X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=2a068975c1ac5c655d7a8508c4ce4a0e282f9604;hb=c24267ee9b42f032d0d1a561b6fb05b03d754460;hp=4338d366010935316969dc90ea92e01a0163c5b2;hpb=c4bd086791a762332a817543ed4de1a6d06b72bf;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 4338d36..2a06897 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -6,7 +6,6 @@
       <tocitem text="Release History" target="release"/>
 	  <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
 	  <tocitem text="Mapping between Sequences" target="seqmappings"/>
-	  <tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
     </tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -15,6 +14,7 @@
   	<tocitem text="Making figures" target="export"/>
 	<tocitem text="Hidden Regions" target="hiddenRegions"/>
 	<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"/>
@@ -58,7 +58,7 @@
 		<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"/>
@@ -89,6 +89,7 @@
           </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">