Updated help pages

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c49436d..38fe9da 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,12 +1,21 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>\r
 <!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="Menus"  expand="true" >\r
-       <tocitem text="File" target="home"/>\r
-       <tocitem text="Edit" target="home"/>\r
-       <tocitem text="Font" target="home"/>\r
-       <tocitem text="View" target="home"/>\r
-       <tocitem text="Colour" target="colours">\r
+<tocitem text="Jalview Documentation" target="home" expand="true" >\r
+       <tocitem text="Getting Started" target="start"/>\r
+       <tocitem text="Whats new" target="new" expand="false">\r
+               <tocitem text="Search" target="search"/>\r
+               <tocitem text="Wrap Alignment" target="wrap"/>\r
+               <tocitem text="Overview Window" target ="overview"/>\r
+               <tocitem text="Sequence Features" target ="seqfeatures"/>\r
+       </tocitem>\r
+       <tocitem text="Web Services" target="webservice" expand="false">\r
+               <tocitem text="Clustal Alignment" target="clustal"/>\r
+       </tocitem>\r
+       <tocitem text="Input /Output" target="io"/>\r
+       <tocitem text="Editing Alignment" target ="edit"/>\r
+       <tocitem text="Colour Schemes" target="colours" expand="false">\r
+               <tocitem text="ClustalX" target="colours.clustal"/>\r
                <tocitem text="Zappo" target="colours.zappo"/>\r
                <tocitem text="Taylor" target="colours.taylor"/>\r
                <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
@@ -16,12 +25,20 @@
                <tocitem text="Buried index" target="colours.buried"/>\r
                <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
                <tocitem text="Blosum62" target="colours.blosum"/>\r
-               <tocitem text="PID" target="colours.pid"/>              \r
+               <tocitem text="by Percentage Identity" target="colours.pid"/>   \r
+               <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>\r
+       <tocitem text="Calculations" expand="false">\r
+               <tocitem text="Calculating trees" target="trees"/>\r
+               <tocitem text="Conservation" target="conservation"/>\r
+               <tocitem text="Principal Component Analysis" target="pca"/>\r
+               <tocitem text="Pairwise Alignments" target="pairwise"/>\r
+               <tocitem text="Remove Redundancy" target="redundancy"/>\r
        </tocitem>\r
-       <tocitem text="Calculate" target="calculate"/>\r
-       <tocitem text="Align" target="home"/>\r
 </tocitem>\r
-<tocitem text="Useful information">\r
+<tocitem text="Useful information" expand="false">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
        <tocitem text="The Genetic Code" target="geneticCode"/>\r
 </tocitem>\r