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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/distfunc.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/seqvect.h"
#include "libMUSCLE/pwpath.h"
namespace muscle {
void DistPWKimura(const SeqVect &v, DistFunc &DF)
{
SEQWEIGHT SeqWeightSave = GetSeqWeightMethod();
SetSeqWeightMethod(SEQWEIGHT_Henikoff);
const unsigned uSeqCount = v.Length();
DF.SetCount(uSeqCount);
const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;
unsigned uCount = 0;
SetProgressDesc("PWKimura distance");
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
const Seq &s1 = v.GetSeq(uSeqIndex1);
MSA msa1;
msa1.FromSeq(s1);
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)
{
if (0 == uCount%20)
Progress(uCount, uPairCount);
++uCount;
const Seq &s2 = v.GetSeq(uSeqIndex2);
MSA msa2;
msa2.FromSeq(s2);
PWPath Path;
MSA msaOut;
AlignTwoMSAs(msa1, msa2, msaOut, Path, false, false);
double dPctId = msaOut.GetPctIdentityPair(0, 1);
float f = (float) KimuraDist(dPctId);
DF.SetDist(uSeqIndex1, uSeqIndex2, f);
}
}
ProgressStepsDone();
SetSeqWeightMethod(SeqWeightSave);
}
}
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