JAL-1165 visual delay whilst results are processed.

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9406292..f59dd70 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -20,9 +20,18 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
        <tocitem text="What's new" target="new" expand="true">
+    <tocitem text="Protein Disorder Prediction" target="disorder"/>
+    <tocitem text="Alignment Conservation Analysis" target="aacon"/>
                <tocitem text="Viewing RNA structure" target="varna" />
                <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
                <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+               <tocitem text="HTML annotation report" target="io.seqreport"/>
+               <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
+               <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
+         <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
+         <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
+         <tocitem text="DNA or Protein PCA calculation" target="pca"/>
+         <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
        </tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>        
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -46,6 +55,7 @@
                  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
          <tocitem text="DAS Feature Settings" target="das.settings"/>
+         <tocitem text="HTML annotation report" target="io.seqreport"/>
         </tocitem>
        <tocitem text="Web Services" target="webservice" expand="false">
        <tocitem text="JABAWS" target="jabaws"/>
@@ -55,6 +65,8 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+          <tocitem text="Protein Disorder Prediction" target="disorder"/>
+          <tocitem text="Alignment Conservation Analysis" target="aacon"/>
           <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
                <tocitem text="Sequence Retrieval" target="seqfetch"/>
                <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
@@ -77,6 +89,7 @@
                <tocitem text="User Defined" target="colours.user"/>
                <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
                <tocitem text="By conservation" target="colours.conservation"/>
+    <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
                <tocitem text="By Annotation" target="colours.annotation"/>
                <tocitem text="By RNA Helices" target="colours.rnahelices"/>
        </tocitem>
@@ -129,9 +142,11 @@
         </tocitem>
                <tocitem text="Privacy" target="privacy"/>
 </tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
        <tocitem text="Amino Acid Table" target="aminoAcids"/>
        <tocitem text="Amino Acid Properties" target="aaProperties"/>
        <tocitem text="The Genetic Code" target="geneticCode"/>
+       <tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+  
 </tocitem>
 </toc>