import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
/*
* Share the same dataset sequence mappings (if any).
*/
- this.setCodonFrames(al.getCodonFrames());
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
}
/**
}
}
- /**
- * adds a set of mappings (while ignoring any duplicates)
- */
- @Override
- public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
- {
- if (codons != null)
- {
- Iterator<AlignedCodonFrame> it = codons.iterator();
- while (it.hasNext())
- {
- addCodonFrame(it.next());
- }
- }
- }
-
/*
* (non-Javadoc)
*
addAnnotation(alan[a]);
}
+ // use add method
getCodonFrames().addAll(toappend.getCodonFrames());
List<SequenceGroup> sg = toappend.getGroups();
{
return AlignmentUtils.alignProteinAsDna(this, al);
}
+ else if (thatIsProtein && thisIsNucleotide)
+ {
+ return AlignmentUtils.alignCdsAsProtein(this, al);
+ }
return AlignmentUtils.alignAs(this, al);
}