From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 28 Jun 2019 13:17:54 +0000 (+0100)
Subject: JAL-3330 apply Ensembl feature settings when showing crossrefs for alignment that... 
X-Git-Tag: Release_2_11_0~2^2~28^2~1
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=afa061b7ecd1bc011096d9f2879448185874fcd3

JAL-3330 apply Ensembl feature settings when showing crossrefs for alignment that looks like it was from Ensembl
---

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 673bcc0..9ad6596 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -111,6 +111,13 @@ public class CrossRefAction implements Runnable
       FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
               .getFeatureColourScheme(source);
 
+      if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+      {
+        // override default featureColourScheme so products have Ensembl variant colours
+        featureColourScheme = new SequenceFetcher()
+                .getFeatureColourScheme(DBRefSource.ENSEMBL);
+      }
+
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
               xrefs);
       if (!dna)