split test for general Stockholm IO consistency (JAL-1199) from test for IO of sequen...

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5371ad4..0d2e096 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,30 +1,37 @@
 <?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/>.
+  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="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"/>
@@ -48,18 +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"/>
@@ -81,6 +89,7 @@
                <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>
@@ -133,9 +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>