Implements fitting of a two-step function to a number sequence. More...
#include <fitonoff.hh>
Public Member Functions | |
FitOnOff (numseq_t &x_, double delta_01_, double delta_10_, double beta_) | |
double | viterbi (double c0, double c1, bool traceback) |
double | best_once_on (double c0, double c1) |
pf_t | forward (double c0, double c1) |
std::pair< double, double > | optimize (double c0, double c1) |
void | write_viterbi_path_compact (std::ostream &out, double c0, double c1) |
writes the ranges in the viterbi path | |
void | write_viterbi_path (std::ostream &out, double c0, double c1) const |
writes the viterbi path | |
void | print_table (const std::string &name, const std::vector< bool > &v) const |
void | print_table (const std::string &name, const std::vector< pf_t > &v) const |
void | print_tables () const |
Implements fitting of a two-step function to a number sequence.
LocARNA::FitOnOff::FitOnOff | ( | numseq_t & | x_, |
double | delta_01_, | ||
double | delta_10_, | ||
double | beta_ | ||
) | [inline] |
construct with parameters
x_ | number sequence that we want to fit |
delta_01_ | penalty for change from a to b |
delta_10_ | penalty for change from b to a |
beta_ | is the inverse temperature |
double LocARNA::FitOnOff::best_once_on | ( | double | c0, |
double | c1 | ||
) |
best path that is "on" (=c1) exactly once
c0 | off-value |
c1 | on-value |
pf_t LocARNA::FitOnOff::forward | ( | double | c0, |
double | c1 | ||
) |
compute forward partition functions fills tables v
std::pair< double, double > LocARNA::FitOnOff::optimize | ( | double | c0, |
double | c1 | ||
) |
optimize c0 and c1 by gradient optimization
void LocARNA::FitOnOff::print_table | ( | const std::string & | name, |
const std::vector< bool > & | v | ||
) | const |
Print boolean vector to cout
name | Identifier name to be printed |
v | Vector |
void LocARNA::FitOnOff::print_table | ( | const std::string & | name, |
const std::vector< pf_t > & | v | ||
) | const |
Print vector of partition functions (pf_t) to cout
name | Identifier name to be printed |
v | Vector |
void LocARNA::FitOnOff::print_tables | ( | ) | const |
Print DP-tables for debugging to cout
double LocARNA::FitOnOff::viterbi | ( | double | c0, |
double | c1, | ||
bool | traceback | ||
) |
compute the viterbi score (and optionally path) fills tables v, optionally compute t and trace
c0 | off-value |
c1 | on-value |
traceback | whether to perform traceback |