JAL-913; Documentation of RNA Structure Conservation

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 8490970..2f8a2fd 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,29 +1,30 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-  
-  This program 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 2
-  of the License, or (at your option) any later version.
-  
-  This program 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 this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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="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="Sequence Retrieval" target="seqfetch"/>
-               <tocitem text="VAMSAS Interoperation" target="vamsas"/>
        </tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>        
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -34,6 +35,7 @@
        <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"/>
@@ -44,6 +46,9 @@
          <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"/>
@@ -52,6 +57,7 @@
             </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">
@@ -65,12 +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"/>
@@ -82,6 +90,7 @@
        </tocitem>
        <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"/>