<mapID target="jalarchive" url="html/features/jalarchive.html"/>
<mapID target="multipleviews" url="html/features/multipleViews.html"/>
<mapID target="splitframe" url="html/features/splitView.html"/>
+ <mapID target="splitframe.virtualfeats" url="html/features/splitView.html#virtualfeats"/>
<mapID target="splitframe.mirrorfonts" url="html/features/splitView.html#mirror"/>
<mapID target="trees" url="html/calculations/tree.html"/>
<mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
<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="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" />
number of ways</a>. In the Jalview Desktop, Split Frame views are
saved in Jalview Projects, like any other alignment view.
</p>
+ <p><strong><a name="virtualfeats">Virtual Sequence Features</a></strong>
+ </p>
+ <p>Since Jalview 2.11.1, sequence features displayed in either CDS
+ or Protein can be shown as 'Virtual Features' mapped onto the other
+ view. Features describing non-synonymous genomic sequence variation
+ in coding regions are dynamically translated when shown in the
+ protein view.</p>
+ <p>The display of virtual features and whether they are rendered
+ below or above features local to the aligned sequences is controlled
+ by a check box shown in the view's Sequence Feature Settings dialog
+ box. For convenience, Protein and CDS feature settings for a linked
+ CDS/Protein view are shown as tabs in a single dialog box, allowing
+ easy access to display and filter settings for each view.</p>
+ <p>
+ <img width="631" align="center"
+ alt="Linked CDS and Protein Feature Settings showing Virtual Feature checkbox"
+ src="linkedfeatsettings.png" /> <em>CDS and Protein feature
+ settings tabs and corresponding views showing 'Virtual Features'
+ from each view overlaid on the other (created with Jalview 2.11.1.0).</em>
+ </p>
+ <p>When virtual features are enabled, they are also shown on any
+ linked 3D structure views when 'Colour by Sequence' is enabled, and
+ exported as GFF and Jalview Features files (mapped to their
+ associated virtual coordinates).</p>
<p>
<strong>Operations supported in Split Frame Mode</strong>
</p>