/**Return the strongest intramolecular structure (as reported by lac) for
* the specified sequence.
* Throws exception if allowPolys is true.*/
public NASecStructure calculateStructure(NucleotideSequence seq, boolean doTemp) {
Alignment la = doStrongestIntramolecularLocalAlignment(seq.seqString(), seq.getType());
if (la == null) return null;
NASecStructure s = new DefaultNASecStructure(la,seq.length());
return s;
}