X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=2bc4187896a7dcd06e14eefa806087cd2e0e17b5;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=feafc0f36e5456e1910fc4dca48f4a45eedad5cd;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index feafc0f..2bc4187 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,28 +1,31 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
-   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
-   * Copyright (C) 2010 J Procter, AM Waterhouse, 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="true">
-      <tocitem text="Release History" target="release"/>
-		<tocitem text="Sequence Retrieval" target="seqfetch"/>
-		<tocitem text="VAMSAS Interoperation" target="vamsas"/>
+      <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
+          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+          <tocitem text="Jalview News Reader" target="newsreader"/>
+          <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
+      <tocitem text="Default Annotation preferences" target="colours.annotation"/>
+      <tocitem text="Jaba Web Services" target="jabaws"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -43,14 +46,16 @@
 	  <tocitem text="DAS Feature Settings" target="das.settings"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
-          <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="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="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
 		<tocitem text="Sequence Retrieval" target="seqfetch"/>
+		<tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
 		<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">