*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
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;
{
FeaturesFile formatter = new FeaturesFile();
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map<String, Object> featureColours = ap.getFeatureRenderer()
+ 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