JAL-2490 tidy code and tests for feature export in Jalview format

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 136a38e..a48c030 100644 (file)
--- 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;
@@ -156,20 +157,19 @@ 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();
       boolean includeNonPositional = ap.av.isShowNPFeats();
       if (GFFFormat.isSelected())
       {
-        text = formatter.printGffFormat(sequences, featureColours, true,
+        text = formatter.printGffFormat(sequences, featureColours,
                 includeNonPositional);
       }
       else
       {
         text = formatter.printJalviewFormat(sequences, featureColours,
-                true, includeNonPositional);
+                includeNonPositional);
       }
     }
     else