JAL-384 documentation on custom colours groovy examples

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 38b479b..a8aadf5 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 2.9.0b2)
- * 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 +23,12 @@
 <!-- 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="Groovy Features Counter example" target="groovy.featurescounter"/>
+                               <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
+                               <tocitem text="Omit hidden regions in Overview" target="overview"/>
+                               <tocitem text="identifers.org for URL Links" target="linksprefs" />
+                               <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -49,7 +49,7 @@
                <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" />
@@ -75,7 +75,7 @@
                        <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" />
@@ -107,7 +107,7 @@
                        <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" />
@@ -127,16 +127,18 @@
                        <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 +153,7 @@
                                <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 +161,11 @@
                </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>