Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index beb77ca..a619997 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;
@@ -156,28 +157,22 @@ public class AnnotationExporter extends JPanel
             .getString("label.no_features_on_alignment");
     if (features)
     {
-      Map<String, FeatureColourI> displayedFeatureColours = ap
-              .getFeatureRenderer().getDisplayedFeatureCols();
       FeaturesFile formatter = new FeaturesFile();
       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 = new FeaturesFile().printGffFormat(
-                ap.av.getAlignment().getDataset().getSequencesArray(),
-                displayedFeatureColours, true, ap.av.isShowNPFeats());
-        text = formatter.printGffFormat(sequences, featureColours, true,
-                includeNonPositional);
+        text = formatter.printGffFormat(sequences, featureColours,
+                featureGroups, includeNonPositional);
       }
       else
       {
-        text = new FeaturesFile().printJalviewFormat(
-                ap.av.getAlignment().getDataset().getSequencesArray(),
-                displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
-        text = formatter.printJalviewFormat(sequences, featureColours, true,
-                includeNonPositional);
+        text = formatter.printJalviewFormat(sequences, featureColours,
+                featureGroups, includeNonPositional);
       }
     }
     else