import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.JalviewFileChooser;
{
Map<String, FeatureColourI> displayedFeatureColours = ap
.getFeatureRenderer().getDisplayedFeatureCols();
+ FeaturesFile formatter = new FeaturesFile();
+ SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+ .getDisplayedFeatureCols();
+ boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
- text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), displayedFeatureColours, true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
+ text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats());
+ text = formatter.printGffFormat(sequences, featureColours, true,
+ includeNonPositional);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+ text = formatter.printJalviewFormat(sequences, featureColours,
+ true, includeNonPositional);
}
}
else