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#include "muscle.h"
#include "msa.h"
#include "profile.h"
#include "pwpath.h"
SCORE GlobalAlign4(ProfPos *PA, unsigned uLengthA, ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE AlignTwoProfs(
const ProfPos *PA, unsigned uLengthA, WEIGHT wA,
const ProfPos *PB, unsigned uLengthB, WEIGHT wB,
PWPath &Path, ProfPos **ptrPout, unsigned *ptruLengthOut)
{
assert(uLengthA < 100000);
assert(uLengthB < 100000);
float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0
if (r < 1)
r = 1/r;
SCORE Score;
if (g_bTermGaps4 && r > 1.2)
Score = GlobalAlign4((ProfPos *) PA, uLengthA, (ProfPos *) PB, uLengthB, Path);
else
Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
AlignTwoProfsGivenPath(Path, PA, uLengthB, wA/(wA + wB), PB, uLengthB, wB/(wA + wB),
ptrPout, ptruLengthOut);
if (ALPHA_Amino == g_Alpha)
Hydro(*ptrPout, *ptruLengthOut);
return Score;
}
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