Uniprot retrieves features from XML

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 38fe9da..5c48b5a 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,18 +2,21 @@
 <!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="Getting Started" target="start"/>\r
-       <tocitem text="Whats new" target="new" expand="false">\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="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
@@ -30,13 +33,26 @@
                <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="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="Memory Settings" target="memory"/>\r
 </tocitem>\r
 <tocitem text="Useful information" expand="false">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r