X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=4636ea36f8398fb4e9aa7b069c5ee2ce77abc90f;hb=ea2cf1fb34a7630388e87c058d994d2a4017f9e3;hp=75eb7df1bb0d985f86852f8752c2744840a6aa78;hpb=be80bb1a8c747f67cfbaa0d73ac4f31c7cd1b9b9;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 75eb7df..4636ea3 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,108 +1,183 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
+<!--
+ * 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.
+ -->
 <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="PDB Viewing with Jmol" target="pdbjmol"/>
-	  <tocitem text="Mapping between Sequences" target="seqmappings"/>
-		<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="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"/>
+<!-- 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="Latest Release Notes" target="release"/>
+        <tocitem text="Calculations Dialog" target="calcs.dialog"/>
+				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
+				<tocitem text="Omit hidden regions in Overview" target="overview"/>
+				<tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
+				<tocitem text="identifers.org for URL Links" target="linksprefs" />
+				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
+		</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" expand="false">
+			<tocitem text="BioJSON v1.0" target="biojson" />
+		</tocitem>
+		
+		<tocitem text="Making Figures" target="export" expand="false">
+			<tocitem text="BioJS MSA Viewer" target="biojsmsa" />
+		</tocitem>
+		
+		<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="Select Columns by Annotation" target="selectcolbyannot" />
+		
+		<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="jpred" />
+			<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" expand="false">
+			<tocitem text="Sorting alignments" target="sorting" />
+			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+  			  <tocitem text="Calculating trees" target="trees" />
+  			  <tocitem text="Principal Component Analysis" target="pca" />
+  			</tocitem>
+			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
+			<tocitem text="Pairwise Alignments" target="pairwise" />
+			<tocitem text="Remove Redundancy" target="redundancy" />
+			<tocitem text="Reference Sequences" target="referenceseq" />
+		</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 text="Select Columns by Annotation" target="selectcolbyannot" />
+		</tocitem>
+		<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
+			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+			<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+			<tocitem text="Jmol Viewer" target="pdbjmol" />
+			<tocitem text="Chimera Viewer" target="chimera" />			
+		</tocitem>
+		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+		    <tocitem text="Configuring URL Links" target="linksprefs" />
+		</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="Calculate 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="Scripting with Groovy" target="groovy">
+			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+		</tocitem>
+		<tocitem text="Command Line" target="commandline" expand="false">
+			<tocitem text="Command Line Arguments" target="clarguments" />
+		</tocitem>
+		<tocitem text="Privacy" target="privacy" />
 	</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 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>
-        <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>
-<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>