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#ifndef _PHARAOH_ALIGNMENT_H_
#define _PHARAOH_ALIGNMENT_H_
#include <string>
#include <iostream>
#include <boost/shared_ptr.hpp>
#include "array2d.h"
struct AlignmentPharaoh {
static boost::shared_ptr<Array2D<bool> > ReadPharaohAlignmentGrid(const std::string& al);
static void SerializePharaohFormat(const Array2D<bool>& alignment, std::ostream* out);
};
#endif
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