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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef PROFILEALIGNALGORITHM_H
#define PROFILEALIGNALGORITHM_H
#include <vector>
#include "../alignment/Alignment.h"
namespace clustalw
{
class ProfileAlignAlgorithm
{
public:
virtual ~ProfileAlignAlgorithm(){};
/* Functions */
virtual int profileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* group,
int* aligned) = 0;
/* Attributes */
protected:
/* Attributes */
int prfLength1;
int prfLength2;
SeqArray seqArray;
vector<int> alnWeight;
int nseqs1;
int nseqs2;
private:
/* Functions */
/* Attributes */
};
}
#endif
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