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#include <alignment/tuples/DNATuple.hpp>
DNATuple::DNATuple() : pos(0) {}
DNATuple::DNATuple(const DNATuple &rhs) : BaseTuple(rhs), pos(rhs.pos) {}
int DNATuple::FromStringRL(Nucleotide *strPtr, TupleMetrics &tm)
{
//
// Tuples are created with the right-most character
// in the most significant bit in the sequence.
//
DNASequence tmpSeq;
tmpSeq.seq = strPtr;
tmpSeq.length = tm.tupleSize;
if (!OnlyACTG(tmpSeq)) return 0;
if (tm.tupleSize == 0) return 1;
tuple = 0;
Nucleotide *p;
for (p = strPtr + tm.tupleSize - 1; p > strPtr; p--) {
tuple += TwoBit[*p];
tuple <<= 2;
}
//
// The tuple size is guaranteed to be at least
// 1, so it's safe to add the last value.
// This cannot be in the previous loop since
// the shift shouldn't happen.
tuple += TwoBit[*p];
return 1;
}
int DNATuple::MakeRC(DNATuple &dest, TupleMetrics &tm)
{
int i;
TupleData tempTuple = tuple;
dest.tuple = 0;
TupleData mask = 0x3;
if (tm.tupleSize == 0) return 0;
for (i = 0; i < tm.tupleSize - 1; i++) {
dest.tuple += (~tempTuple & mask);
tempTuple >>= 2;
dest.tuple <<= 2;
}
dest.tuple += (~tempTuple & mask);
return 1;
}
std::string DNATuple::ToString(TupleMetrics &tm)
{
int i;
std::string s;
TupleData tempTuple = tuple;
for (i = 0; i < tm.tupleSize; i++) {
s.insert(s.begin(), TwoBitToAscii[tempTuple & 3]);
tempTuple = tempTuple >> 2;
}
return s;
}
bool CompareByTuple::operator()(const DNATuple &lhs, const DNATuple &rhs) const
{
return lhs.tuple < rhs.tuple;
}
CountedDNATuple::CountedDNATuple(const CountedDNATuple &rhs) : DNATuple(rhs), count(rhs.count) {}
PositionDNATuple::PositionDNATuple() : DNATuple() { pos = static_cast<DNALength>(-1); }
PositionDNATuple::PositionDNATuple(const PositionDNATuple &rhs) : DNATuple(rhs) {}
PositionDNATuple::PositionDNATuple(const PositionDNATuple &tupleP, const DNALength posP)
: DNATuple(tupleP)
{
pos = posP;
}
int PositionDNATuple::operator==(const DNATuple &pTuple) const { return tuple == pTuple.tuple; }
int OrderPositionDNATuplesByPosition::operator()(const PositionDNATuple &lhs,
const PositionDNATuple &rhs) const
{
return lhs.pos < rhs.pos;
}
int OrderPositionDNATuplesByTuple::operator()(const PositionDNATuple &lhs,
const PositionDNATuple &rhs) const
{
return lhs.tuple < rhs.tuple;
}
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