All datastructures and typedefs shared among the ViennaRNA Package can be found here. More...

Detailed Description

All datastructures and typedefs shared among the ViennaRNA Package can be found here.

Collaboration diagram for (Abstract) Data Structures:

Modules
	The Fold Compound
	This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib.

	The Dynamic Programming Matrices
	This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib.

	Hash Tables
	Various implementations of hash table functions.

	Heaps
	Interface for an abstract implementation of a heap data structure.

	Buffers
	Functions that provide dynamically buffered stream-like data structures.

Files
file	dp_matrices.h
	Functions to deal with standard dynamic programming (DP) matrices.

file	basic.h
	Various data structures and pre-processor macros.

Data Structures
struct	vrna_basepair_s
	Base pair data structure used in subopt.c. More...

struct	vrna_cpair_s
	this datastructure is used as input parameter in functions of PS_dot.c More...

struct	vrna_color_s

struct	vrna_data_linear_s

struct	vrna_sect_s
	Stack of partial structures for backtracking. More...

struct	vrna_bp_stack_s
	Base pair stack element. More...

struct	pu_contrib
	contributions to p_u More...

struct	interact
	interaction data structure for RNAup More...

struct	pu_out
	Collection of all free_energy of beeing unpaired values for output. More...

struct	constrain
	constraints for cofolding More...

struct	duplexT
	Data structure for RNAduplex. More...

struct	node
	Data structure for RNAsnoop (fold energy list) More...

struct	snoopT
	Data structure for RNAsnoop. More...

struct	dupVar
	Data structure used in RNApkplex. More...

Typedefs
typedef struct vrna_basepair_s	vrna_basepair_t
	Typename for the base pair repesenting data structure vrna_basepair_s.

typedef struct vrna_elem_prob_s	vrna_plist_t
	Typename for the base pair list repesenting data structure vrna_elem_prob_s.

typedef struct vrna_bp_stack_s	vrna_bp_stack_t
	Typename for the base pair stack repesenting data structure vrna_bp_stack_s.

typedef struct vrna_cpair_s	vrna_cpair_t
	Typename for data structure vrna_cpair_s.

typedef struct vrna_sect_s	vrna_sect_t
	Typename for stack of partial structures vrna_sect_s.

typedef double	FLT_OR_DBL
	Typename for floating point number in partition function computations.

typedef struct vrna_basepair_s	PAIR
	Old typename of vrna_basepair_s. More...

typedef struct vrna_elem_prob_s	plist
	Old typename of vrna_elem_prob_s. More...

typedef struct vrna_cpair_s	cpair
	Old typename of vrna_cpair_s. More...

typedef struct vrna_sect_s	sect
	Old typename of vrna_sect_s. More...

typedef struct vrna_bp_stack_s	bondT
	Old typename of vrna_bp_stack_s. More...

typedef struct pu_contrib	pu_contrib
	contributions to p_u

typedef struct interact	interact
	interaction data structure for RNAup

typedef struct pu_out	pu_out
	Collection of all free_energy of beeing unpaired values for output.

typedef struct constrain	constrain
	constraints for cofolding

typedef struct node	folden
	Data structure for RNAsnoop (fold energy list)

typedef struct dupVar	dupVar
	Data structure used in RNApkplex.

Functions
void	vrna_C11_features (void)
	Dummy symbol to check whether the library was build using C11/C++11 features. More...

Data Structure Documentation

struct vrna_basepair_s

Base pair data structure used in subopt.c.

struct vrna_cpair_s

this datastructure is used as input parameter in functions of PS_dot.c

struct vrna_color_s

struct vrna_data_linear_s

Collaboration diagram for vrna_data_linear_s:

struct vrna_sect_s

Stack of partial structures for backtracking.

struct vrna_bp_stack_s

Base pair stack element.

struct pu_contrib

contributions to p_u

Data Fields
double **	H
	hairpin loops

double **	I
	interior loops

double **	M
	multi loops

double **	E
	exterior loop

int	length
	length of the input sequence

int	w
	longest unpaired region

struct interact

interaction data structure for RNAup

Data Fields
double *	Pi
	probabilities of interaction

double *	Gi
	free energies of interaction

double	Gikjl
	full free energy for interaction between [k,i] k<i in longer seq and [j,l] j<l in shorter seq

double	Gikjl_wo
	Gikjl without contributions for prob_unpaired.

int	i
	k<i in longer seq

int	k
	k<i in longer seq

int	j
	j<l in shorter seq

int	l
	j<l in shorter seq

int	length
	length of longer sequence

struct pu_out

Collection of all free_energy of beeing unpaired values for output.

Data Fields
int	len
	sequence length

int	u_vals
	number of different -u values

int	contribs
	[-c "SHIME"]

char **	header
	header line

double **	u_values
	(the -u values * [-c "SHIME"]) * seq len

struct constrain

constraints for cofolding

struct duplexT

Data structure for RNAduplex.

struct node

Data structure for RNAsnoop (fold energy list)

Collaboration diagram for node:

struct snoopT

Data structure for RNAsnoop.

struct dupVar

Data structure used in RNApkplex.

Typedef Documentation

typedef struct vrna_basepair_s PAIR

#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_basepair_s.

Deprecated:: Use vrna_basepair_t instead!

typedef struct vrna_elem_prob_s plist

#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_elem_prob_s.

Deprecated:: Use vrna_ep_t or vrna_elem_prob_s instead!

typedef struct vrna_cpair_s cpair

#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_cpair_s.

Deprecated:: Use vrna_cpair_t instead!

typedef struct vrna_sect_s sect

#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_sect_s.

Deprecated:: Use vrna_sect_t instead!

typedef struct vrna_bp_stack_s bondT

#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_bp_stack_s.

Deprecated:: Use vrna_bp_stack_t instead!

Function Documentation

void vrna_C11_features ( void )

#include <ViennaRNA/datastructures/basic.h>

Dummy symbol to check whether the library was build using C11/C++11 features.

By default, several data structures of our new v3.0 API use C11/C++11 features, such as unnamed unions, unnamed structs. However, these features can be deactivated at compile time to allow building the library and executables with compilers that do not support these features.

Now, the problem arises that once our static library is compiled and a third-party application is supposed to link against it, it needs to know, at compile time, how to correctly address particular data structures. This is usually implicitely taken care of through the API exposed in our header files. Unfortunately, we had some preprocessor directives in our header files that changed the API depending on the capabilities of the compiler the third-party application is build with. This in turn prohibited the use of an RNAlib compiled without C11/C++11 support in a program that compiles/links with enabled C11/C++11 support and vice-versa.

Therefore, we introduce this dummy symbol which can be used to check, whether the static library was build with C11/C++11 features.

Note: If the symbol is present, the library was build with enabled C11/C++11 features support and no action is required. However, if the symbol is missing in RNAlib >= 2.2.9, programs that link to RNAlib must define a pre-processor identifier VRNA_DISABLE_C11_FEATURES before including any ViennaRNA Package header file, for instance by adding a CPPFLAG
1 CPPFLAGS+=-DVRNA_DISABLE_C11_FEATURES

Since: v2.2.9

Detailed Description

Modules

Files

Data Structures

Typedefs

Functions

Data Structure Documentation

Data Fields

Data Fields

Data Fields

Typedef Documentation

Function Documentation