X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=9560ecfdec5957c7dc395a2bac7db45229ef9f28;hb=07e6452f0883636e9439327ac8fece19b0461537;hp=e1bc443efe3ef380efd450e0bf7738e87a5053b2;hpb=721a650185138574d75e548b3e1f81113034ff45;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index e1bc443..9560ecf 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -1,4 +1,21 @@
 <?xml version="1.0" encoding="ISO-8859-1" ?>
+<!--
+  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 map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">
 <map version="1.0">
    <mapID target="home" url="html/index.html" />
@@ -38,6 +55,7 @@
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
+   <mapID target="io.tcoffeescores" url="html/io/tcoffeescores.html"/>
    <mapID target="export" url="html/io/export.html"/>
    <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
@@ -106,6 +124,7 @@
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />
+   <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
    
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />