/usr/include/libMUSCLE-3.7/libMUSCLE/msadist.h is in libmuscle-3.7-dev 3.7+4565-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | #ifndef MSADist_h
#define MSADist_h
#include <math.h>
namespace muscle {
class MSA;
double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);
class MSADist
{
public:
MSADist(DISTANCE Distance)
{
m_Distance = Distance;
}
double ComputeDist(const MSA &msa, unsigned uSeqIndex1, unsigned uSeqIndex2)
{
if (m_Distance == DISTANCE_ScoreDist)
return GetScoreDist(msa, uSeqIndex1, uSeqIndex2);
double dPctId = msa.GetPctIdentityPair(uSeqIndex1, uSeqIndex2);
switch(m_Distance)
{
case DISTANCE_PctIdKimura:
return KimuraDist(dPctId);
case DISTANCE_PctIdLog:
if (dPctId < 0.05)
dPctId = 0.05;
return -log(dPctId);
}
Quit("MSADist::ComputeDist, invalid DISTANCE_%u", m_Distance);
return 0;
}
private:
DISTANCE m_Distance;
};
} // namespace muscle
#endif // MSADist_h
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