Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 77ddd88..6d7c948 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,9 +23,10 @@
 <!-- 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="Latest Release Notes" target="release"/>
-                               <tocitem text="Structure Chooser" target="pdbchooser"/>
-                               <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+                       <tocitem text="Latest Release Notes" target="release"/>
+                       <tocitem text="Next Generation Command Line Interface" target="clarguments" />
+                       <tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
+                       <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />                            
                </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" />
@@ -60,6 +62,7 @@
                        <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>
                
@@ -84,12 +87,17 @@
                        <tocitem text="ClustalX" target="colours.clustal" />
                        <tocitem text="Zappo" target="colours.zappo" />
                        <tocitem text="Taylor" target="colours.taylor" />
+                       <tocitem text="gecos Flower" target="colours.gecos-flower" />
+                       <tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+                       <tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+                       <tocitem text="gecos Ocean" target="colours.gecos-ocean" />
                        <tocitem text="Hydrophobicity" target="colours.hydro" />
                        <tocitem text="Helix propensity" target="colours.helix" />
                        <tocitem text="Strand propensity" target="colours.strand" />
                        <tocitem text="Turn propensity" target="colours.turn" />
                        <tocitem text="Buried index" target="colours.buried" />
                        <tocitem text="Nucleotide colours" target="colours.nucleotide" />
+                       <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
                        <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
                        <tocitem text="Blosum62" target="colours.blosum" />
                        <tocitem text="by Percentage Identity" target="colours.pid" />
@@ -127,18 +135,15 @@
                </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">
@@ -156,15 +161,22 @@
                        </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 text="Command Line: introduction and reference" target="clarguments" />
+                       <tocitem text="Command Line: basic usage" target="clarguments-basic" />
+                       <tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
+                       <tocitem text="Command Line: argument files" target="clarguments-argfiles" />
+                       <tocitem text="Command Line: reference" target="clarguments-reference" />
+                       <tocitem text="Command Line: old command line arguments" target="clarguments-old" />
                </tocitem>
+               <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
                <tocitem text="Privacy" target="privacy" />
-       </tocitem>
+    </tocitem>
        <tocitem text="Useful information" expand="true">
                <tocitem text="Amino Acid Table" target="aminoAcids" />
                <tocitem text="Amino Acid Properties" target="aaProperties" />