text: //FRAGMENT(main)
  #include <iostream>
  #include <seqan/align.h>
  
  using namespace seqan;
  
  int main()
  {
  //FRAGMENT(init1)
  	Align< String<char> > ali;
  	resize(rows(ali), 2);
  	assignSource(row(ali, 0), "aphilologicaltheorem");
  	assignSource(row(ali, 1), "bizarreamphibology");
  
  //FRAGMENT(ali1)
  	std::cout << "Score = " << localAlignment(ali, Score<int>(3,-3,-2, -2)) << 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;
  
  //FRAGMENT(init2)
  	Align< String<Dna> > ali2;
  	resize(rows(ali2), 2);
  	assignSource(row(ali2, 0), "ataagcgtctcg");
  	assignSource(row(ali2, 1), "tcatagagttgc");
  
  //FRAGMENT(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;
  }
  