X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2FhelpTOC.xml;h=1f15e45be7655526bfa06911412e8f15bf48ff2f;hb=076b3b34bc3e02a033213cdac4300444e3c57b74;hp=f458cbc2228327c96a618b90694007861163be8b;hpb=88153d5bb04acd2b8e7fbc3e6789622b77b6cf58;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index f458cbc..1f15e45 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="importvcf"/>
+				<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" />
@@ -147,18 +149,20 @@
 				<tocitem text="Colour Menu" target="alwColour" />
 				<tocitem text="Calculate Menu" target="alwCalc" />
 				<tocitem text="Web Service Menu" target="wsMenu" />
+				<tocitem text="HMMER Menu" target="alwHmmer" />
 				<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 				<tocitem text="Popup Menu" target="popMenu" />
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
-		<tocitem text="Memory Settings" target="memory" expand="false"/>
 		<tocitem text="Scripting with Groovy" target="groovy">
 			<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" />
-		</tocitem>
+    <tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
+    </tocitem>
 		<tocitem text="Privacy" target="privacy" />
 	</tocitem>
 	<tocitem text="Useful information" expand="true">