Merge branch 'develop' into feature/JAL-3187linkedFeatures

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

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index ac0e82a..92947e2 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -112,6 +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)
@@ -188,15 +195,24 @@ public class CrossRefAction implements Runnable
 
       /*
        * apply 'database source' feature configuration
-       * if any was found
+       * if any - first to the new splitframe view about to be displayed
        */
-      // TODO is this the feature colouring for the original
-      // alignment or the fetched xrefs? either could be Ensembl
+
       newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
       copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
 
+      /*
+       * and for JAL-3330 also to original alignFrame view(s)
+       * this currently trashes any original settings.
+       */
+      for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+        origpanel.getAlignViewport()
+                .mergeFeaturesStyle(featureColourScheme);
+      }
+
       SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
               dna ? newFrame : copyThis);
+
       newFrame.setVisible(true);
       copyThis.setVisible(true);
       String linkedTitle = MessageManager