JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings...

[jalview.git] / help / help / html / features / splitView.html

diff --git a/help/help/html/features/splitView.html b/help/help/html/features/splitView.html
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@@ -40,6 +40,30 @@
       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>