2.4 release documentation update menus, service refs, new features and releases

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 7d9e595..9ad08fa 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,16 +2,20 @@
 <!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="Sequence Retrieval" target="seqfetch"/>
+               <tocitem text="VAMSAS Interoperation" target="vamsas"/>
+       </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"/>
+       <tocitem text="Making Figures" target="export"/>
        <tocitem text="Hidden Regions" target="hiddenRegions"/>
-       <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
        <tocitem text="Multiple Views" target="multipleviews"/>
+       <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
+       <tocitem text="Fetching Sequences" target="seqfetch"/>
        <tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -28,6 +32,8 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+               <tocitem text="Sequence Retrieval" target="seqfetch"/>
+               <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
        </tocitem>
        <tocitem text="Colour Schemes" target="colours" expand="false">
                <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
@@ -55,12 +61,20 @@
                <tocitem text="Pairwise Alignments" target="pairwise"/>
                <tocitem text="Remove Redundancy" target="redundancy"/>
        </tocitem>
-       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
+       <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+         <tocitem text="Jmol Viewer" target="pdbjmol"/>
+         <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
+       </tocitem>
+       <tocitem text="VAMSAS Data Exchange" target="vamsas">
+               <!-- what can Jalview share with other apps -->
+               <!-- what other apps exist -->
+               </tocitem>
        <tocitem text="Window Menus" target="menus" expand="false">
                <tocitem text="Desktop Window" target="desktopMenu"/>
                <tocitem text="Alignment Window" target="alMenu">
@@ -82,6 +96,7 @@
           </tocitem>
         <tocitem text="Command Line" target="commandline" expand="false">
           <tocitem text="Command Line Arguments" target="clarguments"/>
+             <tocitem text="Groovy Shell" target="groovy"/>
         </tocitem>
 </tocitem>
 <tocitem text="Useful information" expa nd="true">