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//
// kimura.cpp
// Mothur
//
// Created by Sarah Westcott on 7/2/21.
// Copyright © 2021 Schloss Lab. All rights reserved.
//
#include "kimura.hpp"
/***********************************************************************/
double Kimura::calcDist(Protein A, Protein B) {
try {
int numBases = A.getAlignLength();
vector<AminoAcid> seqA = A.getAligned();
vector<AminoAcid> seqB = B.getAligned();
int lm = 0; int n = 0;
for (int i = 0; i < numBases; i++) {
int numA = seqA[i].getNum();
int numB = seqB[i].getNum();
if ((((long)numA <= (long)val) || ((long)numA == (long)ser)) && (((long)numB <= (long)val) || ((long)numB == (long)ser))) {
if (numA == numB) { lm++; }
n++;
}
}
double p = 1 - (double)lm / n;
double dp = 1.0 - p - 0.2 * p * p;
if (dp < 0.0) {
m->mothurOut("[WARNING]: DISTANCE BETWEEN SEQUENCES " + A.getName() + " AND " + B.getName() + " IS TOO LARGE FOR KIMURA FORMULA, setting distance to -1.0.\n");
dist = -1.0;
} else {
dist = -log(dp);
}
return dist;
}
catch(exception& e) {
m->errorOut(e, "Kimura", "calcDist");
exit(1);
}
}
/***********************************************************************/
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