Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 77ddd88..7e358d6 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,8 +24,9 @@
        <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="Structure Chooser" target="pdbchooser"/>
-                               <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+                               <tocitem text="VCF Import" target="importvcf"/>
+                               <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+                               
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +50,7 @@
                <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
                
                <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+                 <tocitem text="Annotating from VCF" target="importvcf" /> 
                        <tocitem text="Viewing RNA structure" target="varna" />
                        <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
                        <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
@@ -135,10 +137,6 @@
                <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 -->
-               </tocitem>
                <tocitem text="Window Menus" target="menus" expand="false">
                        <tocitem text="Desktop Window" target="desktopMenu" />
                        <tocitem text="Alignment Window" target="alMenu">
@@ -156,13 +154,14 @@
                        </tocitem>
                </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>
+    <tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
+    </tocitem>
                <tocitem text="Privacy" target="privacy" />
        </tocitem>
        <tocitem text="Useful information" expand="true">