1#ifndef VIENNA_RNA_PACKAGE_UTILS_H
2#define VIENNA_RNA_PACKAGE_UTILS_H
4#ifdef VRNA_WARN_DEPRECATED
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
10# define DEPRECATED(func, msg) func
13# define DEPRECATED(func, msg) func
35#define VRNA_INPUT_ERROR 1U
39#define VRNA_INPUT_QUIT 2U
43#define VRNA_INPUT_MISC 4U
52#define VRNA_INPUT_FASTA_HEADER 8U
59#define VRNA_INPUT_SEQUENCE 16U
65#define VRNA_INPUT_CONSTRAINT 32U
71#define VRNA_INPUT_NO_TRUNCATION 256U
76#define VRNA_INPUT_NO_REST 512U
81#define VRNA_INPUT_NO_SPAN 1024U
86#define VRNA_INPUT_NOSKIP_BLANK_LINES 2048U
91#define VRNA_INPUT_BLANK_LINE 4096U
96#define VRNA_INPUT_NOSKIP_COMMENTS 128U
101#define VRNA_INPUT_COMMENT 8192U
106#define MIN2(A, B) ((A) < (B) ? (A) : (B))
111#define MAX2(A, B) ((A) > (B) ? (A) : (B))
116#define MIN3(A, B, C) (MIN2((MIN2((A), (B))), (C)))
121#define MAX3(A, B, C) (MAX2((MAX2((A), (B))), (C)))
132#define vrna_alloc(S) calloc(1, (S))
133#define vrna_realloc(p, S) xrealloc(p, S)
188extern unsigned short xsubi[3];
248 unsigned int options);
418vrna_message_input_msa(
const char *s);
425#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
427DEPRECATED(
int *get_indx(
unsigned int length),
"Use vrna_idx_col_wise() instead");
429DEPRECATED(
int *get_iindx(
unsigned int length),
"Use vrna_idx_row_wise() instead");
443DEPRECATED(
char *
get_line(FILE *fp),
"Use vrna_read_line() instead");
470DEPRECATED(
void warn_user(
const char message[]),
"Use vrna_message_warning() instead");
477DEPRECATED(
void nrerror(
const char message[]),
"Use vrna_message_error() instead()");
484DEPRECATED(
void *
space(
unsigned size),
"Use vrna_alloc() instead");
492 unsigned size),
"Use vrna_realloc() instead");
498DEPRECATED(
void init_rand(
void),
"Use vrna_init_rand() instead");
505DEPRECATED(
double urn(
void),
"Use vrna_urn() instead");
512DEPRECATED(
int int_urn(
int from,
513 int to),
"Use vrna_int_urn() instead()");
521 FILE *to),
"Use vrna_file_copy() instead");
528DEPRECATED(
char *
time_stamp(
void),
"Use vrna_time_stamp() instead");
Various data structures and pre-processor macros.
void vrna_message_info(FILE *fp, const char *format,...)
Print an info message.
void vrna_message_error(const char *format,...)
Print an error message and die.
void vrna_message_vwarning(const char *format, va_list args)
Print a warning message.
void vrna_message_warning(const char *format,...)
Print a warning message.
void vrna_message_verror(const char *format, va_list args)
Print an error message and die.
void vrna_message_vinfo(FILE *fp, const char *format, va_list args)
Print an info message.
void vrna_message_input_seq_simple(void)
Print a line to stdout that asks for an input sequence.
void vrna_message_input_seq(const char *s)
Print a line with a user defined string and a ruler to stdout.
void vrna_init_rand(void)
Initialize seed for random number generator.
char * vrna_time_stamp(void)
Get a timestamp.
int * vrna_idx_row_wise(unsigned int length)
Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...
double vrna_urn(void)
get a random number from [0..1]
int vrna_int_urn(int from, int to)
Generates a pseudo random integer in a specified range.
unsigned int get_input_line(char **string, unsigned int options)
int * vrna_idx_col_wise(unsigned int length)
Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.
void vrna_init_rand_seed(unsigned int seed)
Initialize the random number generator with a pre-defined seed.
void * vrna_realloc(void *p, unsigned size)
Reallocate space safely.
unsigned short xsubi[3]
Current 48 bit random number.
void * vrna_alloc(unsigned size)
Allocate space safely.
void nrerror(const char message[])
Die with an error message.
char * time_stamp(void)
Get a timestamp.
int int_urn(int from, int to)
Generates a pseudo random integer in a specified range.
void print_tty_input_seq(void)
Print a line to stdout that asks for an input sequence.
void * space(unsigned size)
Allocate space safely.
void * xrealloc(void *p, unsigned size)
Reallocate space safely.
void init_rand(void)
Make random number seeds.
char * get_line(FILE *fp)
Read a line of arbitrary length from a stream.
double urn(void)
get a random number from [0..1]
void filecopy(FILE *from, FILE *to)
Inefficient cp
void print_tty_input_seq_str(const char *s)
Print a line with a user defined string and a ruler to stdout.
void warn_user(const char message[])
Print a warning message.