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#ifndef _ALIGNMENT_IO_H_
#define _ALIGNMENT_IO_H_
#include <string>
#include <iostream>
#include <boost/shared_ptr.hpp>
#include "array2d.h"
struct AlignmentIO {
enum AlignmentType { kNONE = 0, kTRANSLATION = 1, kTRANSLITERATION = 2 };
static boost::shared_ptr<Array2D<bool> > ReadPharaohAlignmentGrid(const std::string& al);
static void SerializePharaohFormat(const Array2D<bool>& alignment, std::ostream* out);
static void SerializeTypedAlignment(const Array2D<AlignmentType>& alignment, std::ostream* out);
};
inline std::ostream& operator<<(std::ostream& os, const Array2D<AlignmentIO::AlignmentType>& m) {
os << ' ';
for (int j=0; j<m.height(); ++j)
os << (j%10);
os << "\n";
for (int i=0; i<m.width(); ++i) {
os << (i%10);
for (int j=0; j<m.height(); ++j) {
switch (m(i,j)) {
case AlignmentIO::kNONE: os << '.'; break;
case AlignmentIO::kTRANSLATION: os << '*'; break;
case AlignmentIO::kTRANSLITERATION: os << '#'; break;
default: os << '?'; break;
}
}
os << (i%10) << "\n";
}
os << ' ';
for (int j=0; j<m.height(); ++j)
os << (j%10);
os << "\n";
return os;
}
#endif
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