JAL-2588 overview tab docs, whats new and release notes

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 52eaf85..4636ea3 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,9 +24,13 @@
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Latest Release Notes" target="release"/>
+        <tocitem text="Calculations Dialog" target="calcs.dialog"/>
                                <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="Split Frame View" target="splitframe.mirrorfonts" />
+                               <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
+                               <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" />
@@ -107,8 +111,10 @@
                
                <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" />