No need for minorSpacing

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 752b4eb..c148afc 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,19 +2,17 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
 <toc version="1.0">\r
 <tocitem text="Jalview Documentation" target="home" expand="true" >\r
-       <tocitem text="What's new" target="new" expand="false">\r
-                <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>\r
-                <tocitem text="New Output Format Controls" target="preferences"/>\r
-                <tocitem text="Enhanced PDB Viewer" target="pdbviewer"/>\r
-                <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
-        </tocitem>\r
+       <tocitem text="What's new" target="new" expand="false"/>\r
        <tocitem text="Release History" target="release"/>\r
-       <tocitem text="Alignment Annotations" target ="alannotation"/>\r
-       \r
+       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+          <tocitem text="Conservation" target="calcs.alconserv"/>\r
+          <tocitem text="Quality" target="calcs.alquality"/>\r
+        </tocitem>\r
        <tocitem text="Input / Output" target="io"/>\r
        <tocitem text="Key Strokes" target="keys"/>\r
        <tocitem text="Making figures" target="export"/>\r
        <tocitem text="Editing Alignments" target ="edit"/>\r
+       <tocitem text="Sequence Features" target="seqfeatures"/>\r
        <tocitem text="Web Services" target="webservice" expand="false">\r
                <tocitem text="Clustal Alignment" target="clustal"/>\r
                 <tocitem text="Muscle Alignment" target="muscle"/>\r
@@ -35,6 +33,7 @@
                <tocitem text="User Defined" target="colours.user"/>\r
                <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
                <tocitem text="By conservation" target="colours.conservation"/>\r
+               <tocitem text="By Annotation" target="colours.annotation"/>\r
        </tocitem>\r
        <tocitem text="Calculations" target="calculations" expand="false">\r
                <tocitem text="Sorting alignments" target="sorting"/>\r
@@ -56,10 +55,13 @@
                <tocitem text="Popup Menu" target="popMenu"/>\r
                 </tocitem>\r
        </tocitem>\r
-       <tocitem text="Memory Settings" target="memory"/>\r
+       <tocitem text="Memory Settings" target="memory" expand="false">\r
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
+          </tocitem>\r
 </tocitem>\r
 <tocitem text="Useful information" expand="true">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
+       <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
        <tocitem text="The Genetic Code" target="geneticCode"/>\r
 </tocitem>\r
 </toc>\r