JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings...
authorJim Procter <jprocter@issues.jalview.org>
Mon, 16 Mar 2020 17:51:38 +0000 (17:51 +0000)
committerJim Procter <jprocter@issues.jalview.org>
Mon, 16 Mar 2020 17:56:46 +0000 (17:56 +0000)
help/help/help.jhm
help/help/helpTOC.xml
help/help/html/features/linkedfeatsettings.png [new file with mode: 0644]
help/help/html/features/splitView.html

index 6b0a1c0..aecd1a4 100755 (executable)
@@ -75,6 +75,7 @@
    <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"/>
index 5374e1a..5802ddb 100755 (executable)
@@ -24,6 +24,7 @@
        <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" />
                                
diff --git a/help/help/html/features/linkedfeatsettings.png b/help/help/html/features/linkedfeatsettings.png
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       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>