X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=7ba4ee506827438d03b68c60cd84cbccaf29c4cb;hb=60d67f3a980b29fd2039d2c3ad81ee6863f82548;hp=54abd53676590971df614b1c7bea434d0d8a2fba;hpb=cd4e2687751aab1c9c5974e6966e610a3332236b;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 54abd53..7ba4ee5 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,6 +24,7 @@
 	<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>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -104,8 +105,10 @@
 		
 		<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" />
@@ -131,6 +134,9 @@
 			<tocitem text="Chimera Viewer" target="chimera" />			
 		</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="linksprefs" />
+		</tocitem>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->
 			<!-- what other apps exist -->
@@ -154,7 +160,7 @@
 		<tocitem text="Preferences" target="preferences" />
 		<tocitem text="Memory Settings" target="memory" expand="false"/>
 		<tocitem text="Scripting with Groovy" target="groovy">
-			<tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 		</tocitem>
 		<tocitem text="Command Line" target="commandline" expand="false">
 			<tocitem text="Command Line Arguments" target="clarguments" />