X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2FhelpTOC.xml;h=f59dd70c33627c971a14e25fe75d702e2583595a;hb=10866cba33b339de23e5a4e3121ab86c08b5ff2a;hp=3e41ba312e6415dc8dfe84e27f3531264b398a9b;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 3e41ba3..f59dd70 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,7 +1,7 @@
 <?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
+ * 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
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,18 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<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 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"/>
@@ -35,6 +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"/>
@@ -43,18 +55,19 @@
 		  <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"/>
 	<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"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
+	<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="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"/>
@@ -70,12 +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"/>
@@ -86,15 +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 -->
@@ -124,9 +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>