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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/profile.h"
#include "libMUSCLE/pwpath.h"
#include "libMUSCLE/textfile.h"
#include "libMUSCLE/timing.h"
namespace muscle {
SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,
bool bLockLeft, bool bLockRight)
{
const unsigned uLengthA = msa1.GetColCount();
const unsigned uLengthB = msa2.GetColCount();
ProfPos *PA = ProfileFromMSA(msa1);
ProfPos *PB = ProfileFromMSA(msa2);
if (bLockLeft)
{
PA[0].m_scoreGapOpen = MINUS_INFINITY;
PB[0].m_scoreGapOpen = MINUS_INFINITY;
}
if (bLockRight)
{
PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;
PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;
}
float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0
if (r < 1)
r = 1/r;
SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
delete[] PA;
delete[] PB;
return Score;
}
}
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