X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=6d7c9482fd6abffc5fa2da3837bd4be8fb4896d1;hb=HEAD;hp=77ddd8898363b7ca6e2fb58e46facada6d07ec00;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 77ddd88..259c43d 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,9 +23,10 @@
 <!-- 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="Latest Release Notes" target="release"/>
-				<tocitem text="Structure Chooser" target="pdbchooser"/>
-				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+			<tocitem text="Latest Release Notes" target="release"/>
+			<tocitem text="PaSiMap Sequence Similarity Plots" target="pasimap" />
+			<tocitem text="Secondary Structure Trees and PCAs" target="proteinssanaly" />
+			<tocitem text="Secondary Structure Consensus" target="proteinss" />				
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +50,7 @@
 		<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 		
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+		  <tocitem text="Annotating from VCF" target="importvcf" /> 
 			<tocitem text="Viewing RNA structure" target="varna" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
@@ -60,6 +62,7 @@
 			<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>
 		
@@ -84,12 +87,17 @@
 			<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" />
 			<tocitem text="Turn propensity" target="colours.turn" />
 			<tocitem text="Buried index" target="colours.buried" />
 			<tocitem text="Nucleotide colours" target="colours.nucleotide" />
+			<tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
 			<tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
 			<tocitem text="Blosum62" target="colours.blosum" />
 			<tocitem text="by Percentage Identity" target="colours.pid" />
@@ -103,9 +111,10 @@
 		
 		<tocitem text="Calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
-			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+			<tocitem text="Trees, PCA and PaSiMap" target="calcs.dialog" expand="false">
   			  <tocitem text="Calculating trees" target="trees" />
   			  <tocitem text="Principal Component Analysis" target="pca" />
+  			  <tocitem text="PaSiMap Analysis" target="pasimap" />
   			</tocitem>
 			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 			<tocitem text="Pairwise Alignments" target="pairwise" />
@@ -127,18 +136,15 @@
 		</tocitem>
 		<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
 			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-			<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+			<tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
 			<tocitem text="Jmol Viewer" target="pdbjmol" />
-			<tocitem text="Chimera Viewer" target="chimera" />			
+			<tocitem text="Chimera/X Viewer" target="chimera" />
+			<tocitem text="Pymol Viewer" target="pymol" />			
 		</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="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">
@@ -156,15 +162,22 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
-		<tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		<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 text="Command Line: introduction and reference" target="clarguments" />
+			<tocitem text="Command Line: basic usage" target="clarguments-basic" />
+			<tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
+			<tocitem text="Command Line: argument files" target="clarguments-argfiles" />
+			<tocitem text="Command Line: reference" target="clarguments-reference" />
+			<tocitem text="Command Line: old command line arguments" target="clarguments-old" />
 		</tocitem>
+		<tocitem text="Memory Settings" target="memory" expand="false"/>
+		<tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
 		<tocitem text="Privacy" target="privacy" />
-	</tocitem>
+    </tocitem>
 	<tocitem text="Useful information" expand="true">
 		<tocitem text="Amino Acid Table" target="aminoAcids" />
 		<tocitem text="Amino Acid Properties" target="aaProperties" />