X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=9ae45b93ef749d2a9c88704f9690850be871ef30;hb=86ce701110991d006f506c585e13128996a01477;hp=fe421106a9d9488baca72fa2317906cf3e8f4ab4;hpb=82bb69383ab22735cbd3440c670ae0b290fe6afd;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fe42110..9ae45b9 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,16 +1,24 @@
 <?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 ($$Version-Rel$$)
+ * 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.
+ -->
 <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">
@@ -18,11 +26,8 @@
 				<tocitem text="Split Frame View" target="splitframe" />
 				<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="BioJSON v1.0" target="biojson" />
 				<tocitem text="Latest Release Notes" target="release"/>
 		</tocitem>
 		
@@ -35,7 +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>
 		
@@ -110,6 +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">