affinealignment.h

#ifndef AFFINEALIGNMENT_H
#define AFFINEALIGNMENT_H

#include "affinealignobj.h"
#include "alignment.h"
#include "utils.h"
#include "similarityMatrix.h"
#include <limits>

namespace DIAlign
{
namespace AffineAlignment
{
void doAffineAlignment(AffineAlignObj&, const SimMatrix& s, double go, double ge, bool OverlapAlignment);

void getAffineAlignedIndices(AffineAlignObj &affineAlignObj, int bandwidth = 0);

double getOlapAffineAlignStartIndices(double* MatrixM, double* MatrixA, double* MatrixB,
                                      int ROW_SIZE, int COL_SIZE, int &OlapStartRow,
                                      int &OlapStartCol, Traceback::tbJump &MatrixName);

void fillSimPath(bool* simPath, int bandwidth, int ROW_IDX, int COL_IDX, int ROW_SIZE, int COL_SIZE);

double getForwardSim(const SimMatrix& s, bool* simPath);
} // namespace AffineAlignment
} // namespace DIAlign

#endif // AFFINEALIGNMENT_H