X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=482ccdf73b54bcfe3cb7a308dfdb13cdbc3bb592;hb=bc096ecbcd3cf4bbf17a24f9e9df88806789d688;hp=a570a54b6cb8cdf2db82c2922f9f9fc3ad42cbaf;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a570a54..482ccdf 100755
--- 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 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,9 +23,6 @@
 <!-- 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="Retrieval from ENSEMBL" target="ensemblfetch" />
-				<tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
-				<tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
 				<tocitem text="Latest Release Notes" target="release"/>
 		</tocitem>
 		
@@ -73,7 +70,7 @@
 			<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="Secondary Structure Prediction" target="jpred" />
 			<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
 			<tocitem text="Protein Disorder Prediction" target="disorder" />
 			<tocitem text="Alignment Conservation Analysis" target="aacon" />
@@ -134,6 +131,9 @@
 			<tocitem text="Chimera Viewer" target="chimera" />			
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+		    <tocitem text="Configuring URL Links" target="urllinkspref" />
+		</tocitem>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->
 			<!-- what other apps exist -->