X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=5dec60151db23f516f7905d85d17f448f1f92ae9;hb=ae3b7664d0d98f376b1f636edc34aaff6b8a914a;hp=bae82d4076f3062f2167f7e00f845de6f7801a17;hpb=d40ad6d5aa51ca4174a3da658b24059ae588098f;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index bae82d4..5dec601 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,33 +3,33 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-          <tocitem text="Cursor Mode" target="cursor"/>
-          <tocitem text="Selection Area Based Editing" target="edit.selareas"/>
-          <tocitem text="User Defined Sequence Features" target="search"/>
-          <tocitem text="Sequence Feature Groups" target="seqfeatures"/>
-          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
-          <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>
-          <tocitem text="Annotations File" target="annotations.fileformat"/>
-          <tocitem text="Colour by Annotation Value" target="colours.annotation"/>
-        </tocitem>
-	<tocitem text="Release History" target="release"/>
-      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
-          <tocitem text="Quality" target="calcs.alquality"/>
-          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
+        	<tocitem text="DAS Feature Fetching" target="das.settings"/>
+        	<tocitem text="Hide Regions" target="hiddenRegions"/>
+              	<tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
         </tocitem>
-	<tocitem text="Input / Output" target="io"/>
+        <tocitem text="Release History" target="release"/>
+        <tocitem text="Editing Alignments" target ="edit"/>	
+        <tocitem text="Cursor Mode" target="cursor"/>
 	<tocitem text="Key Strokes" target="keys"/>
+	<tocitem text="Input / Output" target="io"/>
   	<tocitem text="Making figures" target="export"/>
-	<tocitem text="Editing Alignments" target ="edit"/>
+	<tocitem text="Hidden Regions" target="hiddenRegions"/>
+	<tocitem text="Viewing PDB Files" target="viewingpdbs"/>
 	<tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
+          <tocitem text="User Defined Sequence Features" target="search"/>
+          <tocitem text="DAS Features Settings" target="das.viewing"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
+          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
-          	<tocitem text="JNet Prediction" target="jnet"/>
+                <tocitem text="MAFFT Alignment" target="mafft"/>
+            </tocitem>
+          <tocitem text="Secondary Structure Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
@@ -55,6 +55,12 @@
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
+      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+          <tocitem text="Conservation" target="calcs.alconserv"/>
+          <tocitem text="Quality" target="calcs.alquality"/>
+          <tocitem text="Consensus" target="calcs.consensus"/>
+          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
+        </tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">