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#ifndef SW_H
#define SW_H
#include <string>
typedef float score_t;
const score_t MINUS_INF = -999999;
#undef DPM
#undef DPD
#undef DPI
#undef DPMb
#undef DPDb
#undef DPIb
// Macros to simulate 2D matrices
#define DPM(i, j) DPM_[(j)*PCA + (i)]
#define DPD(i, j) DPD_[(j)*PCA + (i)]
#define DPI(i, j) DPI_[(j)*PCA + (i)]
#define DPMb(i, j) DPMb_[BandIndex((i), (j), LA, LB, r)]
#define DPDb(i, j) DPDb_[BandIndex((i), (j), LA, LB, r)]
#define DPIb(i, j) DPIb_[BandIndex((i), (j), LA, LB, r)]
//#define SUBST(cA, cB) \
// ((*g_ptrScoreMatrix)[CharToLetter[(unsigned char) (cA)]][CharToLetter[(unsigned char) (cB)]])
static inline float SUBST(unsigned char cA, unsigned char cB)
{
unsigned LetA = CharToLetter[(unsigned char) cA];
unsigned LetB = CharToLetter[(unsigned char) cB];
assert(LetA < 32);
assert(LetB < 32);
return (*g_ptrScoreMatrix)[LetA][LetB];
}
extern float g_scoreGapExtend;
extern float g_scoreGapOpen;
#define GAPOPEN g_scoreGapOpen
#define GAPEXTEND g_scoreGapExtend
#define EQ(a, b) ((a) == (b))
score_t SWSimple(const char *A_, unsigned LA, const char *B_,
unsigned LB, unsigned *ptrStartA, unsigned *ptrStartB, std::string &Path);
class Seq;
score_t SW(const Seq &A, const Seq &B, unsigned *ptrStartA, unsigned *ptrStartB,
std::string &Path);
#endif // SW_H
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