| alphabet() const | core::sequence::SequenceProfile | inline |
| alphabet(utility::vector1< std::string > new_alphabet) | core::sequence::SequenceProfile | inline |
| append_char(char new_char) | core::sequence::Sequence | |
| append_gap() | core::sequence::Sequence | |
| at(core::Size pos) const | core::sequence::Sequence | |
| clone() const override | core::sequence::SequenceProfile | inlinevirtual |
| convert_profile_to_probs(core::Real temp=1.0) | core::sequence::SequenceProfile | |
| delete_position(core::Size pos) override | core::sequence::SequenceCoupling | virtual |
| edgeList() const | core::sequence::SequenceCoupling | inline |
| edgeList(utility::vector1< utility::vector1< Size > > const &eList) | core::sequence::SequenceCoupling | inline |
| edgeList_ | core::sequence::SequenceCoupling | private |
| edgePotBetween(Size vert1, Size vert2) const | core::sequence::SequenceCoupling | |
| edgePotBetween(Size edgeId) const | core::sequence::SequenceCoupling | |
| edgePots() const | core::sequence::SequenceCoupling | inline |
| edgePots(utility::vector1< utility::vector1< utility::vector1< Real > > > const &ePots) | core::sequence::SequenceCoupling | inline |
| edgePots_ | core::sequence::SequenceCoupling | private |
| FileName typedef | core::sequence::SequenceCoupling | private |
| findEdgeId(Size vert1, Size vert2) const | core::sequence::SequenceCoupling | |
| gap_char(char gap_char) | core::sequence::Sequence | |
| gap_char() const | core::sequence::Sequence | |
| generate_from_sequence(Sequence const &seq, std::string matrix="BLOSUM62") | core::sequence::SequenceProfile | virtual |
| global_auto_rescale() | core::sequence::SequenceProfile | |
| id(std::string new_id) | core::sequence::Sequence | |
| id() const | core::sequence::Sequence | |
| insert_char(core::Size pos, char new_char) override | core::sequence::SequenceCoupling | virtual |
| insert_gap(core::Size pos) | core::sequence::Sequence | |
| is_gap(core::Size pos) const | core::sequence::Sequence | |
| length() const | core::sequence::Sequence | virtual |
| negative_better() const | core::sequence::SequenceProfile | inline |
| negative_better(bool negbet) | core::sequence::SequenceProfile | inline |
| npos() const | core::sequence::SequenceCoupling | inline |
| numEdges_ | core::sequence::SequenceCoupling | private |
| numVerts_ | core::sequence::SequenceCoupling | private |
| occurrence_data() const | core::sequence::SequenceProfile | |
| occurrence_data(utility::vector1< utility::vector1< Real > > const &new_occurrence_data) | core::sequence::SequenceProfile | |
| operator<(const Sequence &s) const | core::sequence::Sequence | inline |
| operator=(Sequence const &rhs) | core::sequence::Sequence | inline |
| operator==(SequenceProfile const &other) const | core::sequence::SequenceProfile | |
| core::sequence::Sequence::operator==(const Sequence &s) const | core::sequence::Sequence | inline |
| operator[](core::Size pos) const | core::sequence::Sequence | |
| probability_row(Size pos) const | core::sequence::SequenceProfile | |
| probabilty_row(utility::vector1< Real > const &new_prob_row, core::Size pos) | core::sequence::SequenceProfile | |
| prof_row(Size pos) const | core::sequence::SequenceProfile | |
| prof_row(utility::vector1< Real > const &new_prof_row, core::Size pos) | core::sequence::SequenceProfile | |
| profile() const | core::sequence::SequenceProfile | |
| profile(utility::vector1< utility::vector1< Real > > const &new_profile) | core::sequence::SequenceProfile | |
| read_data(std::istream &in) | core::sequence::Sequence | |
| read_from_binary_chk(FileName const &fn) | core::sequence::SequenceProfile | |
| read_from_checkpoint(FileName const &fn, bool negative_better=true) | core::sequence::SequenceProfile | |
| read_from_file(FileName const &fn) override | core::sequence::SequenceCoupling | virtual |
| read_from_file(utility::file::FileName const &fn, Real temp) | core::sequence::SequenceCoupling | virtual |
| replace_char(core::Size pos, char new_char) | core::sequence::Sequence | virtual |
| rescale(core::Real factor=1) | core::sequence::SequenceProfile | |
| resnum(core::Size idx) const | core::sequence::Sequence | |
| Sequence() | core::sequence::Sequence | inline |
| Sequence(std::string const &seq, std::string const &id, core::Size start=1) | core::sequence::Sequence | inline |
| Sequence(core::pose::Pose const &pose) | core::sequence::Sequence | |
| Sequence(Sequence const &src) | core::sequence::Sequence | inline |
| sequence(std::string sequence) | core::sequence::Sequence | |
| sequence() const | core::sequence::Sequence | |
| SequenceCoupling() | core::sequence::SequenceCoupling | inline |
| SequenceProfile() | core::sequence::SequenceProfile | |
| SequenceProfile(FileName const &fn) | core::sequence::SequenceProfile | inline |
| SequenceProfile(FileName const &fn, bool use_occurrence_data) | core::sequence::SequenceProfile | inline |
| SequenceProfile(utility::vector1< utility::vector1< core::Real > > prof, std::string const &sequence, std::string const &id, Size start=1, bool negative_better=false, bool use_occurrence_data=false) | core::sequence::SequenceProfile | inline |
| size() const | core::sequence::SequenceProfile | inline |
| spacer_positions(utility::vector1< Size > const &spacer_positions) | core::sequence::Sequence | |
| spacer_positions() const | core::sequence::Sequence | |
| start(core::Size new_start) | core::sequence::Sequence | |
| start() const | core::sequence::Sequence | |
| string typedef | core::sequence::SequenceCoupling | private |
| temp() const | core::sequence::SequenceCoupling | inline |
| temp(core::Real const t) | core::sequence::SequenceCoupling | inline |
| temp_ | core::sequence::SequenceCoupling | private |
| to_string() const | core::sequence::Sequence | virtual |
| type() const override | core::sequence::SequenceCoupling | inlinevirtual |
| ungapped_length() const | core::sequence::Sequence | |
| ungapped_sequence() const | core::sequence::Sequence | |
| width() const | core::sequence::SequenceProfile | |
| ~Sequence() override | core::sequence::Sequence | |
1.8.7