mapping implemented by MapList added to DBRefEntry.

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c91faff..7d9e595 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,11 +2,7 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-       <tocitem text="What's new" target="new" expand="true">
-         <tocitem text="Multiple Views" target="multipleviews"/>
-         <tocitem text="Reload and Save" target="reloadsave"/>
-         <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
-        </tocitem>
+       <tocitem text="What's new" target="new" expand="true"/>
         <tocitem text="Release History" target="release"/>
         <tocitem text="Editing Alignments" target ="edit"/>    
         <tocitem text="Cursor Mode" target="cursor"/>
@@ -15,10 +11,11 @@
        <tocitem text="Making figures" target="export"/>
        <tocitem text="Hidden Regions" target="hiddenRegions"/>
        <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
+       <tocitem text="Multiple Views" target="multipleviews"/>
        <tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
-          <tocitem text="User Defined Sequence Features" target="search"/>
+          <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
                  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
          <tocitem text="DAS Feature Settings" target="das.settings"/>
@@ -33,6 +30,7 @@
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
        </tocitem>
        <tocitem text="Colour Schemes" target="colours" expand="false">
+               <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
                <tocitem text="ClustalX" target="colours.clustal"/>
                <tocitem text="Zappo" target="colours.zappo"/>
                <tocitem text="Taylor" target="colours.taylor"/>
@@ -67,8 +65,10 @@
                <tocitem text="Desktop Window" target="desktopMenu"/>
                <tocitem text="Alignment Window" target="alMenu">
                 <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/> 
-                <tocitem text="View Menu" target="alwView"/> 
+                <tocitem text="Edit Menu" target="alwEdit"/>
+                               <tocitem text="Select Menu" target="alwSelect"/> 
+                <tocitem text="View Menu" target="alwView"/>
+                               <tocitem text="Format Menu" target="alwFormat"/>
                 <tocitem text="Colour Menu" target="alwColour"/>
                 <tocitem text="Calculation Menu" target="alwCalc"/>
                <tocitem text="Web Service Menu" target="wsMenu"/>
@@ -76,11 +76,15 @@
                <tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
        </tocitem>
+        <tocitem text="Preferences" target="preferences"/>
        <tocitem text="Memory Settings" target="memory" expand="false">
           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
           </tocitem>
+        <tocitem text="Command Line" target="commandline" expand="false">
+          <tocitem text="Command Line Arguments" target="clarguments"/>
+        </tocitem>
 </tocitem>
-<tocitem text="Useful information" expand="true">
+<tocitem text="Useful information" expa nd="true">
        <tocitem text="Amino Acid Table" target="aminoAcids"/>
        <tocitem text="Amino Acid Properties" target="aaProperties"/>
        <tocitem text="The Genetic Code" target="geneticCode"/>