JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2580d9a..73147d2 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,29 +1,33 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * 
-       Copyright (C) $$Year-Rel$$ 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">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ -->
 <toc version="1.0">
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Split Frame View" target="splitframe" />
-                               <tocitem text="Fetching Sequences" target="seqfetch" />         
-                               <tocitem text="BioJSON v1.0" target="biojson" />
                                <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
                                <tocitem text="PDB Structure Chooser" target="pdbchooser" />
-                               <tocitem text="Jmol Viewer" target="pdbjmol" />
                                <tocitem text="Chimera Viewer" target="chimera" />
                                <tocitem text="Select columns by annotation" target="selectcolbyannot" />
-                               <tocitem text="Annotations File Format" target="annotations.fileformat" />
                                <tocitem text="Latest Release Notes" target="release"/>
                </tocitem>
                
@@ -36,7 +40,6 @@
                </tocitem>
                
                <tocitem text="Making Figures" target="export" expand="false">
-                       <tocitem text="BioJSON v1.0" target="biojson" />
                        <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
                </tocitem>
                
@@ -111,6 +114,7 @@
                        <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
                        <tocitem text="Pairwise Alignments" target="pairwise" />
                        <tocitem text="Remove Redundancy" target="redundancy" />
+                       <tocitem text="Reference Sequences" target="referenceseq" />
                </tocitem>
                
                <tocitem text="Sequence Annotations" target="seqannots" expand="true">