2.1 updates

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 77f105e..9265599 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,21 +3,28 @@
 <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="EBI Sequence Fetcher" target="seqfetch"/>\r
-                <tocitem text="New Output Format Controls" target="preferences"/>\r
-                <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>\r
-                <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
+               <tocitem text="MAFFT Alignment" target="mafft"/>\r
+               <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
+               <tocitem text="Hide Regions" target="hiddenRegions"/>            \r
         </tocitem>\r
-       <tocitem text="Release History" target="release"/>\r
-       <tocitem text="Alignment Annotations" target ="alannotation"/>\r
-       \r
-       <tocitem text="Input / Output" target="io"/>\r
+        <tocitem text="Release History" target="release"/>\r
+        <tocitem text="Editing Alignments" target ="edit"/>    \r
+        <tocitem text="Cursor Mode" target="cursor"/>\r
        <tocitem text="Key Strokes" target="keys"/>\r
+       <tocitem text="Input / Output" target="io"/>\r
        <tocitem text="Making figures" target="export"/>\r
-       <tocitem text="Editing Alignments" target ="edit"/>\r
+       <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
+       <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\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 text="User Defined Sequence Features" target="search"/>\r
+          <tocitem text="DAS Features Settings" target="das.settings"/>\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="MAFFT Alignment" target="mafft"/>\r
                <tocitem text="JNet Prediction" target="jnet"/>\r
        </tocitem>\r
        <tocitem text="Colour Schemes" target="colours" expand="false">\r
@@ -35,6 +42,7 @@
                <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
@@ -43,6 +51,12 @@
                <tocitem text="Pairwise Alignments" target="pairwise"/>\r
                <tocitem text="Remove Redundancy" target="redundancy"/>\r
        </tocitem>\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="Consensus" target="calcs.consensus"/>\r
+          <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
+        </tocitem>\r
        <tocitem text="Window Menus" target="menus" expand="false">\r
                <tocitem text="Desktop Window" target="desktopMenu"/>\r
                <tocitem text="Alignment Window" target="alMenu">\r
@@ -51,15 +65,18 @@
                 <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="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