Command Files

Functions to parse and interpret the content of Command Files. More...

Detailed Description

Functions to parse and interpret the content of Command Files.

Collaboration diagram for Command Files:

Files
file	commands.h
	Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.

Macros
#define	VRNA_CMD_PARSE_HC   1U
	Command parse/apply flag indicating hard constraints. More...
#define	VRNA_CMD_PARSE_SC   2U
	Command parse/apply flag indicating soft constraints. More...
#define	VRNA_CMD_PARSE_UD   4U
	Command parse/apply flag indicating unstructured domains. More...
#define	VRNA_CMD_PARSE_SD   8U
	Command parse/apply flag indicating structured domains. More...
#define	VRNA_CMD_PARSE_DEFAULTS
	Command parse/apply flag indicating default set of commands. More...

Typedefs
typedef struct vrna_command_s *	vrna_cmd_t
	A data structure that contains commands.

Functions
vrna_cmd_t	vrna_file_commands_read (const char *filename, unsigned int options)
	Extract a list of commands from a command file. More...
int	vrna_file_commands_apply (vrna_fold_compound_t *vc, const char *filename, unsigned int options)
	Apply a list of commands from a command file. More...
int	vrna_commands_apply (vrna_fold_compound_t *vc, vrna_cmd_t commands, unsigned int options)
	Apply a list of commands to a vrna_fold_compound_t. More...
void	vrna_commands_free (vrna_cmd_t commands)
	Free memory occupied by a list of commands. More...

Macro Definition Documentation

#define VRNA_CMD_PARSE_HC   1U

#include <ViennaRNA/commands.h>

Command parse/apply flag indicating hard constraints.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

#define VRNA_CMD_PARSE_SC   2U

#include <ViennaRNA/commands.h>

Command parse/apply flag indicating soft constraints.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

#define VRNA_CMD_PARSE_UD   4U

#include <ViennaRNA/commands.h>

Command parse/apply flag indicating unstructured domains.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

#define VRNA_CMD_PARSE_SD   8U

#include <ViennaRNA/commands.h>

Command parse/apply flag indicating structured domains.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

#define VRNA_CMD_PARSE_DEFAULTS

#include <ViennaRNA/commands.h>

Value:

(VRNA_CMD_PARSE_HC \
                                 | VRNA_CMD_PARSE_SC \
                                 | VRNA_CMD_PARSE_UD \
                                 | VRNA_CMD_PARSE_SD \
                                 )

Command parse/apply flag indicating default set of commands.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

Function Documentation

vrna_cmd_t vrna_file_commands_read	(	const char *	filename,
		unsigned int	options
	)

#include <ViennaRNA/commands.h>

Extract a list of commands from a command file.

Read a list of commands specified in the input file and return them as list of abstract commands

See also

vrna_commands_apply(), vrna_file_commands_apply(), vrna_commands_free()

Parameters

filename	The filename
options	Options to limit the type of commands read from the file

Returns

A list of abstract commands

int vrna_file_commands_apply	(	vrna_fold_compound_t *	vc,
		const char *	filename,
		unsigned int	options
	)

#include <ViennaRNA/commands.h>

Apply a list of commands from a command file.

This function is a shortcut to directly parse a commands file and apply all successfully parsed commands to a vrna_fold_compound_t data structure. It is the same as:

  int                   r;
  struct vrna_command_s *cmds;

  cmds  = vrna_file_commands_read(filename, options);
  r     = vrna_commands_apply(vc, cmds, options);

  vrna_commands_free(cmds);

  return r;

Parameters

vc	The vrna_fold_compound_t the command list will be applied to
filename	The filename
options	Options to limit the type of commands read from the file

Returns

The number of commands successfully applied

SWIG Wrapper Notes:

This function is attached as method file_commands_apply() to objects of type fold_compound

int vrna_commands_apply	(	vrna_fold_compound_t *	vc,
		vrna_cmd_t	commands,
		unsigned int	options
	)

#include <ViennaRNA/commands.h>

Apply a list of commands to a vrna_fold_compound_t.

Parameters

vc	The vrna_fold_compound_t the command list will be applied to
commands	The commands to apply
options	Options to limit the type of commands read from the file

Returns

The number of commands successfully applied

void vrna_commands_free

(

vrna_cmd_t

commands

)

#include <ViennaRNA/commands.h>

Free memory occupied by a list of commands.

Release memory occupied by a list of commands

Parameters

commands

A pointer to a list of commands