X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=f6bb7c71309f947a5fdcd056d3492b3c759a5ad9;hb=HEAD;hp=84909700ae3115e8ea00afb221c88572aba45bd6;hpb=8063681d24eb8536bf529fadf8835b51080294a0;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
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-<?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
--->
-<!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="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"/>
-	<tocitem text="Key Strokes" target="keys"/>
-	<tocitem text="Input / Output" target="io"/>
-  	<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"/>
-	  <tocitem text="DAS Feature Settings" target="das.settings"/>
-        </tocitem>
-	<tocitem text="Web Services" target="webservice" expand="false">
-          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
-		<tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
-                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
-            </tocitem>
-          <tocitem text="Secondary Structure Prediction" target="jnet"/>
-		<tocitem text="Sequence Retrieval" target="seqfetch"/>
-		<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"/>
-		<tocitem text="ClustalX" target="colours.clustal"/>
-		<tocitem text="Zappo" target="colours.zappo"/>
-		<tocitem text="Taylor" target="colours.taylor"/>
-		<tocitem text="Hydrophobicity" target="colours.hydro"/>
-		<tocitem text="Helix propensity" target="colours.helix"/>
-		<tocitem text="Strand propensity" target="colours.strand"/>
-		<tocitem text="Turn propensity" target="colours.turn"/>
-		<tocitem text="Buried index" target="colours.buried"/>
-		<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
-		<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>
-	<tocitem text="Calculations" target="calculations" expand="false">
-		<tocitem text="Sorting alignments" target="sorting"/>
-                <tocitem text="Calculating trees" target="trees"/>
-		<tocitem text="Principal Component Analysis" target="pca"/>
-              	<tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
-		<tocitem text="Pairwise Alignments" target="pairwise"/>
-		<tocitem text="Remove Redundancy" target="redundancy"/>
-	</tocitem>
-  	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
-          <tocitem text="Quality" target="calcs.alquality"/>
-          <tocitem text="Consensus" target="calcs.consensus"/>
-          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
-        </tocitem>
-	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
-	  <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">
-                <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>
-				<tocitem text="Select Menu" target="alwSelect"/> 
-                <tocitem text="View Menu" target="alwView"/>
-				<tocitem text="Format Menu" target="alwFormat"/>
-                <tocitem text="Colour Menu" target="alwColour"/>
-                <tocitem text="Calculation Menu" target="alwCalc"/>
-		<tocitem text="Web Service Menu" target="wsMenu"/>
-		<tocitem text="Annotation Menus" target="annotMenus"/>
-		<tocitem text="Popup Menu" target="popMenu"/>
-                </tocitem>
-	</tocitem>
-        <tocitem text="Preferences" target="preferences"/>
-	<tocitem text="Memory Settings" target="memory" expand="false">
-          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
-          </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"/>
-	<tocitem text="Amino Acid Properties" target="aaProperties"/>
-	<tocitem text="The Genetic Code" target="geneticCode"/>
-</tocitem>
-</toc>