, including all inherited members.
alphabet() const | LocARNA::Ribosum | [inline] |
alphabet_type typedef | LocARNA::Ribosum | [protected] |
am | LocARNA::Ribosum | [protected] |
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_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_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] |
LocARNA::Ribosum::operator<<(std::ostream &out, const Ribosum &ribosum) | LocARNA::Ribosum | [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_type &names) const | LocARNA::Ribosum | [protected] |
read_ribosum(std::istream &in) | LocARNA::Ribosum | [protected] |
Ribosum() | LocARNA::Ribosum | [protected] |
Ribosum(const std::string &filename) | LocARNA::Ribosum | [explicit] |
RibosumFreq(const std::string &filename) | LocARNA::RibosumFreq | [explicit] |
RibosumFreq() (defined in LocARNA::RibosumFreq) | LocARNA::RibosumFreq | [protected] |
set_arcname_alphabet(const std::string a[]) | LocARNA::Ribosum | [inline, protected] |
set_basename_alphabet(const std::string a[]) | LocARNA::Ribosum | [inline, protected] |
string_alphabet() const | LocARNA::Ribosum | [inline] |
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_type &alph) const | LocARNA::Ribosum | [protected] |
~Ribosum() | LocARNA::Ribosum | [virtual] |