1 #ifndef VIENNA_RNA_PACKAGE_UTILS_H 2 #define VIENNA_RNA_PACKAGE_UTILS_H 4 #ifdef VRNA_WARN_DEPRECATED 5 # if defined(__clang__) 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 PRIVATE static 40 #define VRNA_INPUT_ERROR 1U 44 #define VRNA_INPUT_QUIT 2U 48 #define VRNA_INPUT_MISC 4U 57 #define VRNA_INPUT_FASTA_HEADER 8U 64 #define VRNA_INPUT_SEQUENCE 16U 70 #define VRNA_INPUT_CONSTRAINT 32U 76 #define VRNA_INPUT_NO_TRUNCATION 256U 81 #define VRNA_INPUT_NO_REST 512U 86 #define VRNA_INPUT_NO_SPAN 1024U 91 #define VRNA_INPUT_NOSKIP_BLANK_LINES 2048U 96 #define VRNA_INPUT_BLANK_LINE 4096U 101 #define VRNA_INPUT_NOSKIP_COMMENTS 128U 106 #define VRNA_INPUT_COMMENT 8192U 111 #define MIN2(A, B) ((A) < (B) ? (A) : (B)) 116 #define MAX2(A, B) ((A) > (B) ? (A) : (B)) 121 #define MIN3(A, B, C) (MIN2((MIN2((A), (B))), (C))) 126 #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) 172 extern unsigned short xsubi[3];
228 unsigned int options);
387 void vrna_message_input_msa(
const char *s);
394 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 396 DEPRECATED(
int *get_indx(
unsigned int length),
"Use vrna_idx_col_wise() instead");
398 DEPRECATED(
int *get_iindx(
unsigned int length),
"Use vrna_idx_row_wise() instead");
412 DEPRECATED(
char *
get_line(FILE *fp),
"Use vrna_read_line() instead");
439 DEPRECATED(
void warn_user(
const char message[]),
"Use vrna_message_warning() instead");
446 DEPRECATED(
void nrerror(
const char message[]),
"Use vrna_message_error() instead()");
453 DEPRECATED(
void *
space(
unsigned size),
"Use vrna_alloc() instead");
461 unsigned size),
"Use vrna_realloc() instead");
467 DEPRECATED(
void init_rand(
void),
"Use vrna_init_rand() instead");
474 DEPRECATED(
double urn(
void),
"Use vrna_urn() instead");
481 DEPRECATED(
int int_urn(
int from,
482 int to),
"Use vrna_int_urn() instead()");
489 DEPRECATED(
void filecopy(FILE *from,
490 FILE *to),
"Use vrna_file_copy() instead");
497 DEPRECATED(
char *
time_stamp(
void),
"Use vrna_time_stamp() instead");
void * vrna_alloc(unsigned size)
Allocate space safely.
unsigned int get_input_line(char **string, unsigned int options)
void vrna_message_warning(const char *format,...)
Print a warning message.
void * xrealloc(void *p, unsigned size)
Reallocate space safely.
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_message_vinfo(FILE *fp, const char *format, va_list args)
Print an info message.
void vrna_init_rand(void)
Initialize seed for random number generator.
double urn(void)
get a random number from [0..1]
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...
char * vrna_time_stamp(void)
Get a timestamp.
Various data structures and pre-processor macros.
void vrna_message_vwarning(const char *format, va_list args)
Print a warning message.
void vrna_message_info(FILE *fp, const char *format,...)
Print an info message.
void vrna_message_verror(const char *format, va_list args)
Print an error message and die.
void vrna_message_input_seq_simple(void)
Print a line to stdout that asks for an input sequence.
void warn_user(const char message[])
Print a warning message.
char * time_stamp(void)
Get a timestamp.
char * get_line(FILE *fp)
Read a line of arbitrary length from a stream.
void * vrna_realloc(void *p, unsigned size)
Reallocate space safely.
int vrna_int_urn(int from, int to)
Generates a pseudo random integer in a specified range.
void vrna_message_error(const char *format,...)
Print an error message and die.
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 print_tty_input_seq_str(const char *s)
Print a line with a user defined string and a ruler to stdout.
void nrerror(const char message[])
Die with an error message.
unsigned short xsubi[3]
Current 48 bit random number.
int int_urn(int from, int to)
Generates a pseudo random integer in a specified range.
void filecopy(FILE *from, FILE *to)
Inefficient cp
void init_rand(void)
Make random number seeds.
double vrna_urn(void)
get a random number from [0..1]
void vrna_message_input_seq(const char *s)
Print a line with a user defined string and a ruler to stdout.