JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index bf1710c..f3311a7 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,10 +23,13 @@
 <!-- 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="Retrieval from ENSEMBL" target="ensemblfetch" />
-                               <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
-                               <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
                                <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="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" />
@@ -73,7 +76,7 @@
                        <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" />
@@ -107,8 +110,10 @@
                
                <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" />
@@ -134,6 +139,9 @@
                        <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 -->
@@ -157,7 +165,7 @@
                <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" />