X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0d2e09603d20afa99bbf88817e75c96bd5518e81;hb=11104931ab7f415eb1d43bff2da84842d973f3c5;hp=75aa6d21d544eaabcb26e8f0222fe3ef8f41652f;hpb=721a650185138574d75e548b3e1f81113034ff45;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 75aa6d2..0d2e096 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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)
+  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/>.
 -->
 <!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">
@@ -26,9 +26,12 @@
 		<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"/>
@@ -86,6 +89,7 @@
 		<tocitem text="User Defined" target="colours.user"/>
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
+    <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
 		<tocitem text="By Annotation" target="colours.annotation"/>
 		<tocitem text="By RNA Helices" target="colours.rnahelices"/>
 	</tocitem>
@@ -142,5 +146,7 @@
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
+	<tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+  
 </tocitem>
 </toc>