void DistPWScoreDist(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("PW ScoreDist");
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);
float d = (float) GetScoreDist(msaOut, 0, 1);
DF.SetDist(uSeqIndex1, uSeqIndex2, d);
}
}
ProgressStepsDone();
SetSeqWeightMethod(SeqWeightSave);
}
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);
}
}
}
