X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=71b7ef97a26dcc25ed0666a8fe7f5887707188f6;hb=37f0332f53a8564ba7a9d55b993f8bfd2f368c80;hp=52eaf85e03195cf8e33a2b6e8f2295db4bae1f61;hpb=e7bdaf79ac2aa5ea995c80c559c9cb170f35f4ba;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 52eaf85..71b7ef9 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,9 +24,6 @@
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
 				<tocitem text="Latest Release Notes" target="release"/>
-				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
-				<tocitem text="Omit hidden regions in Overview" target="overview"/>
-				<tocitem text="Split Frame View" target="splitframe.mirrorfonts" />
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -107,8 +104,10 @@
 		
 		<tocitem text="Calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
-			<tocitem text="Calculating trees" target="trees" />
-			<tocitem text="Principal Component Analysis" target="pca" />
+			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+  			  <tocitem text="Calculating trees" target="trees" />
+  			  <tocitem text="Principal Component Analysis" target="pca" />
+  			</tocitem>
 			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 			<tocitem text="Pairwise Alignments" target="pairwise" />
 			<tocitem text="Remove Redundancy" target="redundancy" />
@@ -153,6 +152,7 @@
 				<tocitem text="Colour Menu" target="alwColour" />
 				<tocitem text="Calculate Menu" target="alwCalc" />
 				<tocitem text="Web Service Menu" target="wsMenu" />
+				<tocitem text="HMMER Menu" target="alwHmmer" />
 				<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 				<tocitem text="Popup Menu" target="popMenu" />
 			</tocitem>