<!-- 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="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 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" />
<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="Memory Settings" target="memory" expand="false"/>
- <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
- </tocitem>
+ <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" />