X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=6630a0a37bc8d3b3498922097abbfba03b250b08;hb=69e9cd54dcfd25dd3067f353bc53eb6b4d7e27af;hp=6a8fe72b8821b3e5b623b7168633981814fa4cf8;hpb=82159a6825376e61f388feffdf182eed4e0e30f2;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 6a8fe72..6630a0a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,12 +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="Alignment Annotations" target ="alannotation"/>
-	
+	<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"/>
@@ -28,6 +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"/>
@@ -40,20 +60,22 @@
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
                 <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>  
-                <tocitem text="Search Menu" target="search"/> 
-                <tocitem text="View Menu" target="alwView"/>  
+                <tocitem text="Edit Menu" target="alwEdit"/> 
+                <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="false">
+<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>