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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef PROFILEWITHSUB_H
#define PROFILEWITHSUB_H
#include "../alignment/Alignment.h"
#include "ProfileBase.h"
namespace clustalw
{
class ProfileWithSub : public ProfileBase
{
public:
/* Functions */
ProfileWithSub(int prfLen, int firstS, int lastS);
void resetPrf1();
void calcProfileWithSub(SeqArray* seqArray, vector<int>* gaps,
int matrix[NUMRES][NUMRES], vector<int>* seqWeight);
/* Attributes */
private:
/* Functions */
/* Attributes */
};
}
#endif
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