*/
package jalview.io.gff;
+import java.util.Locale;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
// e.g. exonerate:protein2genome:local
if (model != null)
{
- String mdl = model.toLowerCase();
+ String mdl = model.toLowerCase(Locale.ROOT);
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
|| mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
|| mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
return false;
}
+ /**
+ * An override to set feature group to "exonerate" instead of the default GFF
+ * source value (column 2)
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> set)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, set);
- sf.setFeatureGroup("exonerate");
+ SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+ "exonerate", set);
return sf;
}