JAL-4023 store distances as doubles

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

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 77ddd88..a9b9788 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,8 +24,12 @@
        <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="Support for ChimeraX" target="chimera"/>
+                               <tocitem text="Support for Pymol" target="pymol"/>
+                               <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
+                               <tocitem text="Startup Memory Settings" target="startupprefs" />
+                       <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+                       <tocitem text="Command line launch scripts" target="jalviewcltool"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +53,7 @@
                <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" />
@@ -60,6 +65,7 @@
                        <tocitem text="Feature Colourschemes" target="features.featureschemes" />
                        <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
                        <tocitem text="Editing Sequence Features" target="seqfeatedit" />
+                       <tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
                        <tocitem text="HTML annotation report" target="io.seqreport" />
                </tocitem>
                
@@ -127,18 +133,15 @@
                </tocitem>
                <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-                       <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+                       <tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
-                       <tocitem text="Chimera Viewer" target="chimera" />                      
+                       <tocitem text="Chimera/X Viewer" target="chimera" />
+                       <tocitem text="Pymol Viewer" target="pymol" />                  
                </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 -->
-               </tocitem>
                <tocitem text="Window Menus" target="menus" expand="false">
                        <tocitem text="Desktop Window" target="desktopMenu" />
                        <tocitem text="Alignment Window" target="alMenu">
@@ -156,13 +159,15 @@
                        </tocitem>
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
-               <tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
                <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">