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//![solution]
#include <iostream>
#include <seqan/align.h>
using namespace seqan2;
int main()
{
// Defining all types that are needed.
typedef String<char> TSequence;
typedef Align<TSequence, ArrayGaps> TAlign;
typedef Row<TAlign>::Type TRow;
typedef Iterator<TRow>::Type TRowIterator;
TSequence seq1 = "ACGTCACCTC";
TSequence seq2 = "ACGGGCCTATC";
// Initializing the align object.
TAlign align;
resize(rows(align), 2);
assignSource(row(align, 0), seq1);
assignSource(row(align, 1), seq2);
// Use references to the rows of align.
TRow & row1 = row(align, 0);
TRow & row2 = row(align, 1);
// Insert gaps.
insertGaps(row1, 2, 2);
insertGap(row1, 7); // We need to pass the view position which is changed due to the previous insertion.
insertGaps(row2, 9, 2);
// Initialize the row iterators.
TRowIterator itRow1 = begin(row1);
TRowIterator itEndRow1 = end(row1);
TRowIterator itRow2 = begin(row2);
// Iterate over both rows simultaneously.
int gapCount = 0;
for (; itRow1 != itEndRow1; ++itRow1, ++itRow2)
{
if (isGap(itRow1))
{
gapCount += countGaps(itRow1); // Count the number of consecutive gaps from the current position in row1.
itRow1 += countGaps(itRow1); // Jump to next position to check for gaps.
itRow2 += countGaps(itRow1); // Jump to next position to check for gaps.
}
if (isGap(itRow2))
{
gapCount += countGaps(itRow2); // Count the number of consecutive gaps from the current position in row2.
itRow1 += countGaps(itRow2); // Jump to next position to check for gaps.
itRow2 += countGaps(itRow2); // Jump to next position to check for gaps.
}
}
// Print the result.
std::cout << "Number of gaps: " << gapCount << std::endl;
}
//![solution]
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