From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 16 Mar 2020 17:51:38 +0000 (+0000)
Subject: JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings... 
X-Git-Tag: Develop-2_11_2_0-d20201215~76
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5adb410f9f92defbfe2ec572584c2f6f4d133022

JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings for linked cds/protein views
---

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 6b0a1c0..aecd1a4 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -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"/>
diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 5374e1a..5802ddb 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -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
new file mode 100644
index 0000000..7b45a32
Binary files /dev/null and b/help/help/html/features/linkedfeatsettings.png differ
diff --git a/help/help/html/features/splitView.html b/help/help/html/features/splitView.html
index e1c07c1..03b9ced 100644
--- a/help/help/html/features/splitView.html
+++ b/help/help/html/features/splitView.html
@@ -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>