JAL-2698 what’s new and release notes

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 54abd53..20dd8db 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -104,8 +104,10 @@
                
                <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" />
@@ -131,6 +133,9 @@
                        <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 -->
@@ -154,7 +159,7 @@
                <tocitem text="Preferences" target="preferences" />
                <tocitem text="Memory Settings" target="memory" expand="false"/>
                <tocitem text="Scripting with Groovy" target="groovy">
-                       <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+                       <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" />