X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=f6bb7c71309f947a5fdcd056d3492b3c759a5ad9;hb=HEAD;hp=4ce98922ca1089f0ac716a59ea809160c9b71c0c;hpb=023d23abaad346f745b93fced2407d7342ab7171;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
deleted file mode 100755
index 4ce9892..0000000
--- a/help/helpTOC.xml
+++ /dev/null
@@ -1,147 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * 
-	Copyright (C) $$Year-Rel$$ 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">
-<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
-	<tocitem text="Jalview Documentation" target="home" expand="true">
-		<tocitem text="What's new" target="new" expand="true">
-			<tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
-			<tocitem text="Annotation Panel Menu" target="alwAnnotations" />
-			<tocitem text="Add reference annotation" target="popMenuAddref" />
-			<tocitem text="Colour By Annotation" target="colours.annotation" />
-			<tocitem text="Chimera Viewer" target="chimera" />
-			<tocitem text="Structure Preferences" target="strucprefs" />
-		</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="Split Frame View" target="splitframe" />
-		<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 text="Select Column by Annotation" target="calcs.annotation" />
-		</tocitem>
-		<tocitem text="Sequence Annotations" target="seqannots"	expand="true">
-			<tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
-		</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="Chimera Viewer" target="chimera" />
-			<tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
-		</tocitem>
-		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
-		<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="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>