void SequenceTools::getCDS(Sequence& sequence, bool checkInit, bool checkStop, bool includeInit, bool includeStop)
{
const CodonAlphabet* alphabet = dynamic_cast<const CodonAlphabet*>(sequence.getAlphabet());
if (!alphabet)
throw AlphabetException("SequenceTools::getCDS. Sequence is not a codon sequence.");
if (checkInit)
{
unsigned int i;
for (i = 0; i < sequence.size() && !alphabet->isInit(sequence[i]); ++i)
{}
for (unsigned int j = 0; includeInit ? j < i : j <= i; ++j)
{
sequence.deleteElement(j);
}
}
if (checkStop)
{
unsigned int i;
for (i = 0; i < sequence.size() && !alphabet->isStop(sequence[i]); ++i)
{}
for (unsigned int j = includeStop ? i + 1 : i; j < sequence.size(); ++j)
{
sequence.deleteElement(j);
}
}
}
void SequenceTools::removeGaps(Sequence& seq)
{
const Alphabet* alpha = seq.getAlphabet();
for (size_t i = seq.size(); i > 0; --i)
{
if (alpha->isGap(seq[i - 1]))
seq.deleteElement(i - 1);
}
}
void SequenceTools::removeStops(Sequence& seq) throw (Exception)
{
const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(seq.getAlphabet());
if (!calpha)
throw Exception("SequenceTools::removeStops. Input sequence should have a codon alphabet.");
for (size_t i = seq.size(); i > 0; --i)
{
if (calpha->isStop(seq[i - 1]))
seq.deleteElement(i - 1);
}
}
