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//Examples for three seed extension algorithms.
#include <iostream>
#include <seqan/seeds.h>
using namespace seqan;
int main()
{
String<char> a = "SEEDabXcdXefXXX";
String<char> b = "SEEDabYcdefYYYY";
Seed<Simple> seed1(0, 0, 4); //left=0; length=4
extendSeed(seed1, a, b, EXTEND_BOTH, MatchExtend());
std::cout << "endPositionH(seed1) = " << endPositionH(seed1) << std::endl;
std::cout << "endPositionV(seed1) = " << endPositionV(seed1) << std::endl;
Seed<Simple> seed2(0, 0, 4); //left=0; length=4
Score<> scoring(1, -1, -1);
extendSeed(seed2, a, b, EXTEND_BOTH, scoring, 2, UnGappedXDrop());
std::cout << "endPositionH(seed2) = " << endPositionH(seed2) << std::endl;
std::cout << "endPositionV(seed2) = " << endPositionV(seed2) << std::endl;
Seed<Simple> seed3(0, 0, 4); //left=0; length=4
extendSeed(seed3, a, b, EXTEND_BOTH, scoring, 2, GappedXDrop());
std::cout << "endPositionH(seed3) = " << endPositionH(seed3) << std::endl;
std::cout << "endPositionV(seed3) = " << endPositionV(seed3) << std::endl;
return 0;
}
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