added sequence fetcher and sequence features retrieval to web serviices index

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c0c7f2c..2a06897 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,21 +3,18 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
        <tocitem text="What's new" target="new" expand="true">
-         <tocitem text="Multiple Views" target="multipleviews"/>
-         <tocitem text="New keystrokes and Menus" target="newkeys"/>
-         <tocitem text="Reload and Save" target="reloadsave"/>
-         <tocitem text="Creating Sequence Features" target="seqfeatcreat"/>
-         <tocitem text="Amending or Deleting Sequence Features" target="seqfeatedit"/>
-      <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
-          </tocitem>
-        <tocitem text="Release History" target="release"/>
-        <tocitem text="Editing Alignments" target ="edit"/>    
-        <tocitem text="Cursor Mode" target="cursor"/>
+      <tocitem text="Release History" target="release"/>
+         <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
+         <tocitem text="Mapping between Sequences" target="seqmappings"/>
+    </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="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="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -36,6 +33,7 @@
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
        </tocitem>
        <tocitem text="Colour Schemes" target="colours" expand="false">
+               <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
                <tocitem text="ClustalX" target="colours.clustal"/>
                <tocitem text="Zappo" target="colours.zappo"/>
                <tocitem text="Taylor" target="colours.taylor"/>
@@ -60,12 +58,16 @@
                <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="Window Menus" target="menus" expand="false">
                <tocitem text="Desktop Window" target="desktopMenu"/>
                <tocitem text="Alignment Window" target="alMenu">
@@ -81,11 +83,16 @@
                <tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
        </tocitem>
+        <tocitem text="Preferences" target="preferences"/>
        <tocitem text="Memory Settings" target="memory" expand="false">
           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
           </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" expand="true">
+<tocitem text="Useful information" expa nd="true">
        <tocitem text="Amino Acid Table" target="aminoAcids"/>
        <tocitem text="Amino Acid Properties" target="aaProperties"/>
        <tocitem text="The Genetic Code" target="geneticCode"/>