//FRAGMENT(main)
#include <iostream>
#include <seqan/align.h>

using namespace seqan;

int main()
{
//FRAGMENT(init)
	Align< String<AminoAcid> > ali;
	resize(rows(ali), 2);
	assignSource(row(ali, 0), "PNCFDAKQRTASRPL");
	assignSource(row(ali, 1), "CFDKQKNNRTATRDTA");

//FRAGMENT(ali)
	Score<int> sc(3,-2,-1,-5);
    unsigned count = 0;
    LocalAlignmentEnumerator<Score<int>, Unbanded> enumerator(sc);
    while (nextLocalAlignment(ali, enumerator) && count < 3)
    {
        std::cout << "Score = " << getScore(enumerator) << std::endl;
        std::cout << ali;
        ++count;
    }
    return 0;
}
