X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=f6bb7c71309f947a5fdcd056d3492b3c759a5ad9;hb=HEAD;hp=4c09e8f993a08ad044d7a124d226f2657ebfd0b8;hpb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- * 
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<!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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
-    <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
-    <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
-    <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
-  </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="Nucleic Acid Support" target="nucleicAcids" expand="false">
-		<tocitem text="Viewing RNA structure" target="varna" />
-		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
-		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
-	</tocitem>
-	<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 text="HTML annotation report" target="io.seqreport"/>
-        </tocitem>
-	<tocitem text="Web Services" target="webservice" expand="false">
-	<tocitem text="JABAWS" target="jabaws"/>
-	<tocitem text="Web Service Preferences" target="wsprefs"/>
-	<tocitem text="Web Service Parameters" target="wsparams"/>
-	<tocitem text="Sequence Alignment" target="msaservice" expand="false">
-                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
-            </tocitem>
-          <tocitem text="Secondary Structure Prediction" target="jnet"/>
-          <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
-          <tocitem text="Protein Disorder Prediction" target="disorder"/>
-          <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-          <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
-		<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"/>
-		<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="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
-		<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="T-COFFEE Scores" target="io.tcoffeescores"/>
-		<tocitem text="By Annotation" target="colours.annotation"/>
-		<tocitem text="By RNA Helices" target="colours.rnahelices"/>
-	</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="RNA Structure Consensus" target="calcs.alstrconsensus"/>
-          <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="Viewing RNA structures" target="varna" expand="false">	</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="Annotations Menu" target="alwAnnotations"/>
-			<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 Panel Menu" target="annotPanelMenu"/>
-			<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" expand="true">
-	<tocitem text="Amino Acid Table" target="aminoAcids"/>
-	<tocitem text="Amino Acid Properties" target="aaProperties"/>
-	<tocitem text="The Genetic Code" target="geneticCode"/>
-	<tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
-  
-</tocitem>
-</toc>