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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* NOTE: This profile is not used in the multiple alignment part. It is used for the
* the clustal Qt part. It is used in the calculation of low scoring segments.
*/
#ifndef LOWSCORESEGPROFILE_H
#define LOWSCORESEGPROFILE_H
#include "../alignment/Alignment.h"
namespace clustalw
{
class LowScoreSegProfile
{
public:
/* Functions */
LowScoreSegProfile(int prfLen, int firstS, int lastS);
void calcLowScoreSegProfile(const SeqArray* seqArray,
int matrix[NUMRES][NUMRES], vector<int>* seqWeight);
const SeqArray* getProfilePtr(){return &profile;};
/* Attributes */
protected:
/* Functions */
/* Attributes */
SeqArray profile;
int prfLength;
int firstSeq, lastSeq;
private:
/* Functions */
/* Attributes */
};
}
#endif
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