X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=5dec60151db23f516f7905d85d17f448f1f92ae9;hb=ae3b7664d0d98f376b1f636edc34aaff6b8a914a;hp=c49436de681b6f1804a40b1cfadd8638afe92fc5;hpb=bfbc6adb2123ba3e4c267384c0d39849f888c794;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c49436d..5dec601 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,12 +1,38 @@
 <?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="Menus"  expand="true" >
-	<tocitem text="File" target="home"/>
-	<tocitem text="Edit" target="home"/>
-	<tocitem text="Font" target="home"/>
-	<tocitem text="View" target="home"/>
-	<tocitem text="Colour" target="colours">
+<tocitem text="Jalview Documentation" target="home" expand="true" >
+	<tocitem text="What's new" target="new" expand="false">
+        	<tocitem text="DAS Feature Fetching" target="das.settings"/>
+        	<tocitem text="Hide Regions" target="hiddenRegions"/>
+              	<tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
+        </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="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>
+          <tocitem text="Secondary Structure 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"/>
@@ -16,13 +42,45 @@
 		<tocitem text="Buried index" target="colours.buried"/>
 		<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
 		<tocitem text="Blosum62" target="colours.blosum"/>
-		<tocitem text="PID" target="colours.pid"/>		
+		<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="Calculate" target="calculate"/>
-	<tocitem text="Align" target="home"/>
+	<tocitem text="Memory Settings" target="memory" expand="false">
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
+          </tocitem>
 </tocitem>
-<tocitem text="Useful information">
+<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>