source: branches/lib/GDE/MUSCLE/src/msadistmafft.h

#ifndef MSADistMAFFT_h
#define MSADistMAFFT_h

#include "msadist.h"
#include <math.h>

extern double PctIdToMAFFTDist(double dPctId);

class MSADistMAFFT : public MSADist
        {
public:
        virtual double ComputeDist(const MSA &msa, unsigned uSeqIndex1,
          unsigned uSeqIndex2)
                {
                double dPctId = msa.GetPctIdentityPair(uSeqIndex1, uSeqIndex2);
                //if (dPctId < 0.05)
                //      dPctId = 0.05;
                //double dDist = -log(dPctId);
                //return dDist;
                return PctIdToMAFFTDist(dPctId);
                }
        };

#endif  // MSADistMAFFT_h