1 #ifndef LOCARNA_STRAL_SCORE_HH 2 #define LOCARNA_STRAL_SCORE_HH 13 #include "sequence.hh" 17 template <
class T>
class Matrix;
18 template <
class T>
class Alphabet;
24 typedef std::vector<double> p_vec_t;
39 double pf_struct_weight;
44 void init_prob_vecs(
const RnaData &rna,
65 double pf_struct_weight_,
103 return gap_extension;
116 #endif //LOCARNA_STRAL_SCORE_HH represent sparsified data of RNA ensemble
Definition: rna_data.hh:42
StralScore(const RnaData &rnaA, const RnaData &rnaB, const Matrix< double > &sim_mat_, const Alphabet< char > &alphabet_, double pf_struct_weight_, double gap_opening_, double gap_extension_)
Definition: stral_score.cc:10
double sigma(size_type i, size_type j) const
Compute STRAL-like similarity of two residues in the two RNAs.
Definition: stral_score.cc:31
size_t size_type
general size type
Definition: aux.hh:94
double beta() const
Read gap extension cost.
Definition: stral_score.hh:102
Definition: aligner.cc:17
double alpha() const
Read gap opening cost.
Definition: stral_score.hh:93
Implements the stral-like scoring function.
Definition: stral_score.hh:22
void reverse()
Reverse the scoring.
Definition: stral_score.cc:77
"Sequence View" of multiple alignment as array of column vectors
Definition: sequence.hh:29