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#include "pilercr.h"
#include "multaln.h"
#include "sw.h"
#include <math.h>
#include <algorithm>
#define TRACE 0
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)
{
#if TRACE
Log("\n");
Log("SWTraceBack LengthA=%u LengthB=%u\n", LA, LB);
#endif
assert(LB > 0 && LA > 0);
Path.clear();
unsigned i = Topi;
unsigned j = Topj;
const unsigned PCA = LA + 1;
char cEdgeType = 'M';
#if TRACE
Log("TraceBack\n");
Log(" i j Edge\n");
Log("--- --- ----\n");
#endif
for (;;)
{
if (i == 0 || j == 0)
goto Done;
char cPrevEdgeType = cEdgeType;
#if TRACE
unsigned Prev_i = i;
unsigned Prev_j = j;
#endif
/***
i is prefix length in A
j is prefix length in B
Current cell is DP<cEdgeType>(i,j).
Determine the predecessor cell.
***/
switch (cEdgeType)
{
case 'M':
{
assert(i > 0);
assert(j > 0);
const unsigned char cA = A[i-1];
const unsigned char cB = B[j-1];
const score_t Score = DPM(i, j);
const score_t scoreMatch = SUBST(cA, cB);
score_t scoreMM = MINUS_INF;
score_t scoreDM = MINUS_INF;
score_t scoreIM = MINUS_INF;
if (i > 0 && j > 0)
scoreMM = DPM(i-1, j-1) + scoreMatch;
if (i > 1)
scoreDM = DPD(i-1, j-1) + scoreMatch;
if (j > 1)
scoreIM = DPI(i-1, j-1) + scoreMatch;
if (EQ(scoreMM, Score))
cEdgeType = 'M';
else if (EQ(scoreDM, Score))
cEdgeType = 'D';
else if (EQ(scoreIM, Score))
cEdgeType = 'I';
else if (EQ(0, Score))
goto Done;
else
Quit("TraceBack: failed to match M");
--i;
--j;
break;
}
case 'D':
{
assert(i > 0);
const score_t Score = DPD(i, j);
score_t scoreMD = MINUS_INF;
score_t scoreDD = MINUS_INF;
if (i > 1)
{
scoreMD = DPM(i-1, j) + GAPOPEN;
scoreDD = DPD(i-1, j) + GAPEXTEND;
}
if (EQ(Score, scoreMD))
cEdgeType = 'M';
else if (EQ(Score, scoreDD))
cEdgeType = 'D';
else
Quit("TraceBack: failed to match D");
--i;
break;
}
case 'I':
{
assert(j > 0);
const score_t Score = DPI(i, j);
score_t scoreMI = MINUS_INF;
score_t scoreII = MINUS_INF;
if (j > 1)
{
scoreMI = DPM(i, j-1) + GAPOPEN;
scoreII = DPI(i, j-1) + GAPEXTEND;
}
if (EQ(Score, scoreMI))
cEdgeType = 'M';
else if (EQ(Score, scoreII))
cEdgeType = 'I';
else
Quit("TraceBack: failed to match I");
--j;
break;
}
default:
assert(false);
}
Path.push_back(cPrevEdgeType);
#if TRACE
{
char cA = (cPrevEdgeType == 'M' || cPrevEdgeType == 'D') ? A[Prev_i-1] : '-';
char cB = (cPrevEdgeType == 'M' || cPrevEdgeType == 'I') ? B[Prev_j-1] : '-';
Log("%3d %3d %4c %c%c\n", Prev_i-1, Prev_j-1, cPrevEdgeType, cA, cB);
}
#endif
}
Done:
#if TRACE
Log("StartA=%d StartB=%d\n", i, j);
#endif
*ptrStartA = i;
*ptrStartB = j;
std::reverse(Path.begin(), Path.end());
#if TRACE
{
score_t sp = ScorePathLocal(A, LA, B, LB, *ptrStartA, *ptrStartB, Path.c_str());
if (!EQ(sp, TopScore))
{
Log("Path=%s\n", Path.c_str());
Quit("TraceBackSW: scoreMax=%d != ScorePath=%d", TopScore, sp);
}
}
#endif
}
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