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//////////////////////////////////////////////////////////////////////
// GlobalAlign.h
//
// Global alignment procedures using maximum weight trace.
//////////////////////////////////////////////////////////////////////
#ifndef GLOBALALIGN_H
#define GLOBALALIGN_H
#include "Score.h"
#include "Matrix.h"
#include "MultiSequence.h"
#include "Sequence.h"
#include "ProbModel.h"
//////////////////////////////////////////////////////////////////////
// Global alignment class
//////////////////////////////////////////////////////////////////////
class GlobalAlign {
enum TracebackType { NONE, UP, LEFT, UP_LEFT };
// insert gaps into aligned sequence
static Sequence *InsertGaps (const Sequence &seq, const char *alignmentPath, char ch);
public:
// maximum weight trace
static char *ComputeMWTrace (const Matrix &m, float *score = NULL, int *length = NULL);
// convert alignment path into MultiSequence
static MultiSequence *BuildAlignment (const MultiSequence &group1,
const MultiSequence &group2,
const char *alignmentPath);
// align two groups of sequences
static MultiSequence *AlignGroups (int n,
SparseMatrix **posteriors,
const MultiSequence &group1,
const MultiSequence &group2);
static float ComputeAlignmentScore (const MultiSequence &seqs,
int n,
SparseMatrix **posteriors);
};
#endif
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