alphabet() const | core::sequence::ChemicalShiftSequence | inline |
alphabet(utility::vector1< std::string > new_alphabet) | core::sequence::ChemicalShiftSequence | inline |
alphabet_ | core::sequence::ChemicalShiftSequence | private |
append_char(char new_char) | core::sequence::Sequence | |
append_gap() | core::sequence::Sequence | |
at(core::Size pos) const | core::sequence::Sequence | |
check_internals_() const | core::sequence::ChemicalShiftSequence | private |
ChemicalShiftSequence() | core::sequence::ChemicalShiftSequence | inline |
ChemicalShiftSequence(FileName const &fn) | core::sequence::ChemicalShiftSequence | inline |
ChemicalShiftSequence(utility::vector1< utility::vector1< core::Real > > cs_prof, std::string const &seq, std::string const &ident, Size start_idx=1) | core::sequence::ChemicalShiftSequence | inline |
ChemicalShiftSequence(ChemicalShiftSequence const &src) | core::sequence::ChemicalShiftSequence | inline |
clone() const | core::sequence::ChemicalShiftSequence | inlinevirtual |
convert_profile_to_probs(core::Real temp=1.0) | core::sequence::SequenceProfile | |
delete_position(core::Size pos) | core::sequence::SequenceProfile | virtual |
FileName typedef | core::sequence::ChemicalShiftSequence | private |
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) | core::sequence::SequenceProfile | 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 |
operator<(const Sequence &s) const | core::sequence::Sequence | inline |
operator<<(std::ostream &out, const ChemicalShiftSequence &p) | core::sequence::ChemicalShiftSequence | friend |
operator=(ChemicalShiftSequence const &rhs) | core::sequence::ChemicalShiftSequence | inline |
core::sequence::SequenceProfile::operator=(SequenceProfile const &rhs) | core::sequence::SequenceProfile | inline |
core::sequence::Sequence::operator=(Sequence const &rhs) | core::sequence::Sequence | inline |
operator==(const Sequence &s) const | core::sequence::Sequence | inline |
operator[](core::Size pos) const | core::sequence::Sequence | |
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_checkpoint(FileName const &fn, bool negative_better=true) | core::sequence::SequenceProfile | |
read_from_file(FileName const &fn) | core::sequence::ChemicalShiftSequence | virtual |
rescale(core::Real factor=1) | core::sequence::SequenceProfile | |
resnum(core::Size idx) const | core::sequence::Sequence | |
sequence(std::string sequence) | core::sequence::Sequence | |
sequence() const | core::sequence::Sequence | |
Sequence() | core::sequence::Sequence | inline |
Sequence(std::string seq, std::string 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 |
SequenceProfile() | core::sequence::SequenceProfile | inline |
SequenceProfile(FileName const &fn) | 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) | core::sequence::SequenceProfile | inline |
SequenceProfile(SequenceProfile const &src) | core::sequence::SequenceProfile | inline |
sigma(Size, Size idx) | core::sequence::ChemicalShiftSequence | |
size() const | core::sequence::SequenceProfile | inline |
start(core::Size new_start) | core::sequence::Sequence | |
start() const | core::sequence::Sequence | |
string typedef | core::sequence::ChemicalShiftSequence | private |
temp() const | core::sequence::SequenceProfile | inline |
to_string() const | core::sequence::Sequence | virtual |
type() const | core::sequence::SequenceProfile | inlinevirtual |
ungapped_length() const | core::sequence::Sequence | |
ungapped_sequence() const | core::sequence::Sequence | |
width() const | core::sequence::SequenceProfile | |
~ChemicalShiftSequence() | core::sequence::ChemicalShiftSequence | inlinevirtual |
~Sequence() | core::sequence::Sequence | virtual |
~SequenceProfile() | core::sequence::SequenceProfile | inline |