X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=316b63dab60e2817b8165ba81de99cb1ac894354;hb=2a436b9052affcfeb6f3748a40de53f6b8a7e9ef;hp=1530b051aba3d2b8c5ec99de5916267de7809ddb;hpb=b785060f71751dd08fced2b4c84c9efcab62ac0e;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 1530b05..316b63d 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,18 +3,30 @@
 <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="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"/>
-	
+      	<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"/>
@@ -35,6 +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"/>
@@ -56,7 +69,9 @@
 		<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"/>