X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=f0403e772fae743856bb486b23b1df5a0812acf2;hb=92fa0de6fedeab36ad3290152e8290ceb07ab145;hp=bae82d4076f3062f2167f7e00f845de6f7801a17;hpb=d40ad6d5aa51ca4174a3da658b24059ae588098f;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index bae82d4..f0403e7 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,80 +1,128 @@
-<?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="Cursor Mode" target="cursor"/>
-          <tocitem text="Selection Area Based Editing" target="edit.selareas"/>
-          <tocitem text="User Defined Sequence Features" target="search"/>
-          <tocitem text="Sequence Feature Groups" target="seqfeatures"/>
-          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
-          <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>
-          <tocitem text="Annotations File" target="annotations.fileformat"/>
-          <tocitem text="Colour by Annotation Value" target="colours.annotation"/>
-        </tocitem>
-	<tocitem text="Release History" target="release"/>
-      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
-          <tocitem text="Quality" target="calcs.alquality"/>
-          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
-        </tocitem>
-	<tocitem text="Input / Output" target="io"/>
-	<tocitem text="Key Strokes" target="keys"/>
-  	<tocitem text="Making figures" target="export"/>
-	<tocitem text="Editing Alignments" target ="edit"/>
-	<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>
-	<tocitem text="Web Services" target="webservice" expand="false">
-		<tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-          	<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="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 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, 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="Graduated Feature Colours" target="features.featureschemes"/>
+      <tocitem text="Sort by Features" target="seqfeatures.settings"/>
+      <tocitem text="Envision2 Service" target="webservice"/>
+      <tocitem text="Release History" target="release"/>
+	</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="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="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>