X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=c148afc84b7973f00e826c5ee77c6480826bb735;hb=cb8ec179c020265666678572815ab056a024da22;hp=8402add5377a70e2ff7d1c7692572a0a20f836d1;hpb=9807ea8cc4e867378c52d51b832168d4bc611d29;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 8402add..c148afc 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,12 +2,7 @@
 <!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="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>
+	<tocitem text="What's new" target="new" expand="false"/>
 	<tocitem text="Release History" target="release"/>
       	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
@@ -17,6 +12,7 @@
 	<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="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
@@ -37,6 +33,7 @@
 		<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"/>
@@ -58,7 +55,9 @@
 		<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"/>