X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=6630a0a37bc8d3b3498922097abbfba03b250b08;hb=62df38e7204f2903d1b4e5aaef7762acf96f317d;hp=4642f67d759e40bf16b4d035d974a32ad3783245;hpb=08b0ba966ee50a1668ca841afe8fe8ea6e6473fc;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 4642f67..6630a0a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,16 +2,31 @@
 <!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 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" 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"/>
@@ -32,6 +47,7 @@
 		<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"/>
@@ -48,7 +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>