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//////////////////////////////////////////////////////////////////////
// LocalAlign.h
//
// Local alignment procedures using maximum weight trace.
//////////////////////////////////////////////////////////////////////
#ifndef LOCALALIGN_H
#define LOCALALIGN_H
#include "Score.h"
#include "Matrix.h"
#include "Sequence.h"
#include "ProbModel.h"
#include "AlignedFragment.h"
//////////////////////////////////////////////////////////////////////
// Local alignment class
//////////////////////////////////////////////////////////////////////
class LocalAlign {
enum TracebackType { NONE, UP, LEFT, UP_LEFT };
public:
static AlignedFragment * ComputeLocalAlignment (const Sequence &seq1, const Sequence &seq2,
const Matrix &m, float *score = NULL);
};
#endif
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