1 #ifndef NUCLEOTIDE_MATRIX_H
2 #define NUCLEOTIDE_MATRIX_H
3 
4 #include "SubstitutionMatrix.h"
5 
6 class NucleotideMatrix : public SubstitutionMatrix {
7 public:
8     NucleotideMatrix(const char *scoringMatrixFileName, float bitFactor, float scoreBias);
9 
10     virtual ~NucleotideMatrix();
11 
12     using BaseMatrix::getBitFactor;
13 
14     void setupLetterMapping();
15 
reverseResidue(int res)16     int reverseResidue(int res) {
17         return reverseLookup[res];
18     }
19 
20 private:
21     int *reverseLookup;
22 };
23 
24 #endif
25