/usr/include/blasr/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | #ifndef _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
#define _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
#include <string>
#include <iostream>
#include <stdint.h>
#include <string>
#include <cstring>
#include <ostream>
#include "Types.h"
#include "NucConversion.hpp"
#include "Enumerations.h"
#include "DNASequence.hpp"
#include "FASTASequence.hpp"
#include "FASTQSequence.hpp"
#include "DistanceMatrixScoreFunction.hpp"
template<typename T_RefSequence, typename T_QuerySequence>
void DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::InitializeScoreMatrix(int scoreMatrixP[5][5]) {
int i, j;
for (i = 0; i < 5; i++ ){
for (j = 0; j < 5; j++ ){
scoreMatrix[i][j] = scoreMatrixP[i][j];
}
}
}
template<typename T_RefSequence, typename T_QuerySequence>
DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::DistanceMatrixScoreFunction() : BaseScoreFunction() {
}
template<typename T_RefSequence, typename T_QuerySequence>
DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::DistanceMatrixScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP) : BaseScoreFunction() {
InitializeScoreMatrix(scoreMatrixP);
ins = insertionP;
del = deletionP;
}
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Deletion(
T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq,
DNALength queryPos) {
return del;
}
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Insertion(
T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq,
DNALength queryPos) {
return ins;
}
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Deletion(
T_RefSequence &seq, DNALength pos) {
return del;
}
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Match(
T_RefSequence &ref, DNALength refPos, T_QuerySequence &query,
DNALength queryPos) {
return scoreMatrix[ThreeBit[ref[refPos]]][ThreeBit[query[queryPos]]];
}
//
// Define the score function on dereferenced pointers for speed.
//
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Match(
Nucleotide ref, Nucleotide query) {
return scoreMatrix[ThreeBit[ref]][ThreeBit[query]];
}
template<typename T_RefSequence, typename T_QuerySequence>
int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Insertion(
T_QuerySequence &seq, DNALength pos) {
return ins;
}
template<typename T_RefSequence, typename T_QuerySequence>
float
DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>
::NormalizedMatch(T_RefSequence &ref, DNALength refPos,
T_QuerySequence &query, DNALength queryPos) {return 0;}
template<typename T_RefSequence, typename T_QuerySequence>
float DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>
::NormalizedInsertion(T_RefSequence &ref, DNALength refPos,
T_QuerySequence &query, DNALength queryPos) {return 0;}
template<typename T_RefSequence, typename T_QuerySequence>
float DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos) {return 0;}
#endif // _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
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