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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan;
int main()
{
typedef String<Rna> TSequence;
typedef Align<TSequence, ArrayGaps> TAlign;
typedef Row<TAlign>::Type TRow;
typedef Iterator<TRow>::Type TRowIterator;
//![main]
//![init]
TSequence seq1 = "AAGUGACUUAUUG";
TSequence seq2 = "AGUCGGAUCUACUG";
TAlign align;
resize(rows(align), 2);
assignSource(row(align, 0), seq1);
assignSource(row(align, 1), seq2);
//![init]
//![alignment]
int score = globalAlignment(align, MyersHirschberg());
std::cout << "Score: " << score << std::endl;
std::cout << align << std::endl;
//![alignment]
//![view]
unsigned aliLength = _max(length(row(align, 0)), length(row(align, 1)));
for (unsigned i = 0; i < length(rows(align)); ++i)
{
TRowIterator it = iter(row(align, i), 0);
TRowIterator itEnd = iter(row(align, i), aliLength);
unsigned pos = 0;
std::cout << "Row " << i << " contains gaps at positions: ";
std::cout << std::endl;
while (it != itEnd)
{
if (isGap(it))
std::cout << pos << std::endl;
++it;
++pos;
}
}
return 0;
}
//![view]
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