Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[jalview.git] / src / jalview / gui / CrossRefAction.java

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 673bcc0..92947e2 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -39,6 +39,7 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.ws.SequenceFetcher;
 
 import java.util.ArrayList;
@@ -111,6 +112,13 @@ 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)
@@ -170,17 +178,17 @@ public class CrossRefAction implements Runnable
               .isShowSequenceFeatures();
       newFrame.setShowSeqFeatures(showSequenceFeatures);
       copyThis.setShowSeqFeatures(showSequenceFeatures);
-      FeatureRenderer myFeatureStyling = alignFrame.alignPanel
+      FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
               .getSeqPanel().seqCanvas.getFeatureRenderer();
 
       /*
        * copy feature rendering settings to split frame
        */
-      FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+      FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       fr1.transferSettings(myFeatureStyling);
       fr1.findAllFeatures(true);
-      FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+      FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       fr2.transferSettings(myFeatureStyling);
       fr2.findAllFeatures(true);