JAL-1645 more cross-links and fixing menu entries

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 1f1a8b7..b956004 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,16 +1,24 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * 
-       Copyright (C) $$Year-Rel$$ 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. * * 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/>. 
-       * 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">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <toc version="1.0">
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <tocitem text="Jalview Documentation" target="home" expand="true">
@@ -18,11 +26,8 @@
                                <tocitem text="Split Frame View" target="splitframe" />
                                <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
                                <tocitem text="PDB Structure Chooser" target="pdbchooser" />
-                               <tocitem text="Jmol Viewer" target="pdbjmol" />
                                <tocitem text="Chimera Viewer" target="chimera" />
                                <tocitem text="Select columns by annotation" target="selectcolbyannot" />
-                               <tocitem text="Annotations File Format" target="annotations.fileformat" />
-                               <tocitem text="BioJSON v1.0" target="biojson" />
                                <tocitem text="Latest Release Notes" target="release"/>
                </tocitem>
                

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index e9f8e8f..c7f8a10 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -166,8 +166,8 @@
                                visible when you right-click on a sequence name. When this option is clicked, Jalview will open a <a href="../features/structurechooser.html">'Structure Chooser' </a>  
                                 dialogue with options to select the structure which will eventually be opened in
                                a 3D interactive view.<br> These entries will only be present if the sequence
-                               has <a href="../features/viewingpdbs.html">associated PDB structures</a>.
-                               <br /> If the sequence or alignment has RNA structure,
+                               has <a href="../features/viewingpdbs.html">associated PDB structures</a>.</em></li><li><strong>VARNA 2D Structure</strong><br/><em>
+                                If the sequence or alignment has RNA structure,
                                then <strong>VARNA 2D Structure</strong> entries will also be present enabling
                                you to open a linked view of the RNA structure in <a
                                href="../features/varna.html">VARNA</a>.

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 693b0f0..2533c8a 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -68,7 +68,7 @@
       criteria.</li>
     <li><strong>Improved support for RNA visualisation</strong><br />Jalview
       2.9 integrates the latest version of the <a
-      href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
+      href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
       can also now be stored in Jalview projects. We've also dealt with
       a number of lingering bugs in the VARNA/Jalview interface,
       including the loss of pseudoknots when RNA secondary structure is