Optimized Overview

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c49436d..5c48b5a 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,12 +1,24 @@
 <?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="What's 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 text="Alignment Annotations" target ="alannotation"/>\r
+       </tocitem>\r
+       <tocitem text="Input / Output" target="io"/>\r
+       <tocitem text="Making figures" target="export"/>\r
+       <tocitem text="Editing Alignments" target ="edit"/>\r
+       <tocitem text="Web Services" target="webservice" expand="false">\r
+               <tocitem text="Clustal Alignment" target="clustal"/>\r
+                <tocitem text="Muscle Alignment" target="muscle"/>\r
+               <tocitem text="JNet Prediction" target="jnet"/>\r
+       </tocitem>\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 +28,33 @@
                <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" target="calculations" expand="false">\r
+               <tocitem text="Sorting alignments" target="sorting"/>\r
+                <tocitem text="Calculating trees" target="trees"/>\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="Window Menus" target="menus" expand="false">\r
+               <tocitem text="Desktop Window" target="desktopMenu"/>\r
+               <tocitem text="Alignment Window" target="alMenu">\r
+                <tocitem text="File Menu" target="alwFile"/>\r
+                <tocitem text="Edit Menu" target="alwEdit"/>  \r
+                <tocitem text="Colour Menu" target="alwColour"/>\r
+                <tocitem text="Calculation Menu" target="alwCalc"/>\r
+                               <tocitem text="Web Service Menu" target="wsMenu"/>\r
+               <tocitem text="Annotation Menus" target="annotMenus"/>\r
+               <tocitem text="Popup Menu" target="popMenu"/>\r
+                </tocitem>\r
        </tocitem>\r
-       <tocitem text="Calculate" target="calculate"/>\r
-       <tocitem text="Align" target="home"/>\r
+       <tocitem text="Memory Settings" target="memory"/>\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