source: branches/lib/GDE/MUSCLE/src/distcalc.cpp

#include "muscle.h"
#include "distfunc.h"
#include "distcalc.h"
#include "msa.h"

void DistCalcDF::Init(const DistFunc &DF)
        {
        m_ptrDF = &DF;
        }

void DistCalcDF::CalcDistRange(unsigned i, dist_t Dist[]) const
        {
        for (unsigned j = 0; j < i; ++j)
                Dist[j] = m_ptrDF->GetDist(i, j);
        }

unsigned DistCalcDF::GetCount() const
        {
        return m_ptrDF->GetCount();
        }

unsigned DistCalcDF::GetId(unsigned i) const
        {
        return m_ptrDF->GetId(i);
        }

const char *DistCalcDF::GetName(unsigned i) const
        {
        return m_ptrDF->GetName(i);
        }

void DistCalcMSA::Init(const MSA &msa, DISTANCE Distance)
        {
        m_ptrMSA = &msa;
        m_Distance = Distance;
        }

void DistCalcMSA::CalcDistRange(unsigned i, dist_t Dist[]) const
        {
        for (unsigned j = 0; j < i; ++j)
                {
                switch (m_Distance)
                        {
                case DISTANCE_PctIdKimura:
                        {
                        const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);
                        Dist[j] = (float) KimuraDist(PctId);
                        break;
                        }
                case DISTANCE_PctIdLog:
                        {
                        const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);
                        Dist[j] = (float) PctIdToMAFFTDist(PctId);
                        break;
                        }
                case DISTANCE_ScoreDist:
                        {
                        double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);
                        Dist[j] = (float) GetScoreDist(*m_ptrMSA, i, j);
                        continue;
                        }
                case DISTANCE_Edit:
                        {
                        const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);
                        if (PctId > 1.0)
                                Quit("Internal error, DISTANCE_Edit, pct id=%.3g", PctId);
                        Dist[j] = (float) 1.0 - PctId;
                        break;
                        }
                default:
                        Quit("DistCalcMSA: Invalid DISTANCE_%u", m_Distance);
                        }
                }
        }

unsigned DistCalcMSA::GetCount() const
        {
        return m_ptrMSA->GetSeqCount();
        }

unsigned DistCalcMSA::GetId(unsigned i) const
        {
        return m_ptrMSA->GetSeqId(i);
        }

const char *DistCalcMSA::GetName(unsigned i) const
        {
        return m_ptrMSA->GetSeqName(i);
        }