To uppercase only visible

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 09c7125..5dec601 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,35 +3,33 @@
 <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="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 text="DAS Feature Fetching" target="das.settings"/>\r
+               <tocitem text="Hide Regions" target="hiddenRegions"/>\r
+               <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
+               <tocitem text="MAFFT Alignment" target="mafft"/>\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="Consensus" target="calcs.consensus"/>\r
-          <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
-        </tocitem>\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.viewing"/>\r
         </tocitem>\r
        <tocitem text="Web Services" target="webservice" expand="false">\r
+          <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
                <tocitem text="Clustal Alignment" target="clustal"/>\r
                 <tocitem text="Muscle Alignment" target="muscle"/>\r
-               <tocitem text="JNet Prediction" target="jnet"/>\r
+                <tocitem text="MAFFT Alignment" target="mafft"/>\r
+            </tocitem>\r
+          <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
        </tocitem>\r
        <tocitem text="Colour Schemes" target="colours" expand="false">\r
                <tocitem text="ClustalX" target="colours.clustal"/>\r
@@ -57,6 +55,12 @@
                <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