X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=0d2e09603d20afa99bbf88817e75c96bd5518e81;hb=7b3215a40ae93915da4026d5877ebbe447c1fc7e;hp=2bc4187896a7dcd06e14eefa806087cd2e0e17b5;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2bc4187..0d2e096 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,31 +1,37 @@
 <?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, 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/>.
+  Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+  Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
-          <tocitem text="Jalview News Reader" target="newsreader"/>
-          <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
-      <tocitem text="Default Annotation preferences" target="colours.annotation"/>
-      <tocitem text="Jaba Web Services" target="jabaws"/>
+    <tocitem text="Protein Disorder Prediction" target="disorder"/>
+    <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+		<tocitem text="Viewing RNA structure" target="varna" />
+		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+		<tocitem text="HTML annotation report" target="io.seqreport"/>
+		<tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
+		<tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
+	  <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
+	  <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
+	  <tocitem text="DNA or Protein PCA calculation" target="pca"/>
+	  <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -36,6 +42,11 @@
 	<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 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"/>
@@ -44,6 +55,7 @@
 		  <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"/>
@@ -53,7 +65,9 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+          <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"/>
 		<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
@@ -69,12 +83,15 @@
 		<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="T-COFFEE Scores" target="io.tcoffeescores"/>
 		<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"/>
@@ -85,15 +102,17 @@
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
   	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
+          <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>
 	<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="Viewing RNA structures" target="varna" expand="false">	</tocitem>
 	<tocitem text="VAMSAS Data Exchange" target="vamsas">
 		<!-- what can Jalview share with other apps -->
 		<!-- what other apps exist -->
@@ -123,9 +142,11 @@
         </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>