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alignment_util.cpp
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alignment_util.cpp
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//C headers
#include <stdint.h>
//C++ headers
#include <vector>
//my custom headers
#include "alignment_util.h"
using namespace std;
//This code is essentially an adaptation of the algorithms on wikipedia: https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Levenshtein_distance#C.2B.2B
uint64_t editDistance(const vector<uint8_t> &s1, const vector<uint8_t> &s2)
{
//modified version of https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Levenshtein_distance#C.2B.2B
const std::size_t len1 = s1.size(), len2 = s2.size();
std::vector<uint64_t> col(len2+1), prevCol(len2+1);
for (unsigned int i = 0; i < prevCol.size(); i++)
prevCol[i] = i;
for (unsigned int i = 0; i < len1; i++) {
col[0] = i+1;
for (unsigned int j = 0; j < len2; j++)
// note that std::min({arg1, arg2, arg3}) works only in C++11,
// for C++98 use std::min(std::min(arg1, arg2), arg3)
//col[j+1] = std::min({ prevCol[1 + j] + 1, col[j] + 1, prevCol[j] + (s1[i]==s2[j] ? 0 : 1) });
col[j+1] = std::min(std::min(prevCol[1+j]+1, col[j]+1), prevCol[j]+(s1[i]==s2[j] ? 0 : 1));
col.swap(prevCol);
}
return prevCol[len2];
}
pair<uint64_t, uint64_t> editDistance_minimize(const vector<uint8_t> &s1, const vector<uint8_t> &s2)
{
//modified version of https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Levenshtein_distance#C.2B.2B
const std::size_t len1 = s1.size(), len2 = s2.size();
std::vector<uint64_t> col(len2+1), prevCol(len2+1);
for (unsigned int i = 0; i < prevCol.size(); i++)
prevCol[i] = i;
for (unsigned int i = 0; i < len1; i++) {
col[0] = i+1;
for (unsigned int j = 0; j < len2; j++)
// note that std::min({arg1, arg2, arg3}) works only in C++11,
// for C++98 use std::min(std::min(arg1, arg2), arg3)
//col[j+1] = std::min({ prevCol[1 + j] + 1, col[j] + 1, prevCol[j] + (s1[i]==s2[j] ? 0 : 1) });
col[j+1] = std::min(std::min(prevCol[1+j]+1, col[j]+1), prevCol[j]+(s1[i]==s2[j] ? 0 : 1));
col.swap(prevCol);
}
//get the last smallest value
uint64_t argMin = len2;
for(int64_t x = len2-1; x >= 0; x--) {
if(prevCol[x] < prevCol[argMin]) argMin = x;
}
//pick the smallest score
pair<uint64_t, uint64_t> ret;// = scoreArray[oLen][mLen][choice];
ret.first = prevCol[argMin];
ret.second = argMin;
return ret;
}