X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp.jhm;h=aaaaaf8f293fc11ce3e781cc8135268b5db7ba60;hb=682b4b598105a0024231bcf5f53206530425fd64;hp=0ed676c27963a744799864d176404ef447f44bd4;hpb=05c695da50cc7ac1bd759ed5c58b3d5d7a9d0085;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 0ed676c..aaaaaf8 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" />
@@ -15,12 +32,14 @@
    <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
    <mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
    <mapID target="msaservice" url="html/webServices/msaclient.html"/>
-   <mapID target="clustal" url="html/webServices/clustalw.html"/>
-   <mapID target="muscle" url="html/webServices/muscle.html"/>
-   <mapID target="mafft" url="html/webServices/mafft.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
+   <mapID target="shmrws" url="html/webServices/shmr.html"/>
+   <mapID target="newsreader" url="html/webServices/newsreader.html"/>
+   <mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
+   <mapID target="aacon" url="html/webServices/AACon.html"/>
+   <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
-   <mapID target="dbreffetcher" url="html/webservices/dbreffetcher.html"/>
+   <mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
    <mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
@@ -30,11 +49,14 @@
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
+   <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
    <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"/>
@@ -70,11 +92,16 @@
    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
    <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
    <mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>
+   <mapID target="colours.purinepyrimidine" url="html/colourSchemes/purinepyrimidine.html"/>
+   <mapID target="colours.rnahelices" url="html/colourSchemes/rnahelicesColouring.html"/>
    
    <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
+   <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>  
    <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
    
+   <mapID target="nucleicAcids" url="html/na/index.html"/>
+   
    <mapID target="menus" url="html/menus/index.html"/>
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
    <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
@@ -98,6 +125,7 @@
    <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" />