X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0bf615bf4f58f529d1123637f4281069a91d293b;hb=e6f25fadd43d5865b62c5ef749ad12f6c9a3a583;hp=4636ea36f8398fb4e9aa7b069c5ee2ce77abc90f;hpb=a990c2c6facfd04d61d316dcafba31d03747d162;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 4636ea3..0bf615b 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,13 +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="Calculations Dialog" target="calcs.dialog"/>
-				<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="Show gaps as grey in overview" target="overviewprefs"/>
-				<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" />
@@ -65,8 +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>
 		
@@ -83,8 +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">
@@ -159,6 +151,7 @@
 				<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>