jalview 2.5 documentation (still)

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b2f82ae..f0403e7 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,23 +1,43 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
+<!--
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * 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="Graduated Feature Colours" target="features.featureschemes"/>
+      <tocitem text="Sort by Features" target="seqfeatures.settings"/>
+      <tocitem text="Envision2 Service" target="webservice"/>
       <tocitem text="Release History" target="release"/>
-         <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
-         <tocitem text="Mapping between Sequences" target="seqmappings"/>
-    </tocitem>
+       </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="Making Figures" target="export"/>
        <tocitem text="Hidden Regions" target="hiddenRegions"/>
        <tocitem text="Multiple Views" target="multipleviews"/>
        <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
+       <tocitem text="Fetching Sequences" target="seqfetch"/>
        <tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
+          <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
                  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
@@ -31,6 +51,9 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </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">
                <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
@@ -68,6 +91,10 @@
          <tocitem text="Jmol Viewer" target="pdbjmol"/>
          <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
        </tocitem>
+       <tocitem text="VAMSAS Data Exchange" target="vamsas">
+               <!-- what can Jalview share with other apps -->
+               <!-- what other apps exist -->
+               </tocitem>
        <tocitem text="Window Menus" target="menus" expand="false">
                <tocitem text="Desktop Window" target="desktopMenu"/>
                <tocitem text="Alignment Window" target="alMenu">
@@ -89,7 +116,9 @@
           </tocitem>
         <tocitem text="Command Line" target="commandline" expand="false">
           <tocitem text="Command Line Arguments" target="clarguments"/>
+             <tocitem text="Groovy Shell" target="groovy"/>
         </tocitem>
+               <tocitem text="Privacy" target="privacy"/>
 </tocitem>
 <tocitem text="Useful information" expa nd="true">
        <tocitem text="Amino Acid Table" target="aminoAcids"/>