANY WARRANTY; without even the implied warranty 
-  of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-  PURPOSE.  See the GNU General Public License for more details.
-  
-  You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <!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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
-               <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="Protein Disorder Prediction" target="disorder"/>
+   <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+  <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+  </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"/>