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//
// onegapignore.cpp
// Mothur
//
// Created by Sarah Westcott on 4/20/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "onegapignore.h"
/***********************************************************************/
double oneGapIgnoreTermGapDist::calcDist(Sequence A, Sequence B){
try {
string seqA = A.getAligned();
string seqB = B.getAligned();
bool overlap = false;
int start = setStartIgnoreTermGap(seqA, seqB, overlap);
int end = setEndIgnoreTermGap(seqA, seqB, overlap);
//non-overlapping sequences
if (!overlap) { return 1.0000; }
int maxMinLength = end - start;
int difference = 0;
bool openGapA = false;
bool openGapB = false;
for(int i=start;i<=end;i++){
if(seqA[i] == '-' && seqB[i] == '-'){ maxMinLength--; } //comparing gaps, ignore
else if(seqB[i] != '-' && seqA[i] == '-'){ //seqB is a base, seqA is a gap
if(!openGapA){
difference++;
openGapA = true;
openGapB = false;
}else { maxMinLength--; }
}
else if(seqA[i] != '-' && seqB[i] == '-'){ //seqA is a base, seqB is a gap
if(!openGapB){
difference++;
openGapA = false;
openGapB = true;
}else { maxMinLength--; }
}
else if(seqA[i] != '-' && seqB[i] != '-'){ //both bases
openGapA = false;
openGapB = false;
//no match
if(seqA[i] != seqB[i]){ difference++; }
}
dist = (double)difference / maxMinLength;
if (dist > cutoff) { return 1.0000; }
}
if(maxMinLength == 0) { dist = 1.0000; }
else { dist = (double)difference / maxMinLength; }
return dist;
}
catch(exception& e) {
m->errorOut(e, "oneGapDist", "calcDist");
exit(1);
}
}
/***********************************************************************/
vector<double> oneGapIgnoreTermGapDist::calcDist(Sequence A, classifierOTU otu, vector<int> cols){ //this function calcs the distance using only the columns provided
try {
vector<double> dists; dists.resize(otu.numSeqs, 0.0);
//if you didn't select columns, use all columns
if (cols.size() == 0) {
for (int i = 0; i < otu.otuData.size(); i++) { cols.push_back(i); }
}
classifierOTU seq(A.getAligned());
vector<int> starts = setStartsIgnoreTermGap(seq, otu, cols);
vector<int> ends = setEndsIgnoreTermGap(seq, otu, cols);
int alignLength = cols.size();
for (int h = 0; h < otu.numSeqs; h++) {
if (m->getControl_pressed()) { break; }
if ((starts[h] == -1) && (ends[h] == -1)) { dists[h] = 1.0000; } //no overlap
else {
if (starts[h] == -1) { starts[h] = 0; }
if (ends[h] == -1) { ends[h] = 0; }
int maxMinLength = ends[h] - starts[h];
int difference = 0;
bool openGapA = false;
bool openGapB = false;
for(int i=starts[h];i<=ends[h];i++){
char seqA = seq.otuData[cols[i]][0];
vector<char> otuChars = otu.otuData[cols[i]];
char seqB = otuChars[0]; //assume column if identical
if (otuChars.size() == otu.numSeqs) { seqB = otuChars[h]; }
if(seqA == '-' && seqB == '-'){ maxMinLength--; } //comparing gaps, ignore
else if(seqB != '-' && seqA == '-'){ //seqB is a base, seqA is a gap
if(!openGapA){
difference++;
openGapA = true;
openGapB = false;
}else { maxMinLength--; }
}
else if(seqA != '-' && seqB == '-'){ //seqA is a base, seqB is a gap
if(!openGapB){
difference++;
openGapA = false;
openGapB = true;
}else { maxMinLength--; }
}
else if(seqA != '-' && seqB != '-'){ //both bases
openGapA = false;
openGapB = false;
//no match
if(seqA != seqB){ difference++; }
}
double distance = 1.0;
distance = (double)difference / maxMinLength;
if (distance > cutoff) { dists[h] = 1.0000; i+=alignLength; } //break;
}
if(maxMinLength == 0) { dists[h] = 1.0000; }
else if (dists[h] == 0.0) { dists[h] = (double)difference / maxMinLength; } //not set
}
}
return dists;
}
catch(exception& e) {
m->errorOut(e, "oneGapDist", "calcDist");
exit(1);
}
}
/***********************************************************************/
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