#ifndef _BLASR_COMPRESSED_DNA_TUPLE_HPP_
#define _BLASR_COMPRESSED_DNA_TUPLE_HPP_

#include <alignment/tuples/DNATuple.hpp>
#include <pbdata/CompressedSequence.hpp>

template <typename T_Sequence>
class CompressedDNATuple : public DNATuple
{
    static const unsigned char mask = 0xf;

public:
    CompressedDNATuple(const CompressedDNATuple &rhs) : DNATuple(rhs) {}

    int FromStringLR(Nucleotide *strPtr, TupleMetrics &tm)
    {
        //
        // Make sure the sequence contains all valid characters.
        //

        if (!CompressedSequence<T_Sequence>::Only4BitACTG(strPtr, tm.tupleSize)) return 0;

        if (tm.tupleSize == 0) return 1;

        tuple = 0;
        Nucleotide *p;
        Nucleotide *endPtr = &strPtr[tm.tupleSize - 1];
        for (p = strPtr; p != endPtr; p++) {
            tuple += TwoBit[*p & mask];
            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 & mask];
        return 1;
    }

    int FromStringRL(Nucleotide *strPtr, TupleMetrics &tm)
    {

        if (!CompressedSequence<T_Sequence>::Only4BitACTG((CompressedNucleotide *)strPtr,
                                                          tm.tupleSize))
            return 0;

        if (tm.tupleSize == 0) return 1;

        tuple = 0;
        Nucleotide *p;
        for (p = strPtr + tm.tupleSize - 1; p > strPtr; p--) {
            tuple += TwoBit[*p & mask];
            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 & mask];
        return 1;
    }
};

#endif  // _BLASR_COMPRESSED_DNA_TUPLE_HPP_