X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=42913de3552978efe01060d60960153ac83a5750;hb=478b462be553125d574fd2f96f7c234b74f9f61b;hp=136a38e37a9e6ee6c16dae0bc5b0d644c869de8f;hpb=26ba864a6c290121fe6cf616794d2d0bea65fb7d;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 136a38e..42913de 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
@@ -33,6 +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;
@@ -156,20 +158,21 @@ public class AnnotationExporter extends JPanel
     if (features)
     {
       FeaturesFile formatter = new FeaturesFile();
-      SequenceI[] sequences = ap.av.getAlignment().getDataset()
-              .getSequencesArray();
-      Map<String, Object> featureColours = ap.getFeatureRenderer()
+      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, true,
-                includeNonPositional);
+        text = formatter.printGffFormat(sequences, featureColours,
+                featureGroups, includeNonPositional);
       }
       else
       {
         text = formatter.printJalviewFormat(sequences, featureColours,
-                true, includeNonPositional);
+                featureGroups, includeNonPositional);
       }
     }
     else