X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0bf615bf4f58f529d1123637f4281069a91d293b;hb=e6f25fadd43d5865b62c5ef749ad12f6c9a3a583;hp=b55a592a45bcd4713469aa6aef0e03ac1295bdc4;hpb=ef82d3da980713521a661f41e58890b63d3be0d0;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b55a592..0bf615b 100755
--- a/help/helpTOC.xml
+++ b/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="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" />
@@ -59,8 +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>
 		
@@ -77,8 +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">
@@ -105,8 +103,10 @@
 		
 		<tocitem text="Calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
-			<tocitem text="Calculating trees" target="trees" />
-			<tocitem text="Principal Component Analysis" target="pca" />
+			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+  			  <tocitem text="Calculating trees" target="trees" />
+  			  <tocitem text="Principal Component Analysis" target="pca" />
+  			</tocitem>
 			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 			<tocitem text="Pairwise Alignments" target="pairwise" />
 			<tocitem text="Remove Redundancy" target="redundancy" />
@@ -133,7 +133,7 @@
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
-		    <tocitem text="Configuring URL Links" target="urllinkspref" />
+		    <tocitem text="Configuring URL Links" target="linksprefs" />
 		</tocitem>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->
@@ -151,6 +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>
@@ -158,7 +159,7 @@
 		<tocitem text="Preferences" target="preferences" />
 		<tocitem text="Memory Settings" target="memory" expand="false"/>
 		<tocitem text="Scripting with Groovy" target="groovy">
-			<tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+			<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" />