X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=f0403e772fae743856bb486b23b1df5a0812acf2;hb=2be644b535dd34da958a831f877cf63d87912b5b;hp=bd5a9d543f6e8ca64ecb216f27f858e34938438e;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index bd5a9d5..f0403e7 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,29 +1,29 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
-   * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-   * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
    * 
-   * 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.
+   * 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.
    * 
-   * 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 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="Sequence Retrieval" target="seqfetch"/>
-		<tocitem text="VAMSAS Interoperation" target="vamsas"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -37,6 +37,7 @@
 	<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"/>
@@ -51,6 +52,7 @@
             </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">
@@ -116,6 +118,7 @@
           <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"/>