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 a8aadf5..77ddd88 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,11 +24,8 @@
        <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="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 text="Structure Chooser" target="pdbchooser"/>
+                               <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -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>
                
@@ -81,8 +76,7 @@
                        <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">
@@ -109,8 +103,10 @@
                
                <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" />