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);
}
}
}
double PctIdToHeightKimura(double dPctId)
{
return KimuraDist(dPctId);
}
