From: Jim Procter 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/?a=commitdiff_plain;h=5adb410f9f92defbfe2ec572584c2f6f4d133022;p=jalview.git 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 @@ + 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 @@ + 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. In the Jalview Desktop, Split Frame views are saved in Jalview Projects, like any other alignment view.

+

Virtual Sequence Features +

+

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.

+

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.

+

+ Linked CDS and Protein Feature Settings showing Virtual Feature checkbox 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). +

+

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).

Operations supported in Split Frame Mode