X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=4636ea36f8398fb4e9aa7b069c5ee2ce77abc90f;hb=776081a95c10ce4c505cf97c2e438ca49c7fb93e;hp=62df81fb211515c094c7d0ca7b928acba7d2b51f;hpb=1aa769198666becd30648eed7f9037e9d0502ce9;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 62df81f..4636ea3 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,8 +24,11 @@
 	<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="Calculations Dialog" target="calcs.dialog"/>
 				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
 				<tocitem text="Omit hidden regions in Overview" target="overview"/>
+				<tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
 				<tocitem text="identifers.org for URL Links" target="linksprefs" />
 				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
 		</tocitem>
@@ -108,8 +111,10 @@
 		
 		<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" />