X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=2f8a2fdc44a5ace16e1eaf82ca5d2b5e77f72161;hb=04d2166bf6e1ae6df7fb0e346d228b69a8e8a089;hp=7d9e595a720c2a959041bc6d69ea5e12144da1b1;hpb=67594472bd8920efa45169478981b700b79ae683;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 7d9e595..2f8a2fd 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,26 +1,54 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+-->
 <!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="true"/>
-        <tocitem text="Release History" target="release"/>
-        <tocitem text="Editing Alignments" target ="edit"/>	
-        <tocitem text="Cursor Mode" target="cursor"/>
+	<tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Jaba Web Services" target="jabaws"/>
+      <tocitem text="Superpositions with Jmol 12" target="pdbjmol"/>
+      <tocitem text="Web Service Parameters" target="wsparams"/>
+      <tocitem text="Web Service Preferences" target="wsprefs"/>
+      <tocitem text="Release History" 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="Making Figures" target="export"/>
 	<tocitem text="Hidden Regions" target="hiddenRegions"/>
-	<tocitem text="Viewing PDB Files" target="viewingpdbs"/>
 	<tocitem text="Multiple Views" target="multipleviews"/>
+	<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
+	<tocitem text="Fetching Sequences" target="seqfetch"/>
+	<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false"></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"/>
+          <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
 		  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	  <tocitem text="DAS Feature Settings" target="das.settings"/>
         </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="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
@@ -28,6 +56,9 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
+		<tocitem text="Sequence Retrieval" target="seqfetch"/>
+		<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"/>
@@ -40,12 +71,14 @@
 		<tocitem text="Turn propensity" target="colours.turn"/>
 		<tocitem text="Buried index" target="colours.buried"/>
 		<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+		<tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
 		<tocitem text="Blosum62" target="colours.blosum"/>
 		<tocitem text="by Percentage Identity" target="colours.pid"/>	
 		<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 text="By RNA Helices" target="colours.rnahelices"/>
 	</tocitem>
 	<tocitem text="Calculations" target="calculations" expand="false">
 		<tocitem text="Sorting alignments" target="sorting"/>
@@ -55,12 +88,21 @@
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</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="RNA Structure Conservation" target="calcs.alstrconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
+	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+	  <tocitem text="Jmol Viewer" target="pdbjmol"/>
+	  <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
+	</tocitem>
+	<tocitem text="VAMSAS Data Exchange" target="vamsas">
+		<!-- what can Jalview share with other apps -->
+		<!-- what other apps exist -->
+		</tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
@@ -82,7 +124,9 @@
           </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>
 <tocitem text="Useful information" expa nd="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>