X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=a0c7fe6b066b870fcc9fb3028b2dfbae2f945af1;hb=d87b55e45cc1e6a5b7df3865ded1b87a0e3dc7ff;hp=f458cbc2228327c96a618b90694007861163be8b;hpb=88153d5bb04acd2b8e7fbc3e6789622b77b6cf58;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index f458cbc..a0c7fe6 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,8 +24,10 @@
 	<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="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
+				<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
+				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+				
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +51,7 @@
 		<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" />
@@ -60,6 +63,7 @@
 			<tocitem text="Feature Colourschemes" target="features.featureschemes" />
 			<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
 			<tocitem text="Editing Sequence Features" target="seqfeatedit" />
+			<tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
 			<tocitem text="HTML annotation report" target="io.seqreport" />
 		</tocitem>
 		
@@ -152,13 +156,14 @@
 			</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">