X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FCrossRefAction.java;h=7045481888189468fe594b0a7ff8e6d96b8dc4a3;hb=9fcb12165750b20f8a73d0bb976b22be5fda94a2;hp=285e57498f124aa7c6de0e6d38a230a54a09ede2;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 285e574..7045481 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -143,7 +143,7 @@ public class CrossRefAction implements Runnable
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (Cache.getDefault("HIDE_INTRONS", true))
       {
-        newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+        newFrame.hideFeatureColumns(false, SequenceOntologyI.EXON);
       }
       String newtitle = String.format("%s %s %s",
               dna ? MessageManager.getString("label.proteins")
@@ -176,10 +176,14 @@ public class CrossRefAction implements Runnable
       /*
        * copy feature rendering settings to split frame
        */
-      newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
-      copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
+      FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr1.transferSettings(myFeatureStyling);
+      fr1.findAllFeatures(true);
+      FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr2.transferSettings(myFeatureStyling);
+      fr2.findAllFeatures(true);
 
       /*
        * apply 'database source' feature configuration