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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan;
int main()
{
//![main]
//![init1]
Align<String<char> > ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), "aphilologicaltheorem");
assignSource(row(ali, 1), "bizarreamphibology");
//![init1]
//![ali1]
std::cout << "Score = " << localAlignment(ali, Score<int>(3, -3, -2, -2), DynamicGaps()) << std::endl;
std::cout << ali;
std::cout << "Aligns Seq1[" << clippedBeginPosition(row(ali, 0)) << ":" << (clippedEndPosition(row(ali, 0)) - 1) << "]";
std::cout << " and Seq2[" << clippedBeginPosition(row(ali, 1)) << ":" << (clippedEndPosition(row(ali, 1)) - 1) << "]" << std::endl << std::endl;
//![ali1]
//![init2]
Align<String<Dna> > ali2;
resize(rows(ali2), 2);
assignSource(row(ali2, 0), "ataagcgtctcg");
assignSource(row(ali2, 1), "tcatagagttgc");
//![init2]
//![ali2]
Score<int> scoring(2, -1, -2, 0);
LocalAlignmentEnumerator<Score<int>, Unbanded> enumerator(scoring, 5);
while (nextLocalAlignment(ali2, enumerator))
{
std::cout << "Score = " << getScore(enumerator) << std::endl;
std::cout << ali2;
std::cout << "Aligns Seq1[" << clippedBeginPosition(row(ali2, 0)) << ":" << (clippedEndPosition(row(ali2, 0)) - 1) << "]";
std::cout << " and Seq2[" << clippedBeginPosition(row(ali2, 1)) << ":" << (clippedEndPosition(row(ali2, 1)) - 1) << "]" << std::endl << std::endl;
}
return 0;
}
//![ali2]
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