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//
// ignoregaps.cpp
// Mothur
//
// Created by Sarah Westcott on 4/21/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "ignoregaps.h"
/***********************************************************************/
double ignoreGaps::calcDist(Sequence A, Sequence B){
try {
int diff = 0;
int start = 0;
int end = 0;
bool overlap = false;
string seqA = A.getAligned();
string seqB = B.getAligned();
int alignLength = (int)seqA.length();
for(int i=0;i<alignLength;i++){
if(seqA[i] != '.' && seqB[i] != '.'){
start = i;
overlap = true;
break;
}
}
for(int i=alignLength-1;i>=0;i--){
if(seqA[i] != '.' && seqB[i] != '.'){
end = i;
overlap = true;
break;
}
}
//non-overlapping sequences
if (!overlap) { return 1.0000; }
int maxMinLength = end - start + 1;
for(int i=start; i<alignLength; i++){
if(seqA[i] == '.' || seqB[i] == '.'){
break;
}
else if((seqA[i] != '-' && seqB[i] != '-')){
if(seqA[i] != seqB[i]){
diff++;
}
}else { maxMinLength--; }
dist = (double)diff / maxMinLength;
if (dist > cutoff) { return 1.0000; }
}
if(maxMinLength == 0) { dist = 1.0000; }
else { dist = ((double)diff / (double)maxMinLength); }
return dist;
}
catch(exception& e) {
m->errorOut(e, "ignoreGaps", "calcDist");
exit(1);
}
}
/***********************************************************************/
vector<double> ignoreGaps::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 = setStarts(seq, otu, cols);
vector<int> ends = setEnds(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] + 1;
int difference = 0;
for(int i=starts[h];i<alignLength;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 == '.'){ i+=alignLength; }
else if((seqA != '-' && seqB != '-')){
if(seqA != seqB){ difference++; }
}else { maxMinLength--; }
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, "ignoreGaps", "calcDist");
exit(1);
}
}
/***********************************************************************/
vector<int> ignoreGaps::setStarts(classifierOTU seqA, classifierOTU otu, vector<int> cols){
try {
vector<int> starts; starts.resize(otu.numSeqs, -1);
int alignLength = cols.size();
int seqAStart = 0;
for(int i=0;i<alignLength;i++){ //for each column we want to include
if (seqA.otuData[cols[i]][0] != '.') {
seqAStart = i; break;
}
}
//set start positions
int numset = 0;
for(int i=seqAStart;i<alignLength;i++){ //start can't be before seqAStart because of the &&
if(numset == otu.numSeqs) { break; }
vector<char> thisColumn = otu.otuData[cols[i]];
if (thisColumn.size() != otu.numSeqs) { //all seqs at this spot are identical
char thisChar = thisColumn[0];
if (thisChar == '.') { } //every seq in otu is a '.' or '-' at this location, move to next column
else { //this is a base in all locations, you are done
for (int k = 0; k < starts.size(); k++) {
if ((starts[k] == -1) && (seqA.otuData[cols[i]][0] != '.')) { starts[k] = i; numset++; } //any unset starts are set to this location
}
break;
}
}else{
for(int j=0;j<otu.numSeqs;j++){ //for each reference
if((thisColumn[j] != '.') && (starts[j] == -1) && (seqA.otuData[cols[i]][0] != '.')){ //seq j hasn't set the start value and its a base
starts[j] = i; numset++;
}
}
}
}
return starts;
}
catch(exception& e) {
m->errorOut(e, "ignoreGaps", "setStarts");
exit(1);
}
}
/***********************************************************************/
vector<int> ignoreGaps::setEnds(classifierOTU seqA, classifierOTU otu, vector<int> cols){
try {
vector<int> ends; ends.resize(otu.numSeqs, -1);
int alignLength = cols.size();
int seqAEnd = 0;
for(int i=alignLength-1;i>=0;i--){//for each column we want to include
if (seqA.otuData[cols[i]][0] != '.') {
seqAEnd = i; break;
}
}
//set start positions
int numset = 0;
for(int i=seqAEnd;i>=0;i--){ //for each column we want to include
if(numset == otu.numSeqs) { break; }
vector<char> thisColumn = otu.otuData[cols[i]];
if (thisColumn.size() != otu.numSeqs) { //all seqs at this spot are identical
char thisChar = thisColumn[0];
if (thisChar == '.'){ } //every seq in otu is a '.' at this location, move to next column
else { //this is a base in all locations, you are done
for (int k = 0; k < ends.size(); k++) {
if ((ends[k] == -1) && (seqA.otuData[cols[i]][0] != '.')){ ends[k] = i; numset++; } //any unset starts are set to this location
}
break;
}
}else{
for(int j=0;j<otu.numSeqs;j++){ //for each reference
if((thisColumn[j] != '.') && (ends[j] == -1) && (seqA.otuData[cols[i]][0] != '.')) { //seq j hasn't set the start value and its a base
ends[j] = i; numset++;
}
}
}
}
return ends;
}
catch(exception& e) {
m->errorOut(e, "ignoreGaps", "setEnds");
exit(1);
}
}
/***********************************************************************/
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