Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation. More...

Include dependency graph for commands.h:

Data Structures
struct	vrna_command_s
	List element for commands ready for application to a vrna_fold_compound_t. More...

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
	Typename for the command repesenting data structure vrna_command_s.

Enumerations
enum	vrna_command_e
	Types of commands within a list of vrna_command_s structures.

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...

Detailed Description

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

Data Structures