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RNAlib-2.3.4
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Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation. More...
Include dependency graph for commands.h:Go to the source code of this file.
Data Structures | |
| struct | vrna_command_s |
| List element for commands ready for application to a vrna_fold_compound_t. More... | |
| #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... | |
| typedef struct vrna_command_s | vrna_cmd_t |
| Typename for the command repesenting data structure vrna_command_s. | |
| 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... | |
Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
| #define VRNA_CMD_PARSE_HC 1U |
Command parse/apply flag indicating hard constraints.
| #define VRNA_CMD_PARSE_SC 2U |
Command parse/apply flag indicating soft constraints.
| #define VRNA_CMD_PARSE_UD 4U |
Command parse/apply flag indicating unstructured domains.
| #define VRNA_CMD_PARSE_SD 8U |
Command parse/apply flag indicating structured domains.
| #define VRNA_CMD_PARSE_DEFAULTS |
Command parse/apply flag indicating default set of commands.
| vrna_cmd_t* vrna_file_commands_read | ( | const char * | filename, |
| unsigned int | options | ||
| ) |
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
| filename | The filename |
| options | Options to limit the type of commands read from the file |
| 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.
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:
| 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 |
| 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.
| vc | The vrna_fold_compound_t the command list will be applied to |
| commands | The list of commands to apply |
| options | Options to limit the type of commands read from the file |
| void vrna_commands_free | ( | vrna_cmd_t * | commands | ) |
Free memory occupied by a list of commands.
Release memory occupied by a list of commands
| commands | A pointer to a list of commands |