X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=4c372e0ddf90cb57169df1c1a09fb781ce3e02a5;hb=eb3461a71b073a0e7a9a2dba6481b5ed3fca71e9;hp=a0995c2da59defabb1bcddba37ceee1b869e74a8;hpb=7bb2a1c049e7b7be9c04012ce90afc173b81eb1a;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a0995c2..4c372e0 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,7 +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="VCF Import" target="vcfimport"/>
+        <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>
@@ -62,6 +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>
 		
@@ -137,10 +139,6 @@
 		<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">
@@ -153,18 +151,20 @@
 				<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">