<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="VCF Import" target="vcfimport"/>
+ <tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
+ <tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-
+ <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<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>
</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 & 3D-Beacons Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Chimera 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>
</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">