JAL-2490 find features for export as GFF, JAL-2548 respect group

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index a48c030..42913de 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -34,6 +34,7 @@ import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.List;
 import java.util.Map;
 
 import javax.swing.BorderFactory;
@@ -160,16 +161,18 @@ public class AnnotationExporter extends JPanel
       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
       Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
               .getDisplayedFeatureCols();
+      List<String> featureGroups = ap.getFeatureRenderer()
+              .getDisplayedFeatureGroups();
       boolean includeNonPositional = ap.av.isShowNPFeats();
       if (GFFFormat.isSelected())
       {
         text = formatter.printGffFormat(sequences, featureColours,
-                includeNonPositional);
+                featureGroups, includeNonPositional);
       }
       else
       {
         text = formatter.printJalviewFormat(sequences, featureColours,
-                includeNonPositional);
+                featureGroups, includeNonPositional);
       }
     }
     else