/usr/include/blasr/algorithms/alignment/DistanceMatrixScoreFunction.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | #ifndef _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
#define _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
#include "BaseScoreFunction.hpp"
#include "ScoreMatrices.hpp"
template<typename T_RefSequence, typename T_QuerySequence>
class DistanceMatrixScoreFunction : public BaseScoreFunction {
public:
int scoreMatrix[5][5];
DistanceMatrixScoreFunction();
DistanceMatrixScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP);
void InitializeScoreMatrix(int scoreMatrixP[5][5]);
int Deletion(T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq, DNALength queryPos);
int Insertion(T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq, DNALength queryPos);
int Deletion(T_RefSequence &seq, DNALength pos);
int Match(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
//
// Define the score function on dereferenced pointers for speed.
//
int Match(Nucleotide ref, Nucleotide query);
int Insertion(T_QuerySequence &seq, DNALength pos);
float NormalizedMatch(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
float NormalizedInsertion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
float NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
};
#include "DistanceMatrixScoreFunctionImpl.hpp"
#endif // _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
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