X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=1d45e7a3eb52a678d27770677e8882251abcbfd0;hb=ec27ad7e780793a94912b0d13dcc694c8d06bc4c;hp=30665ec5d61d7fff0f9d035e8a6e56d93c20a5ae;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 30665ec..1d45e7a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -7,14 +7,16 @@
  * 
  * 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">
@@ -95,6 +97,9 @@
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
+	<tocitem text="Sequence Annotations" target="seqannots" expand="true">
+		<tocitem text="Annotation from Structure" target="xsspannotation" expand="false"/>
+	</tocitem>
   	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>          
           <tocitem text="Quality" target="calcs.alquality"/>
@@ -104,6 +109,7 @@
         </tocitem>
 	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
 	  <tocitem text="Jmol Viewer" target="pdbjmol"/>
+	  <tocitem text="Chimera Viewer" target="chimera"/>
 	  <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
 	</tocitem>
 	<tocitem text="Viewing RNA structures" target="varna" expand="false">	</tocitem>
@@ -114,17 +120,18 @@
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
-                <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>
-				<tocitem text="Select Menu" target="alwSelect"/> 
-                <tocitem text="View Menu" target="alwView"/>
-				<tocitem text="Format Menu" target="alwFormat"/>
-                <tocitem text="Colour Menu" target="alwColour"/>
-                <tocitem text="Calculation Menu" target="alwCalc"/>
-		<tocitem text="Web Service Menu" target="wsMenu"/>
-		<tocitem text="Annotation Menus" target="annotMenus"/>
-		<tocitem text="Popup Menu" target="popMenu"/>
-                </tocitem>
+            <tocitem text="File Menu" target="alwFile"/>
+            <tocitem text="Edit Menu" target="alwEdit"/>
+			<tocitem text="Select Menu" target="alwSelect"/> 
+            <tocitem text="View Menu" target="alwView"/>
+            <tocitem text="Annotations Menu" target="alwAnnotations"/>
+			<tocitem text="Format Menu" target="alwFormat"/>
+            <tocitem text="Colour Menu" target="alwColour"/>
+            <tocitem text="Calculation Menu" target="alwCalc"/>
+			<tocitem text="Web Service Menu" target="wsMenu"/>
+			<tocitem text="Annotation Panel Menu" target="annotPanelMenu"/>
+			<tocitem text="Popup Menu" target="popMenu"/>
+        </tocitem>
 	</tocitem>
         <tocitem text="Preferences" target="preferences"/>
 	<tocitem text="Memory Settings" target="memory" expand="false">