X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=1d45e7a3eb52a678d27770677e8882251abcbfd0;hb=81edd609f9841a84d5799d221277d45413a177cf;hp=940629297cd56be3ed8039fe11b49fdf61085434;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9406292..1d45e7a 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,32 +1,36 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ * 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/>.
+ * 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">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-	<tocitem text="What's new" target="new" expand="true">
-		<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="Editing Alignments" target ="edit"/>	
-    <tocitem text="Cursor Mode" target="cursor"/>
-	<tocitem text="Key Strokes" target="keys"/>
+ <tocitem text="What's new" target="new" expand="true">
+    <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+    <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+    <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
+    <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
+  </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="Hidden Regions" target="hiddenRegions"/>
@@ -46,6 +50,7 @@
 		  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	  <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"/>
@@ -55,6 +60,9 @@
                 <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="Protein Disorder Prediction" target="disorder"/>
+          <tocitem text="Alignment Conservation Analysis" target="aacon"/>
           <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
 		<tocitem text="Sequence Retrieval" target="seqfetch"/>
 		<tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
@@ -77,6 +85,7 @@
 		<tocitem text="User Defined" target="colours.user"/>
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
+    <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
 		<tocitem text="By Annotation" target="colours.annotation"/>
 		<tocitem text="By RNA Helices" target="colours.rnahelices"/>
 	</tocitem>
@@ -88,6 +97,9 @@
 		<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>
   	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>          
           <tocitem text="Quality" target="calcs.alquality"/>
@@ -97,6 +109,7 @@
         </tocitem>
 	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
 	  <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>
@@ -107,17 +120,18 @@
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
-                <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>
-				<tocitem text="Select Menu" target="alwSelect"/> 
-                <tocitem text="View Menu" target="alwView"/>
-				<tocitem text="Format Menu" target="alwFormat"/>
-                <tocitem text="Colour Menu" target="alwColour"/>
-                <tocitem text="Calculation Menu" target="alwCalc"/>
-		<tocitem text="Web Service Menu" target="wsMenu"/>
-		<tocitem text="Annotation Menus" target="annotMenus"/>
-		<tocitem text="Popup Menu" target="popMenu"/>
-                </tocitem>
+            <tocitem text="File Menu" target="alwFile"/>
+            <tocitem text="Edit Menu" target="alwEdit"/>
+			<tocitem text="Select Menu" target="alwSelect"/> 
+            <tocitem text="View Menu" target="alwView"/>
+            <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="Web Service Menu" target="wsMenu"/>
+			<tocitem text="Annotation Panel Menu" target="annotPanelMenu"/>
+			<tocitem text="Popup Menu" target="popMenu"/>
+        </tocitem>
 	</tocitem>
         <tocitem text="Preferences" target="preferences"/>
 	<tocitem text="Memory Settings" target="memory" expand="false">
@@ -129,9 +143,11 @@
         </tocitem>
        	<tocitem text="Privacy" target="privacy"/>
 </tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
+	<tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+  
 </tocitem>
 </toc>