X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=20dd8dbcdfb91dbde6fc782c66d81e21a4439fe9;hb=89f7e3e9f47ed019f817db123bb2ce8749870b55;hp=f76da168973d8389038df6aae0d0e125e7aa10d2;hpb=e54e2eee927260cd650ffe17b1422b29b8b2f122;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index f76da16..20dd8db 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,8 +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>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -106,8 +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" />
@@ -134,7 +134,7 @@
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
-		    <tocitem text="Configuring URL Links" target="urllinkspref" />
+		    <tocitem text="Configuring URL Links" target="linksprefs" />
 		</tocitem>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->