dont use gold highlights

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fc52348..04bfc7e 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,10 +2,13 @@
 <!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="Editing Alignments" target ="edit"/>    
-        <tocitem text="Cursor Mode" target="cursor"/>
+       <tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Release History" target="release"/>
+         <tocitem text="Mapping between Sequences" target="seqmappings"/>
+         <tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
+    </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"/>
@@ -76,11 +79,15 @@
                <tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
        </tocitem>
+        <tocitem text="Preferences" target="preferences"/>
        <tocitem text="Memory Settings" target="memory" expand="false">
           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
           </tocitem>
+        <tocitem text="Command Line" target="commandline" expand="false">
+          <tocitem text="Command Line Arguments" target="clarguments"/>
+        </tocitem>
 </tocitem>
-<tocitem text="Useful information" expand="true">
+<tocitem text="Useful information" expa nd="true">
        <tocitem text="Amino Acid Table" target="aminoAcids"/>
        <tocitem text="Amino Acid Properties" target="aaProperties"/>
        <tocitem text="The Genetic Code" target="geneticCode"/>