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

#ifndef MSADist_h
#define MSADist_h

#include <math.h>

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;
        };

#endif  // MSADist_h