LocARNA::FitOnOff Class Reference

Implements fitting of a two-step function to a number sequence. More...

#include <fitonoff.hh>

Inheritance diagram for LocARNA::FitOnOff:

Public Member Functions
	FitOnOff (numseq_t &x_, double delta_, 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

Protected Member Functions
virtual double	delta (int i) const
virtual double	exp_delta (int i) const

Detailed Description

Implements fitting of a two-step function to a number sequence.

Constructor & Destructor Documentation

FitOnOff()

LocARNA::FitOnOff::FitOnOff ( numseq_t &  x_, double  delta_, double  beta_  )

inline

construct with parameters

Parameters

x_	number sequence that we want to fit
delta_	penalty for change between a and b
beta_	is the inverse temperature

Member Function Documentation

best_once_on()

double LocARNA::FitOnOff::best_once_on	(	double	c0,
		double	c1
	)

best path that is "on" (=c1) exactly once

Parameters

c0	off-value
c1	on-value

Returns

score of best path post: best path is in trace

forward()

pf_t LocARNA::FitOnOff::forward	(	double	c0,
		double	c1
	)

compute forward partition functions fills tables v

optimize()

std::pair< double, double > LocARNA::FitOnOff::optimize	(	double	c0,
		double	c1
	)

optimize c0 and c1 by gradient optimization

Returns

optimal c0 and c1

print_table() [1/2]

void LocARNA::FitOnOff::print_table	(	const std::string &	name,
		const std::vector< bool > &	v
	)		const

Print boolean vector to cout

Parameters

name	Identifier name to be printed
v	Vector

print_table() [2/2]

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

Parameters

name	Identifier name to be printed
v	Vector

print_tables()

void LocARNA::FitOnOff::print_tables

(

)

const

Print DP-tables for debugging to cout

See also

print_table()

viterbi()

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

Parameters

c0	off-value
c1	on-value
traceback	whether to perform traceback

---

The documentation for this class was generated from the following files:

• src/LocARNA/fitonoff.hh
• src/LocARNA/fitonoff.cc