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