X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=bae82d4076f3062f2167f7e00f845de6f7801a17;hb=fe3f72a41de913cc633f1f6449d3a6433f301b10;hp=c148afc84b7973f00e826c5ee77c6480826bb735;hpb=67b2712fea5eea9212ca794d2bf7ef65f19493a7;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c148afc..bae82d4 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,17 +2,30 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-	<tocitem text="What's new" target="new" expand="false"/>
+	<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>
 	<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"/>
@@ -50,7 +63,7 @@
                 <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>