update HtmlSvgOutput to ignore browser invocation when running in headless mode

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c0e9b66..1d45e7a 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,30 +1,32 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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="Protein Disorder Prediction" target="disorder"/>
-   <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-  <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Select columns containing sequence features" target="seqfeatures.settings"/>
+    <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"/>
@@ -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">