X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=0d2e09603d20afa99bbf88817e75c96bd5518e81;hb=e1a4dac21b9e7fb59d123bf3fa4e0f4f594c7f76;hp=d08e3d267bbe9ad049561c628ee05fa54fff60f5;hpb=3b58e33030c6cfe56564d17edcb9d81b750398fe;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index d08e3d2..0d2e096 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,82 +1,152 @@
-<?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">
-<toc version="1.0">
-<tocitem text="Jalview Documentation" target="home" expand="true" >
-	<tocitem text="What's new" target="new" expand="false">
-        	<tocitem text="MAFFT Alignment" target="mafft"/>
-        	<tocitem text="DAS Feature Fetching" target="das.settings"/>
-        	<tocitem text="Hide Regions" target="hiddenRegions"/> 	         
-        </tocitem>
-        <tocitem text="Release History" target="release"/>
-        <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="Viewing PDB Files" target="viewingpdbs"/>
-	<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="search"/>
-          <tocitem text="DAS Features Settings" target="das.viewing"/>
-        </tocitem>
-	<tocitem text="Web Services" target="webservice" expand="false">
-		<tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
-          	<tocitem text="JNet Prediction" target="jnet"/>
-	</tocitem>
-	<tocitem text="Colour Schemes" target="colours" expand="false">
-		<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="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="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="View Menu" target="alwView"/> 
-                <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="Memory Settings" target="memory" expand="false">
-          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
-          </tocitem>
-</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>
-</toc>
+<?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 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="Protein Disorder Prediction" target="disorder"/>
+    <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+		<tocitem text="Viewing RNA structure" target="varna" />
+		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+		<tocitem text="HTML annotation report" target="io.seqreport"/>
+		<tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
+		<tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
+	  <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
+	  <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
+	  <tocitem text="DNA or Protein PCA calculation" target="pca"/>
+	  <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
+	</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="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="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" 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>