JAL-2791 JAL-2808 correct Javadoc for api method

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 6f3b02a..77ddd88 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,12 +23,9 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
-                               <tocitem text="Split Frame View" target="splitframe" />
-                               <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-                               <tocitem text="PDB Structure Chooser" target="pdbchooser" />
-                               <tocitem text="Chimera Viewer" target="chimera" />
-                               <tocitem text="Select columns by annotation" target="selectcolbyannot" />
                                <tocitem text="Latest Release Notes" target="release"/>
+                               <tocitem text="Structure Chooser" target="pdbchooser"/>
+                               <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -49,7 +46,7 @@
                <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
                <tocitem text="Fetching Sequences" target="seqfetch" />         
                
-               <tocitem text="Select columns by annotation" target="selectcolbyannot" />
+               <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
                
                <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
                        <tocitem text="Viewing RNA structure" target="varna" />
@@ -63,8 +60,6 @@
                        <tocitem text="Feature Colourschemes" target="features.featureschemes" />
                        <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" />
                        <tocitem text="HTML annotation report" target="io.seqreport" />
                </tocitem>
                
@@ -75,14 +70,13 @@
                        <tocitem text="Sequence Alignment" target="msaservice"  expand="false">
                                <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
                        </tocitem>
-                       <tocitem text="Secondary Structure Prediction" target="jnet" />
+                       <tocitem text="Secondary Structure Prediction" target="jpred" />
                        <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
                        <tocitem text="Protein Disorder Prediction" target="disorder" />
                        <tocitem text="Alignment Conservation Analysis" target="aacon" />
                        <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
                        <tocitem text="Sequence Retrieval" target="seqfetch" />
-                       <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
-                       <tocitem text="DAS Feature Retrieval" target="das.viewing" />
+                       <tocitem text="Database Reference Retrieval" target="dbreffetcher" />                   
                </tocitem>
                
                <tocitem text="Colour Schemes" target="colours" expand="false">
@@ -107,10 +101,12 @@
                        <tocitem text="By RNA Helices" target="colours.rnahelices" />
                </tocitem>
                
-               <tocitem text="Calculations" target="calculations" expand="false">
+               <tocitem text="Calculations" expand="false">
                        <tocitem text="Sorting alignments" target="sorting" />
-                       <tocitem text="Calculating trees" target="trees" />
-                       <tocitem text="Principal Component Analysis" target="pca" />
+                       <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+                         <tocitem text="Calculating trees" target="trees" />
+                         <tocitem text="Principal Component Analysis" target="pca" />
+                       </tocitem>
                        <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
                        <tocitem text="Pairwise Alignments" target="pairwise" />
                        <tocitem text="Remove Redundancy" target="redundancy" />
@@ -127,16 +123,18 @@
                        <tocitem text="Consensus" target="calcs.consensus" />
                        <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
                        <tocitem text="Annotations File Format" target="annotations.fileformat" />
-                       <tocitem text="Select Column by Annotation" target="calcs.annotation" />
+                       <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
                </tocitem>
                <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
                        <tocitem text="PDB Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
-                       <tocitem text="Chimera Viewer" target="chimera" />
-                       <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+                       <tocitem text="Chimera Viewer" target="chimera" />                      
                </tocitem>
                <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+               <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+                   <tocitem text="Configuring URL Links" target="linksprefs" />
+               </tocitem>
                <tocitem text="VAMSAS Data Exchange" target="vamsas">
                        <!-- what can Jalview share with other apps -->
                        <!-- what other apps exist -->
@@ -151,7 +149,7 @@
                                <tocitem text="Annotations Menu" target="alwAnnotations" />
                                <tocitem text="Format Menu" target="alwFormat" />
                                <tocitem text="Colour Menu" target="alwColour" />
-                               <tocitem text="Calculation Menu" target="alwCalc" />
+                               <tocitem text="Calculate Menu" target="alwCalc" />
                                <tocitem text="Web Service Menu" target="wsMenu" />
                                <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
                                <tocitem text="Popup Menu" target="popMenu" />
@@ -159,9 +157,11 @@
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
                <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Scripting with Groovy" target="groovy">
+                       <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+               </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
                        <tocitem text="Command Line Arguments" target="clarguments" />
-                       <tocitem text="Groovy Shell" target="groovy" />
                </tocitem>
                <tocitem text="Privacy" target="privacy" />
        </tocitem>