X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=48a2b2a8f29b942d59affd6a2edd5b9093844696;hb=05653e6b73a0dca4ae06c3e911597cc21131fd21;hp=5371ad493e30ab66a56fcc6b9ab9c4f7cedfb0f5;hpb=dc507a79f5eb7837ec52343686e84f9d4b56f0fc;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5371ad4..48a2b2a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,34 +1,36 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- * 
+ * 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/>.
+ * 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="Jaba Web Services" target="jabaws"/>
-      <tocitem text="Superpositions with Jmol 12" target="pdbjmol"/>
-      <tocitem text="Web Service Parameters" target="wsparams"/>
-      <tocitem text="Web Service Preferences" target="wsprefs"/>
-      <tocitem text="Release History" target="release"/>
-	</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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+    <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+    <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
+    <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
+  </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"/>
@@ -48,18 +50,20 @@
 		  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	  <tocitem text="DAS Feature Settings" target="das.settings"/>
+	  <tocitem text="HTML annotation report" target="io.seqreport"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
 	<tocitem text="JABAWS" target="jabaws"/>
 	<tocitem text="Web Service Preferences" target="wsprefs"/>
 	<tocitem text="Web Service Parameters" target="wsparams"/>
-          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
-		<tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
+	<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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+          <tocitem text="Protein Disorder Prediction" target="disorder"/>
+          <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+          <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
 		<tocitem text="Sequence Retrieval" target="seqfetch"/>
 		<tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
 		<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
@@ -81,6 +85,7 @@
 		<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>
@@ -133,9 +138,11 @@
         </tocitem>
        	<tocitem text="Privacy" target="privacy"/>
 </tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
 	<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>