From b5224b96766a131efd6c4b738058aaf1d0b3ecad Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 May 2005 14:43:56 +0000
Subject: [PATCH] Added menus

---
 help/help.jhm    |   14 +++++++++-----
 help/helpTOC.xml |   17 +++++++++--------
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/help/help.jhm b/help/help.jhm
index 9eda491..44f072b 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -10,15 +10,13 @@
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    
    <mapID target="webservice" url="html/webServices/index.html"/>
-   <mapID target="clustal" url="html/webServices/msaws.html#clustal"/>
-   <mapID target="muscle" url="html/webServices/msaws.html#muscle"/>
+   <mapID target="clustal" url="html/webServices/clustal.html"/>
    
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
-
-   <mapID target="sorting" url="html/calculations/sorting.html"/>
+   
+   <mapID target="calculations" url="html/calculations/index.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
-   <mapID target="treeview" url="html/calculations/treeviewer.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
@@ -39,6 +37,12 @@
    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
    <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
    
+   <mapID target="menus" url="html/menus/index.html"/>
+   <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
+   <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
+   <mapID target="popMenu" url="html/menus/popupMenu.html"/>
+   
+   
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />
    
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 160021c..ca759ee 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -8,14 +8,11 @@
 		<tocitem text="Overview Window" target ="overview"/>
 		<tocitem text="Sequence Features" target ="seqfeatures"/>
 	</tocitem>
-	<tocitem text="Web Services" target="webservice" expand="false">
-                <tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="JNet Secondary Structure Prediction" target="jnet"/>
-	</tocitem>
 	<tocitem text="Input /Output" target="io"/>
 	<tocitem text="Editing Alignment" target ="edit"/>
-  	<tocitem text="Viewing Trees" target ="treeview"/>
+	<tocitem text="Web Services" target="webservice" expand="false">
+		<tocitem text="Clustal Alignment" target="clustal"/>
+	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
 		<tocitem text="Zappo" target="colours.zappo"/>
@@ -32,13 +29,17 @@
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
 	</tocitem>
-	<tocitem text="Calculations" expand="false">
-                <tocitem text="Sorting alignments" target="sorting"/>
+	<tocitem text="Calculations" target="calculations" expand="false">
 		<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="Menus" target="menus" expand="false">
+		<tocitem text="Desktop Menu" target="desktopMenu"/>
+		<tocitem text="Alignment Menu" target="alMenu"/>
+		<tocitem text="Popup Menu" target="popMenu"/>
+	</tocitem>
 </tocitem>
 <tocitem text="Useful information" expand="false">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
-- 
1.7.10.2