updated menus and rearranged seqfeatures (again)

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5c48b5a..6630a0a 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,15 +3,30 @@
 <toc version="1.0">\r
 <tocitem text="Jalview Documentation" target="home" expand="true" >\r
        <tocitem text="What's new" target="new" expand="false">\r
-               <tocitem text="Search" target="search"/>\r
-               <tocitem text="Wrap Alignment" target="wrap"/>\r
-               <tocitem text="Overview Window" target ="overview"/>\r
-               <tocitem text="Sequence Features" target ="seqfeatures"/>\r
-               <tocitem text="Alignment Annotations" target ="alannotation"/>\r
-       </tocitem>\r
+          <tocitem text="Cursor Mode" target="cursor"/>\r
+          <tocitem text="Selection Area Based Editing" target="edit.selareas"/>\r
+          <tocitem text="User Defined Sequence Features" target="search"/>\r
+          <tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
+          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+          <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
+          <tocitem text="Annotations File" target="annotations.fileformat"/>\r
+          <tocitem text="Colour by Annotation Value" target="colours.annotation"/>\r
+          <tocitem text="Modeller PIR File IO" target="io.modellerpir"/>\r
+        </tocitem>\r
+       <tocitem text="Release History" target="release"/>\r
+       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+          <tocitem text="Conservation" target="calcs.alconserv"/>\r
+          <tocitem text="Quality" target="calcs.alquality"/>\r
+          <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
+        </tocitem>\r
        <tocitem text="Input / Output" target="io"/>\r
+       <tocitem text="Key Strokes" target="keys"/>\r
        <tocitem text="Making figures" target="export"/>\r
        <tocitem text="Editing Alignments" target ="edit"/>\r
+       <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
+          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+          <tocitem text="Sequence Features File" target="features.fileformat"/>\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
@@ -32,6 +47,7 @@
                <tocitem text="User Defined" target="colours.user"/>\r
                <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
                <tocitem text="By conservation" target="colours.conservation"/>\r
+               <tocitem text="By Annotation" target="colours.annotation"/>\r
        </tocitem>\r
        <tocitem text="Calculations" target="calculations" expand="false">\r
                <tocitem text="Sorting alignments" target="sorting"/>\r
@@ -44,18 +60,22 @@
                <tocitem text="Desktop Window" target="desktopMenu"/>\r
                <tocitem text="Alignment Window" target="alMenu">\r
                 <tocitem text="File Menu" target="alwFile"/>\r
-                <tocitem text="Edit Menu" target="alwEdit"/>  \r
+                <tocitem text="Edit Menu" target="alwEdit"/> \r
+                <tocitem text="View Menu" target="alwView"/> \r
                 <tocitem text="Colour Menu" target="alwColour"/>\r
                 <tocitem text="Calculation Menu" target="alwCalc"/>\r
-                               <tocitem text="Web Service Menu" target="wsMenu"/>\r
+               <tocitem text="Web Service Menu" target="wsMenu"/>\r
                <tocitem text="Annotation Menus" target="annotMenus"/>\r
                <tocitem text="Popup Menu" target="popMenu"/>\r
                 </tocitem>\r
        </tocitem>\r
-       <tocitem text="Memory Settings" target="memory"/>\r
+       <tocitem text="Memory Settings" target="memory" expand="false">\r
+          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
+          </tocitem>\r
 </tocitem>\r
-<tocitem text="Useful information" expand="false">\r
+<tocitem text="Useful information" expand="true">\r
        <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
+       <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
        <tocitem text="The Genetic Code" target="geneticCode"/>\r
 </tocitem>\r
 </toc>\r