Added menus

diff --git a/help/help.jhm b/help/help.jhm
index 9eda491..44f072b 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -10,15 +10,13 @@
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
    \r
    <mapID target="webservice" url="html/webServices/index.html"/>\r
-   <mapID target="clustal" url="html/webServices/msaws.html#clustal"/>\r
-   <mapID target="muscle" url="html/webServices/msaws.html#muscle"/>\r
+   <mapID target="clustal" url="html/webServices/clustal.html"/>\r
    \r
    <mapID target="io" url="html/io/index.html"/>\r
    <mapID target="edit" url="html/editing/index.html"/>\r
-\r
-   <mapID target="sorting" url="html/calculations/sorting.html"/>\r
+   \r
+   <mapID target="calculations" url="html/calculations/index.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r
-   <mapID target="treeview" url="html/calculations/treeviewer.html"/>\r
    <mapID target="pca" url="html/calculations/pca.html"/>\r
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
@@ -39,6 +37,12 @@
    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
    <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
    \r
+   <mapID target="menus" url="html/menus/index.html"/>\r
+   <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r
+   <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>\r
+   <mapID target="popMenu" url="html/menus/popupMenu.html"/>\r
+   \r
+   \r
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />\r
    \r

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 160021c..ca759ee 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -8,14 +8,11 @@
                <tocitem text="Overview Window" target ="overview"/>\r
                <tocitem text="Sequence Features" target ="seqfeatures"/>\r
        </tocitem>\r
-       <tocitem text="Web Services" target="webservice" expand="false">\r
-                <tocitem text="Clustal Alignment" target="clustal"/>\r
-                <tocitem text="Muscle Alignment" target="muscle"/>\r
-                <tocitem text="JNet Secondary Structure Prediction" target="jnet"/>\r
-       </tocitem>\r
        <tocitem text="Input /Output" target="io"/>\r
        <tocitem text="Editing Alignment" target ="edit"/>\r
-       <tocitem text="Viewing Trees" target ="treeview"/>\r
+       <tocitem text="Web Services" target="webservice" expand="false">\r
+               <tocitem text="Clustal Alignment" target="clustal"/>\r
+       </tocitem>\r
        <tocitem text="Colour Schemes" target="colours" expand="false">\r
                <tocitem text="ClustalX" target="colours.clustal"/>\r
                <tocitem text="Zappo" target="colours.zappo"/>\r
@@ -32,13 +29,17 @@
                <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
                <tocitem text="By conservation" target="colours.conservation"/>\r
        </tocitem>\r
-       <tocitem text="Calculations" expand="false">\r
-                <tocitem text="Sorting alignments" target="sorting"/>\r
+       <tocitem text="Calculations" target="calculations" expand="false">\r
                <tocitem text="Calculating trees" target="trees"/>\r
                <tocitem text="Principal Component Analysis" target="pca"/>\r
                <tocitem text="Pairwise Alignments" target="pairwise"/>\r
                <tocitem text="Remove Redundancy" target="redundancy"/>\r
        </tocitem>\r
+       <tocitem text="Menus" target="menus" expand="false">\r
+               <tocitem text="Desktop Menu" target="desktopMenu"/>\r
+               <tocitem text="Alignment Menu" target="alMenu"/>\r
+               <tocitem text="Popup Menu" target="popMenu"/>\r
+       </tocitem>\r
 </tocitem>\r
 <tocitem text="Useful information" expand="false">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r