X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=fe421106a9d9488baca72fa2317906cf3e8f4ab4;hb=82bb69383ab22735cbd3440c670ae0b290fe6afd;hp=57dbe4b10dbec3e7447eb220aa9990fd8c0de294;hpb=6d69275a18e2773d73d84b9fe4291e7313abfda4;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 57dbe4b..fe42110 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * 
-	Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. 
+<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * 
+	Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. 
 	* * Jalview is free software: you can redistribute it and/or * modify it 
 	under the terms of the GNU General Public License * as published by the Free 
 	Software Foundation, either version 3 * of the License, or (at your option) 
@@ -12,31 +12,47 @@
 	* The Jalview Authors are detailed in the 'AUTHORS' file. -->
 <!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">
+<!-- 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="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="BioJSON v1.0" target="biojson" />
+				<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="Nucleic Acid Support" target="nucleicAcids"
-			expand="false">
+		<tocitem text="Fetching Sequences" target="seqfetch" />		
+		
+		<tocitem text="Select columns by annotation" target="selectcolbyannot" />
+		
+		<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" />
@@ -47,17 +63,16 @@
 			<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" />
 			<tocitem text="Web Service Parameters" target="wsparams" />
-			<tocitem text="Sequence Alignment" target="msaservice"
-				expand="false">
+			<tocitem text="Sequence Alignment" target="msaservice"	expand="false">
 				<tocitem text="Multiple Alignment Subjobs" target="msaservice" />
 			</tocitem>
 			<tocitem text="Secondary Structure Prediction" target="jnet" />
-			<tocitem text="RNAalifold RNA Secondary Structure Prediction"
-				target="rnaalifold" />
+			<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
 			<tocitem text="Protein Disorder Prediction" target="disorder" />
 			<tocitem text="Alignment Conservation Analysis" target="aacon" />
 			<tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
@@ -65,6 +80,7 @@
 			<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" />
@@ -86,6 +102,7 @@
 			<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" />
@@ -94,26 +111,27 @@
 			<tocitem text="Pairwise Alignments" target="pairwise" />
 			<tocitem text="Remove Redundancy" target="redundancy" />
 		</tocitem>
-		<tocitem text="Sequence Annotations" target="seqannots"
-			expand="true">
-			<tocitem text="Annotation from Structure" target="xsspannotation"
-				expand="false" />
+		
+		<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="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" />
 		</tocitem>
-		<tocitem text="Viewing RNA structures" target="varna" expand="false">
-		</tocitem>
+		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->
 			<!-- what other apps exist -->
@@ -135,9 +153,7 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
-		<tocitem text="Memory Settings" target="memory" expand="false">
-			<tocitem text="JNLP with extra memory parameters" target="jalviewjnlp" />
-		</tocitem>
+		<tocitem text="Memory Settings" target="memory" expand="false"/>
 		<tocitem text="Command Line" target="commandline" expand="false">
 			<tocitem text="Command Line Arguments" target="clarguments" />
 			<tocitem text="Groovy Shell" target="groovy" />