From 0c6d48fc655b08e80941576156004926dd253c23 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 16:54:45 +0100
Subject: [PATCH] =?utf8?q?JAL-1645=20update=20TOC=20for=202.9=20what=E2=80=99?=
 =?utf8?q?s=20new?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 help/helpTOC.xml |   49 ++++++++++++++++++++++++++++++++++---------------
 1 file changed, 34 insertions(+), 15 deletions(-)

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 60a0ae2..2580d9a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -14,34 +14,46 @@
 <toc version="1.0">
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
 	<tocitem text="Jalview Documentation" target="home" expand="true">
-		<tocitem text="What's new" target="new" expand="true">
-			<tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
-			<tocitem text="Annotation Panel Menu" target="alwAnnotations" />
-			<tocitem text="Add reference annotation" target="popMenuAddref" />
-			<tocitem text="Colour By Annotation" target="colours.annotation" />
-			<tocitem text="Chimera Viewer" target="chimera" />
-			<tocitem text="Structure Preferences" target="strucprefs" />
+			<tocitem text="What's new" target="new" expand="true">
+				<tocitem text="Split Frame View" target="splitframe" />
+				<tocitem text="Fetching Sequences" target="seqfetch" />		
+				<tocitem text="BioJSON v1.0" target="biojson" />
+				<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+				<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+				<tocitem text="Jmol Viewer" target="pdbjmol" />
+				<tocitem text="Chimera Viewer" target="chimera" />
+				<tocitem text="Select columns by annotation" target="selectcolbyannot" />
+				<tocitem text="Annotations File Format" target="annotations.fileformat" />
+				<tocitem text="Latest Release Notes" target="release"/>
 		</tocitem>
+		
 		<tocitem text="Editing Alignments" target="edit" />
 		<tocitem text="Cursor Mode" target="cursor" />
 		<tocitem text="Key Strokes" target="keys" />
-		<tocitem text="Input / Output" target="io" />
-		<tocitem text="Making Figures" target="export" />
+		
+		<tocitem text="Input / Output" target="io" expand="false">
+			<tocitem text="BioJSON v1.0" target="biojson" />
+		</tocitem>
+		
+		<tocitem text="Making Figures" target="export" expand="false">
+			<tocitem text="BioJSON v1.0" target="biojson" />
+			<tocitem text="BioJS MSA Viewer" target="biojsmsa" />
+		</tocitem>
+		
 		<tocitem text="Hidden Regions" target="hiddenRegions" />
 		<tocitem text="Multiple Views" target="multipleviews" />
 		<tocitem text="Split Frame View" target="splitframe" />
 		<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
 		<tocitem text="Fetching Sequences" target="seqfetch" />		
-		<tocitem text="BioJSON v1.0" target="biojson" />
-		<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-		<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+		
 		<tocitem text="Select columns by annotation" target="selectcolbyannot" />
-		<tocitem text="BioJS MSA Viewer" target="biojsmsa" />
+		
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
 			<tocitem text="Viewing RNA structure" target="varna" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
 		</tocitem>
+		
 		<tocitem text="Sequence Features" target="seqfeatures" expand="false">
 			<tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
 			<tocitem text="Sequence Features File" target="features.fileformat" />
@@ -52,6 +64,7 @@
 			<tocitem text="DAS Feature Settings" target="das.settings" />
 			<tocitem text="HTML annotation report" target="io.seqreport" />
 		</tocitem>
+		
 		<tocitem text="Web Services" target="webservice" expand="false">
 			<tocitem text="JABAWS" target="jabaws" />
 			<tocitem text="Web Service Preferences" target="wsprefs" />
@@ -68,6 +81,7 @@
 			<tocitem text="Database Reference Retrieval" target="dbreffetcher" />
 			<tocitem text="DAS Feature Retrieval" target="das.viewing" />
 		</tocitem>
+		
 		<tocitem text="Colour Schemes" target="colours" expand="false">
 			<tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
 			<tocitem text="ClustalX" target="colours.clustal" />
@@ -89,6 +103,7 @@
 			<tocitem text="By Annotation" target="colours.annotation" />
 			<tocitem text="By RNA Helices" target="colours.rnahelices" />
 		</tocitem>
+		
 		<tocitem text="Calculations" target="calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
 			<tocitem text="Calculating trees" target="trees" />
@@ -96,19 +111,23 @@
 			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 			<tocitem text="Pairwise Alignments" target="pairwise" />
 			<tocitem text="Remove Redundancy" target="redundancy" />
-			<tocitem text="Select Column by Annotation" target="calcs.annotation" />
 		</tocitem>
+		
 		<tocitem text="Sequence Annotations" target="seqannots"	expand="true">
 			<tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
 		</tocitem>
+		
 		<tocitem text="Alignment Annotations" target="alannotation" expand="false">
 			<tocitem text="Conservation" target="calcs.alconserv" />
 			<tocitem text="Quality" target="calcs.alquality" />
 			<tocitem text="Consensus" target="calcs.consensus" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="Annotations File Format" target="annotations.fileformat" />
+			<tocitem text="Select Column by Annotation" target="calcs.annotation" />
 		</tocitem>
-		<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+		<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
+			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+			<tocitem text="PDB Structure Chooser" target="pdbchooser" />
 			<tocitem text="Jmol Viewer" target="pdbjmol" />
 			<tocitem text="Chimera Viewer" target="chimera" />
 			<tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
-- 
1.7.10.2