X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=ca866253b651cbc147419e057bc3a476d975e7aa;hb=039594a00b40c65c2864485c1c6ea939a49399a9;hp=b9560041d2527453a3011f30cd827f0faa2c1d68;hpb=1a2d1358f3c22ff288abc6e25ab63adc7cf18a0a;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b956004..ca86625 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,12 +23,9 @@
 <!-- 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 text="Structure Chooser" target="pdbchooser"/>
+				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -49,7 +46,7 @@
 		<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
 		<tocitem text="Fetching Sequences" target="seqfetch" />		
 		
-		<tocitem text="Select columns by annotation" target="selectcolbyannot" />
+		<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 		
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
 			<tocitem text="Viewing RNA structure" target="varna" />
@@ -75,7 +72,7 @@
 			<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" />
@@ -107,13 +104,16 @@
 			<tocitem text="By RNA Helices" target="colours.rnahelices" />
 		</tocitem>
 		
-		<tocitem text="Calculations" target="calculations" expand="false">
+		<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" />
+			<tocitem text="Reference Sequences" target="referenceseq" />
 		</tocitem>
 		
 		<tocitem text="Sequence Annotations" target="seqannots"	expand="true">
@@ -126,16 +126,18 @@
 			<tocitem text="Consensus" target="calcs.consensus" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="Annotations File Format" target="annotations.fileformat" />
-			<tocitem text="Select Column by Annotation" target="calcs.annotation" />
+			<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 		</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="Jmol Viewer" target="pdbjmol" />
-			<tocitem text="Chimera Viewer" target="chimera" />
-			<tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+			<tocitem text="Chimera Viewer" target="chimera" />			
 		</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 -->
@@ -150,17 +152,20 @@
 				<tocitem text="Annotations Menu" target="alwAnnotations" />
 				<tocitem text="Format Menu" target="alwFormat" />
 				<tocitem text="Colour Menu" target="alwColour" />
-				<tocitem text="Calculation Menu" target="alwCalc" />
+				<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>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
 		<tocitem text="Memory Settings" target="memory" expand="false"/>
+		<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="Groovy Shell" target="groovy" />
 		</tocitem>
 		<tocitem text="Privacy" target="privacy" />
 	</tocitem>