X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=4636ea36f8398fb4e9aa7b069c5ee2ce77abc90f;hb=e510f5ac2ae4530767c92cbe99e871c7f21eb36a;hp=75ff4c435f7481a5426cba814b6439d7edfad561;hpb=354963d0c9d69f28fa5aa642c1f13627676ff4ae;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 75ff4c4..4636ea3 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,46 +1,64 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * 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) 
-	any later version. * * Jalview is distributed in the hope that it will be 
-	useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of 
-	MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General 
-	Public License for more details. * * You should have received a copy of the 
-	GNU General Public License * along with Jalview. If not, see <http://www.gnu.org/licenses/>. 
-	* 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">
+<!--
+ * 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) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <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="Latest Release Notes" target="release"/>
+        <tocitem text="Calculations Dialog" target="calcs.dialog"/>
+				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
+				<tocitem text="Omit hidden regions in Overview" target="overview"/>
+				<tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
+				<tocitem text="identifers.org for URL Links" target="linksprefs" />
+				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
 		</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="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="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" />
@@ -51,6 +69,7 @@
 			<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" />
@@ -58,7 +77,7 @@
 			<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="Secondary Structure Prediction" target="jpred" />
 			<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
 			<tocitem text="Protein Disorder Prediction" target="disorder" />
 			<tocitem text="Alignment Conservation Analysis" target="aacon" />
@@ -67,6 +86,7 @@
 			<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" />
@@ -88,31 +108,41 @@
 			<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="Calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
-			<tocitem text="Calculating trees" target="trees" />
-			<tocitem text="Principal Component Analysis" target="pca" />
+			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+  			  <tocitem text="Calculating trees" target="trees" />
+  			  <tocitem text="Principal Component Analysis" target="pca" />
+  			</tocitem>
 			<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 text="Reference Sequences" target="referenceseq" />
 		</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 Columns by Annotation" target="selectcolbyannot" />
 		</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 text="Chimera Viewer" target="chimera" />			
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+		    <tocitem text="Configuring URL Links" target="linksprefs" />
+		</tocitem>
 		<tocitem text="VAMSAS Data Exchange" target="vamsas">
 			<!-- what can Jalview share with other apps -->
 			<!-- what other apps exist -->
@@ -127,7 +157,7 @@
 				<tocitem text="Annotations Menu" target="alwAnnotations" />
 				<tocitem text="Format Menu" target="alwFormat" />
 				<tocitem text="Colour Menu" target="alwColour" />
-				<tocitem text="Calculation Menu" target="alwCalc" />
+				<tocitem text="Calculate Menu" target="alwCalc" />
 				<tocitem text="Web Service Menu" target="wsMenu" />
 				<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 				<tocitem text="Popup Menu" target="popMenu" />
@@ -135,9 +165,11 @@
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
 		<tocitem text="Memory Settings" target="memory" expand="false"/>
+		<tocitem text="Scripting with Groovy" target="groovy">
+			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+		</tocitem>
 		<tocitem text="Command Line" target="commandline" expand="false">
 			<tocitem text="Command Line Arguments" target="clarguments" />
-			<tocitem text="Groovy Shell" target="groovy" />
 		</tocitem>
 		<tocitem text="Privacy" target="privacy" />
 	</tocitem>