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 96e141d..a48c030 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -156,8 +156,6 @@ 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()
@@ -165,19 +163,13 @@ public class AnnotationExporter extends JPanel
       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,
+        text = formatter.printGffFormat(sequences, featureColours,
                 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);
+                includeNonPositional);
       }
     }
     else