X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=6630a0a37bc8d3b3498922097abbfba03b250b08;hb=74fee91ef567d4637911a9c20834c9fb1de8c64a;hp=1bbe5c0a555e083225e0b1293384b3b30428883e;hpb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 1bbe5c0..6630a0a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -4,23 +4,29 @@
 <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="editInSelArea"/>
+          <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 text="Modeller PIR File IO" target="io.modellerpir"/>
         </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>
 	<tocitem text="Input / Output" target="io"/>
 	<tocitem text="Key Strokes" target="keys"/>
   	<tocitem text="Making figures" target="export"/>
 	<tocitem text="Editing Alignments" target ="edit"/>
-	<tocitem text="Sequence Features" target="seqfeatures"/>
+	<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>
 	<tocitem text="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
@@ -58,7 +64,7 @@
                 <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>