X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=77ddd8898363b7ca6e2fb58e46facada6d07ec00;hb=a8e0667a62546cdd95d44a45cf14a629cfa416a6;hp=a8aadf5731c5173d47a3403247317c46f7148a9f;hpb=cd5042310088854fc941b55011fd152f463b982b;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a8aadf5..77ddd88 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,11 +24,8 @@
 	<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="Custom Colourschemes in Groovy" target="groovy.colours"/>
-				<tocitem text="Omit hidden regions in Overview" target="overview"/>
-				<tocitem text="identifers.org for URL Links" target="linksprefs" />
-				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
+				<tocitem text="Structure Chooser" target="pdbchooser"/>
+				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -63,8 +60,6 @@
 			<tocitem text="Feature Colourschemes" target="features.featureschemes" />
 			<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
 			<tocitem text="Editing Sequence Features" target="seqfeatedit" />
-			<tocitem text="DAS Feature Retrieval" target="das.viewing" />
-			<tocitem text="DAS Feature Settings" target="das.settings" />
 			<tocitem text="HTML annotation report" target="io.seqreport" />
 		</tocitem>
 		
@@ -81,8 +76,7 @@
 			<tocitem text="Alignment Conservation Analysis" target="aacon" />
 			<tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
 			<tocitem text="Sequence Retrieval" target="seqfetch" />
-			<tocitem text="Database Reference Retrieval" target="dbreffetcher" />
-			<tocitem text="DAS Feature Retrieval" target="das.viewing" />
+			<tocitem text="Database Reference Retrieval" target="dbreffetcher" />			
 		</tocitem>
 		
 		<tocitem text="Colour Schemes" target="colours" expand="false">
@@ -109,8 +103,10 @@
 		
 		<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" />