ProbScan.h File Reference

#include "RNA.h"
#include "../src/defines.h"
#include <vector>
#include "../src/phmm/utils/xmath/log/xlog_math.h"

Classes
class	ProbScan

Typedefs
typedef struct hp	hairpin_t
	A ProbScan hairpin closed by i and j. More...
typedef struct il	internal_loop_t
	A ProbScan internal loop closed by i and j on the exterior and k and l in the interior, where i<k<l<j. More...
typedef struct bp	basestack_t
	A ProbScan base pair stack. More...
typedef struct mb	multibranch_loop_t
	A ProbScan multibranch loop. More...

Functions
hairpin_t	hairpin (double p, int i, int j)
internal_loop_t	internal_loop (double p, int i, int j, int k, int l)
basestack_t	basestack (double p, int i, int j, int k, int l)
multibranch_loop_t	multibranch_loop (int i, int j)
void	add_branch (multibranch_loop_t &mb, int k, int l)
void	show_hairpins (vector< hairpin_t >, bool fixed)
void	show_stacks (vector< basestack_t >, bool fixed)
void	show_internal_loops (vector< internal_loop_t >, bool fixed)
void	show_bulge_loops (vector< internal_loop_t >, bool fixed)
void	show_mbl (multibranch_loop_t mbl, bool fixed)
void	show_mb_element_array (vector< mb_element >)

Typedef Documentation

basestack_t

typedef struct bp basestack_t

A ProbScan base pair stack.

hairpin_t

typedef struct hp hairpin_t

A ProbScan hairpin closed by i and j.

internal_loop_t

typedef struct il internal_loop_t

A ProbScan internal loop closed by i and j on the exterior and k and l in the interior, where i<k<l<j.

multibranch_loop_t

typedef struct mb multibranch_loop_t

A ProbScan multibranch loop.

A multibranch loop, represented by a vector pairs. branches[0] must close the multibranch loop

Function Documentation

add_branch()

void add_branch	(	multibranch_loop_t &	mb,
		int	k,
		int	l
	)

basestack()

basestack_t basestack	(	double	p,
		int	i,
		int	j,
		int	k,
		int	l
	)

hairpin()

hairpin_t hairpin	(	double	p,
		int	i,
		int	j
	)

internal_loop()

internal_loop_t internal_loop	(	double	p,
		int	i,
		int	j,
		int	k,
		int	l
	)

multibranch_loop()

multibranch_loop_t multibranch_loop	(	int	i,
		int	j
	)

show_bulge_loops()

void show_bulge_loops	(	vector< internal_loop_t >	,
		bool	fixed
	)

show_hairpins()

void show_hairpins	(	vector< hairpin_t >	,
		bool	fixed
	)

show_internal_loops()

void show_internal_loops	(	vector< internal_loop_t >	,
		bool	fixed
	)

show_mb_element_array()

void show_mb_element_array

(

vector< mb_element >

)

show_mbl()

void show_mbl	(	multibranch_loop_t	mbl,
		bool	fixed
	)

show_stacks()

void show_stacks	(	vector< basestack_t >	,
		bool	fixed
	)