basic.h

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#ifndef VIENNA_RNA_PACKAGE_UTILS_H
#define VIENNA_RNA_PACKAGE_UTILS_H

#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

#include <stdio.h>
#include <stdarg.h>

#include <ViennaRNA/datastructures/basic.h>

/* two helper macros to indicate whether a function should be exported in
 * the library or stays hidden */
#define PUBLIC
#define PRIVATE static

#define VRNA_INPUT_ERROR                  1U

#define VRNA_INPUT_QUIT                   2U

#define VRNA_INPUT_MISC                   4U

#define VRNA_INPUT_FASTA_HEADER           8U

/*
 *  @brief  Input flag for get_input_line():\n
 *  Tell get_input_line() that we assume to read a nucleotide sequence
 *
 */
#define VRNA_INPUT_SEQUENCE               16U

#define VRNA_INPUT_CONSTRAINT             32U

#define VRNA_INPUT_NO_TRUNCATION          256U

#define VRNA_INPUT_NO_REST                512U

#define VRNA_INPUT_NO_SPAN                1024U

#define VRNA_INPUT_NOSKIP_BLANK_LINES     2048U

#define VRNA_INPUT_BLANK_LINE             4096U

#define VRNA_INPUT_NOSKIP_COMMENTS        128U

#define VRNA_INPUT_COMMENT                8192U

#define MIN2(A, B)      ((A) < (B) ? (A) : (B))

#define MAX2(A, B)      ((A) > (B) ? (A) : (B))

#define MIN3(A, B, C)   (MIN2((MIN2((A), (B))), (C)))

#define MAX3(A, B, C)   (MAX2((MAX2((A), (B))), (C)))


#ifdef WITH_DMALLOC
/* use dmalloc library to check for memory management bugs */
#include "dmalloc.h"
#define vrna_alloc(S)       calloc(1, (S))
#define vrna_realloc(p, S)  xrealloc(p, S)
#else

void *
vrna_alloc(unsigned size);


void *
vrna_realloc(void     *p,
             unsigned size);


#endif

void
vrna_init_rand(void);


extern unsigned short xsubi[3];

double
vrna_urn(void);


int
vrna_int_urn(int  from,
             int  to);


char *
vrna_time_stamp(void);


unsigned int
get_input_line(char         **string,
               unsigned int options);


int *
vrna_idx_row_wise(unsigned int length);


int *
vrna_idx_col_wise(unsigned int length);


void
vrna_message_error(const char *format,
                   ...);


void
vrna_message_verror(const char  *format,
                    va_list     args);


void
vrna_message_warning(const char *format,
                     ...);


void
vrna_message_vwarning(const char  *format,
                      va_list     args);


void
vrna_message_info(FILE        *fp,
                  const char  *format,
                  ...);


void
vrna_message_vinfo(FILE       *fp,
                   const char *format,
                   va_list    args);


void
vrna_message_input_seq_simple(void);


void
vrna_message_input_seq(const char *s);


void
vrna_message_input_msa(const char *s);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

DEPRECATED(int *get_indx(unsigned int length), "Use vrna_idx_col_wise() instead");

DEPRECATED(int *get_iindx(unsigned int length), "Use vrna_idx_row_wise() instead");

DEPRECATED(char *get_line(FILE *fp), "Use vrna_read_line() instead");

DEPRECATED(void print_tty_input_seq(void), "Use vrna_message_input_seq_simple() instead");

DEPRECATED(void print_tty_input_seq_str(const char *s), "Use vrna_message_input_seq() instead");

DEPRECATED(void warn_user(const char message[]), "Use vrna_message_warning() instead");

DEPRECATED(void nrerror(const char message[]), "Use vrna_message_error() instead()");

DEPRECATED(void *space(unsigned size), "Use vrna_alloc() instead");

DEPRECATED(void *xrealloc(void      *p,
                          unsigned  size), "Use vrna_realloc() instead");

DEPRECATED(void init_rand(void), "Use vrna_init_rand() instead");

DEPRECATED(double urn(void), "Use vrna_urn() instead");

DEPRECATED(int int_urn(int  from,
                       int  to), "Use vrna_int_urn() instead()");

DEPRECATED(void filecopy(FILE *from,
                         FILE *to), "Use vrna_file_copy() instead");

DEPRECATED(char *time_stamp(void), "Use vrna_time_stamp() instead");

#endif

#endif