X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=d08e3d267bbe9ad049561c628ee05fa54fff60f5;hb=0ae0d247aec4361dc0a743d10abd3e9743d6c180;hp=77f105e94ef9ba894ba50c8ccba9ecf662e3bf1a;hpb=f850089f8bc67403194f4a1a3b793a46dbb4224a;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 77f105e..d08e3d2 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,21 +3,28 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-                <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>
-                <tocitem text="New Output Format Controls" target="preferences"/>
-                <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>
-                <tocitem text="Sequence Feature Styles" target="seqfeatures"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
+        	<tocitem text="DAS Feature Fetching" target="das.settings"/>
+        	<tocitem text="Hide Regions" target="hiddenRegions"/> 	         
         </tocitem>
-	<tocitem text="Release History" target="release"/>
-      	<tocitem text="Alignment Annotations" target ="alannotation"/>
-	
-	<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="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
+                <tocitem text="MAFFT Alignment" target="mafft"/>
           	<tocitem text="JNet Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
@@ -35,6 +42,7 @@
 		<tocitem text="User Defined" target="colours.user"/>
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
+		<tocitem text="By Annotation" target="colours.annotation"/>
 	</tocitem>
 	<tocitem text="Calculations" target="calculations" expand="false">
 		<tocitem text="Sorting alignments" target="sorting"/>
@@ -43,6 +51,12 @@
 		<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">
@@ -51,15 +65,18 @@
                 <tocitem text="View Menu" target="alwView"/> 
                 <tocitem text="Colour Menu" target="alwColour"/>
                 <tocitem text="Calculation Menu" target="alwCalc"/>
-				<tocitem text="Web Service Menu" target="wsMenu"/>
+		<tocitem text="Web Service Menu" target="wsMenu"/>
 		<tocitem text="Annotation Menus" target="annotMenus"/>
 		<tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
 	</tocitem>
-	<tocitem text="Memory Settings" target="memory"/>
+	<tocitem text="Memory Settings" target="memory" expand="false">
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
+          </tocitem>
 </tocitem>
 <tocitem text="Useful information" expand="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
+	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
 </tocitem>
 </toc>