X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=54abd53676590971df614b1c7bea434d0d8a2fba;hb=0ce9577d119e1cc646f4b0d2e961f698d994fcc5;hp=a6145c1515138ae6167f8225050e8e953d3ca456;hpb=1b9c3c2c4051fa3e39091ed9b5203c44482cd80e;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a6145c1..54abd53 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,11 +23,6 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
-				<tocitem text="Split Frame View" target="splitframe" />
-				<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-				<tocitem text="PDB Structure Chooser" target="pdbchooser" />
-				<tocitem text="Chimera Viewer" target="chimera" />
-				<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 				<tocitem text="Latest Release Notes" target="release"/>
 		</tocitem>
 		
@@ -75,7 +70,7 @@
 			<tocitem text="Sequence Alignment" target="msaservice"	expand="false">
 				<tocitem text="Multiple Alignment Subjobs" target="msaservice" />
 			</tocitem>
-			<tocitem text="Secondary Structure Prediction" target="jnet" />
+			<tocitem text="Secondary Structure Prediction" target="jpred" />
 			<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
 			<tocitem text="Protein Disorder Prediction" target="disorder" />
 			<tocitem text="Alignment Conservation Analysis" target="aacon" />
@@ -158,9 +153,11 @@
 		</tocitem>
 		<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>
 		<tocitem text="Command Line" target="commandline" expand="false">
 			<tocitem text="Command Line Arguments" target="clarguments" />
-			<tocitem text="Groovy Shell" target="groovy" />
 		</tocitem>
 		<tocitem text="Privacy" target="privacy" />
 	</tocitem>