Approximate Searching

Example Program

Approximate string matching.

1	#include <iostream>
2	#include <seqan/find.h>
3
4	using namespace seqan;
5	using namespace std;
6

This program finds all occurrences of CCT in AACTTAACCTAA with ≤ 1 error using the MyersUkkonen approximate search algorithm.

7	int main()
8	{
9	String<char> haystk("AACTTAACCTAA");
10	String<char> ndl("CCT");
11
12	Finder<String<char> > fnd(haystk);
13	Pattern<String<char>, MyersUkkonen> pat(ndl);

The function setScoreLimit sets the limit score an occurrence must reach. Since the used scoring scheme is a distance measure (edit distance), all scores are negative. A score limit of ≥ -1 therefore means a edit distance ≤ 1.

14	setScoreLimit(pat, -1);
15	while (find(fnd, pat))
16	{
17	cout << position(fnd) << ": " << getScore(pat) << "\n";

Note that position returns the end position of the found occurrence.

18	}
19
20	return 0;
21	}
22

Output

3: -1
4: -1
8: -1
9: 0
10: -1