X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=00aa8b04f0e5d45a56a6cbd3d74bf523fbbe7c06;hb=4e47d166b44617b1cb3cabc3ea3ed72f1a0ad545;hp=cbef39851b30124d51fb71a6f2b330ecb2a67cb9;hpb=3c74b4df923e91c55137dc1b2b5b5ce32775cdb1;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index cbef398..00aa8b0 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,11 +24,12 @@
 	<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="Support for ChimeraX" target="chimera"/>
+        		<tocitem text="Support for ChimeraX" target="chimera"/>
 				<tocitem text="Support for Pymol" target="pymol"/>
 				<tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
 				<tocitem text="Startup Memory Settings" target="startupprefs" />
-        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+		        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+		        <tocitem text="Command line launch scripts" target="jalviewcltool"/>
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -89,6 +90,10 @@
 			<tocitem text="ClustalX" target="colours.clustal" />
 			<tocitem text="Zappo" target="colours.zappo" />
 			<tocitem text="Taylor" target="colours.taylor" />
+			<tocitem text="gecos Flower" target="colours.gecos-flower" />
+			<tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+			<tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+			<tocitem text="gecos Ocean" target="colours.gecos-ocean" />
 			<tocitem text="Hydrophobicity" target="colours.hydro" />
 			<tocitem text="Helix propensity" target="colours.helix" />
 			<tocitem text="Strand propensity" target="colours.strand" />
@@ -153,6 +158,7 @@
 				<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>