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#include "pilercr.h"
#include "multaln.h"
#include "sw.h"
// Simple version of Smith-Waterman.
// Could certainly be made smaller & faster if desired.
#define TRACE 0
#define ScoreToStr LocalScoreToStr
void SWTraceBack(const unsigned char *A, unsigned LA, const unsigned char *B,
unsigned LB, unsigned Topi, unsigned Topj, score_t TopScore, const score_t *DPM_,
const score_t *DPD_, const score_t *DPI_, std::string &Path, unsigned *ptrStartA,
unsigned *ptrStartB);
static const char *ScoreToStr(score_t s)
{
static char str[16];
if (s <= MINUS_INF/2)
return " *";
#if INTEGER_DP
sprintf(str, "%6d", s);
#else
sprintf(str, "%6.0f", s);
#endif
return str;
}
#if TRACE
static void LogDP(const score_t *DPM_, const unsigned char *A,
const unsigned char *B, unsigned PCA, unsigned PCB)
{
Log(" ");
for (unsigned j = 0; j < PCB; ++j)
{
char c = ' ';
if (j > 0)
c = B[j - 1];
Log(" %4u:%c", j, c);
}
Log("\n");
for (unsigned i = 0; i < PCA; ++i)
{
char c = ' ';
if (i > 0)
c = A[i - 1];
Log("%4u:%c ", i, c);
for (unsigned j = 0; j < PCB; ++j)
Log(" %s", ScoreToStr(DPM(i, j)));
Log("\n");
}
}
#endif // TRACE
score_t SW(const Seq &A, const Seq &B, unsigned *ptrStartA, unsigned *ptrStartB,
std::string &Path)
{
unsigned LA = A.Length();
unsigned LB = B.Length();
char *sA = all(char, LA + 1);
char *sB = all(char, LB + 1);
A.ToString(sA, LA + 1);
B.ToString(sB, LB + 1);
score_t Score = SWSimple(sA, LA, sB, LB, ptrStartA, ptrStartB, Path);
freemem(sA);
freemem(sB);
return Score;
}
score_t SWSimple(const char *A_, unsigned LA, const char *B_,
unsigned LB, unsigned *ptrStartA, unsigned *ptrStartB, std::string &Path)
{
assert(LB > 0 && LA > 0);
const unsigned char *A = (const unsigned char *) A_;
const unsigned char *B = (const unsigned char *) B_;
Path.clear();
const unsigned PCA = LA + 1;
const unsigned PCB = LB + 1;
// Allocate DP matrices
const unsigned LM = PCA*PCB;
score_t *DPM_ = all(score_t, LM);
score_t *DPD_ = all(score_t, LM);
score_t *DPI_ = all(score_t, LM);
// Boundaries
for (unsigned j = 0; j < PCB; ++j)
{
// M=LetterA+LetterB, impossible with empty prefix
DPM(0, j) = 0;
DPD(0, j) = 0;
DPI(0, j) = 0;
}
for (unsigned i = 0; i < PCA; ++i)
{
DPM(i, 0) = 0;
DPD(i, 0) = 0;
DPI(i, 0) = 0;
}
// ============
// Main DP loop
// ============
score_t TopScore = -1;
unsigned Topi = 0;
unsigned Topj = 0;
for (unsigned i = 1; i < PCA; ++i)
{
const unsigned char cA = A[i-1];
for (unsigned j = 1; j < PCB; ++j)
{
const unsigned char cB = B[j-1];
{
// Match M=LetterA+LetterB
score_t scoreLL = SUBST(cA, cB);
score_t scoreMM = DPM(i-1, j-1);
score_t scoreDM = DPD(i-1, j-1);
score_t scoreIM = DPI(i-1, j-1);
score_t scoreBest;
if (scoreMM >= scoreDM && scoreMM >= scoreIM)
scoreBest = scoreMM;
else if (scoreDM >= scoreMM && scoreDM >= scoreIM)
scoreBest = scoreDM;
else
{
assert(scoreIM >= scoreMM && scoreIM >= scoreDM);
scoreBest = scoreIM;
}
score_t s = scoreBest + scoreLL;
if (s > 0)
{
DPM(i, j) = s;
if (s > TopScore)
{
TopScore = s;
Topi = i;
Topj = j;
}
}
else
DPM(i, j) = 0;
}
{
// Delete D=LetterA+GapB
score_t scoreMD = DPM(i-1, j) + GAPOPEN;
score_t scoreDD = DPD(i-1, j) + GAPEXTEND;
score_t scoreBest;
if (scoreMD >= scoreDD)
scoreBest = scoreMD;
else
{
assert(scoreDD >= scoreMD);
scoreBest = scoreDD;
}
if (scoreBest < 0)
scoreBest = 0;
DPD(i, j) = scoreBest;
}
// Insert I=GapA+LetterB
{
score_t scoreMI = DPM(i, j-1) + GAPOPEN;
score_t scoreII = DPI(i, j-1) + GAPEXTEND;
score_t scoreBest;
if (scoreMI >= scoreII)
scoreBest = scoreMI;
else
{
assert(scoreII > scoreMI);
scoreBest = scoreII;
}
if (scoreBest < 0)
scoreBest = 0;
DPI(i, j) = scoreBest;
}
}
}
#if TRACE
Log("DPM:\n");
LogDP(DPM_, A, B, PCA, PCB);
Log("DPD:\n");
LogDP(DPD_, A, B, PCA, PCB);
Log("DPI:\n");
LogDP(DPI_, A, B, PCA, PCB);
#endif
if (TopScore < 0)
{
*ptrStartA = 0;
*ptrStartB = 0;
return 0;
}
#if TRACE
Log("TopScore=%d Topi=%u Topj=%u\n", TopScore, Topi, Topj);
#endif
SWTraceBack(A, LA, B, LB, Topi, Topj, TopScore, DPM_, DPD_, DPI_, Path,
ptrStartA, ptrStartB);
freemem(DPM_);
freemem(DPD_);
freemem(DPI_);
return TopScore;
}
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