X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=38277476d2946324ae589049556b702507911623;hb=6f812eb434553c97cccaaaefa35da54afc72bb79;hp=77ddd8898363b7ca6e2fb58e46facada6d07ec00;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 77ddd88..3827747 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,8 +24,9 @@
 	<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="Structure Chooser" target="pdbchooser"/>
-				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+				<tocitem text="VCF Import" target="vcfimport"/>
+				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+				
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +50,7 @@
 		<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 		
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+		  <tocitem text="Annotating from VCF" target="importvcf" /> 
 			<tocitem text="Viewing RNA structure" target="varna" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
@@ -135,10 +137,6 @@
 		<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 -->
-		</tocitem>
 		<tocitem text="Window Menus" target="menus" expand="false">
 			<tocitem text="Desktop Window" target="desktopMenu" />
 			<tocitem text="Alignment Window" target="alMenu">