| alphabet() const | LocARNA::Ribosum | inline |
| am_ | LocARNA::Ribosum | protected |
| arc_alphabet_type typedef | LocARNA::Ribosum | |
| arcmatch_prob(char i, char j, char k, char l) const | LocARNA::RibosumFreq | inline |
| arcmatch_probs_ | LocARNA::RibosumFreq | protected |
| arcmatch_score(char i, char j, char k, char l) const | LocARNA::Ribosum | inline |
| arcname_alphabet_ | LocARNA::Ribosum | protected |
| base_alphabet_type typedef | LocARNA::Ribosum | |
| base_nonstruct_prob(char i) const | LocARNA::RibosumFreq | inline |
| base_nonstruct_probs_ | LocARNA::RibosumFreq | protected |
| base_prob(char i) const | LocARNA::RibosumFreq | inline |
| base_probs_ | LocARNA::RibosumFreq | protected |
| base_unpaired_prob(char i) const | LocARNA::RibosumFreq | |
| basematch_prob(char i, char j) const | LocARNA::RibosumFreq | inline |
| basematch_probs_ | LocARNA::RibosumFreq | protected |
| basematch_score(char i, char j) const | LocARNA::Ribosum | inline |
| basematch_score_corrected(char i, char j) const | LocARNA::RibosumFreq | |
| basename_alphabet_ | LocARNA::Ribosum | protected |
| basepair_prob(char i, char j) const | LocARNA::RibosumFreq | inline |
| basepair_probs_ | LocARNA::RibosumFreq | protected |
| bm_ | LocARNA::Ribosum | protected |
| char_alphabet_type typedef | LocARNA::Ribosum | |
| char_basename_alphabet_ | LocARNA::Ribosum | protected |
| get_arcmatch_probs() const | LocARNA::RibosumFreq | inline |
| get_arcmatch_scores() const | LocARNA::Ribosum | inline |
| get_base_nonstruct_probs() const | LocARNA::RibosumFreq | inline |
| get_base_probs() const | LocARNA::RibosumFreq | inline |
| get_basematch_probs() const | LocARNA::RibosumFreq | inline |
| get_basematch_scores() const | LocARNA::Ribosum | inline |
| get_basepair_probs() const | LocARNA::RibosumFreq | inline |
| get_name() const | LocARNA::Ribosum | inline |
| make_char_alphabet() const | LocARNA::Ribosum | protected |
| matrix_t typedef | LocARNA::Ribosum | |
| name_ | LocARNA::Ribosum | protected |
| operator<<(std::ostream &out, const RibosumFreq &ribosum) | LocARNA::RibosumFreq | friend |
| print_basematch_scores_corrected(std::ostream &out) const | LocARNA::RibosumFreq | |
| read_matrix(std::istream &in, const std::string &header, matrix_t &mat, size_t xdim, size_t ydim) | LocARNA::RibosumFreq | |
| LocARNA::Ribosum::read_matrix(std::istream &in, matrix_t &mat, const Alphabet< std::string, N > &names) const | LocARNA::Ribosum | protected |
| read_ribosum(std::istream &in) | LocARNA::Ribosum | protected |
| Ribosum(const std::string &filename) | LocARNA::Ribosum | explicit |
| Ribosum() | LocARNA::Ribosum | protected |
| RibosumFreq(const std::string &filename) | LocARNA::RibosumFreq | explicit |
| RibosumFreq() (defined in LocARNA::RibosumFreq) | LocARNA::RibosumFreq | protected |
| set_arcname_alphabet(const std::array< std::string, 16 > &a) | LocARNA::Ribosum | inlineprotected |
| set_basename_alphabet(const std::array< std::string, 4 > &a) | LocARNA::Ribosum | inlineprotected |
| string_alphabet() const | LocARNA::Ribosum | inline |
| write_CC_matrix(std::ostream &out, const std::string &ribname, const std::string &matname, int x, int y, const Ribosum::matrix_t &m) const (defined in LocARNA::RibosumFreq) | LocARNA::RibosumFreq | protected |
| write_ICC_code(std::ostream &out, const std::string &ribname) const | LocARNA::RibosumFreq | |
| write_matrix(std::ostream &out, const std::string &name, const Matrix< double > &mat) const | LocARNA::RibosumFreq | |
| LocARNA::Ribosum::write_matrix(std::ostream &out, const matrix_t &mat, const Alphabet< std::string, N > &alph) const | LocARNA::Ribosum | protected |
| ~Ribosum() | LocARNA::Ribosum | virtual |
