utils.h

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#ifndef __VIENNA_RNA_PACKAGE_UTILS_H__
#define __VIENNA_RNA_PACKAGE_UTILS_H__

#define VRNA_INPUT_ERROR                  1U

#define VRNA_INPUT_QUIT                   2U

#define VRNA_INPUT_MISC                   4U

#define VRNA_INPUT_FASTA_HEADER           8U

#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 VRNA_CONSTRAINT_PIPE              1U

#define VRNA_CONSTRAINT_DOT               2U

#define VRNA_CONSTRAINT_X                 4U

#define VRNA_CONSTRAINT_ANG_BRACK         8U

#define VRNA_CONSTRAINT_RND_BRACK         16U

#define VRNA_CONSTRAINT_MULTILINE         32U

#define VRNA_CONSTRAINT_NO_HEADER         64U

#define VRNA_CONSTRAINT_ALL              128U

#define VRNA_CONSTRAINT_G                256U



#define VRNA_OPTION_MULTILINE             32U


#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)))


#define XSTR(s) STR(s)

#define STR(s) #s

#ifndef FILENAME_MAX_LENGTH

#define FILENAME_MAX_LENGTH   80

#define FILENAME_ID_LENGTH    42
#endif


#ifdef HAVE_CONFIG_H
#include <config.h>
#ifndef HAVE_STRDUP
char *strdup(const char *s);
#endif
#endif
#ifdef WITH_DMALLOC
/* use dmalloc library to check for memory management bugs */
#include "dmalloc.h"
#define space(S) calloc(1,(S))
#else

/*@only@*/ /*@notnull@*/
void  *space(unsigned size) /*@ensures MaxSet(result) == (size-1);@*/;

/*@only@*/ /*@notnull@*/
void  *xrealloc(/*@null@*/ /*@only@*/ /*@out@*/ /*@returned@*/ void *p,
                unsigned size) /*@modifies *p @*/ /*@ensures MaxSet(result) == (size-1) @*/;
#endif

/*@exits@*/
void nrerror(const char message[]);

void warn_user(const char message[]);

void   init_rand(void);

extern unsigned short xsubi[3];

double urn(void);

int    int_urn(int from, int to);

void   filecopy(FILE *from, FILE *to); /* inefficient `cp' */

/*@observer@*/
char  *time_stamp(void);

/*@only@*/ /*@notnull@*/
char  *random_string(int l, const char symbols[]);

int   hamming(const char *s1, const char *s2);

int   hamming_bound(const char *s1, const char *s2, int n);

/*@only@*/ /*@null@*/
char  *get_line(FILE *fp);

int skip_comment_lines(char **line);

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

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

unsigned int read_record( char **header,
                          char **sequence,
                          char  ***rest,
                          unsigned int options);


/* \brief Extract a dot-bracket structure string from (multiline)character array
 *
 * This function extracts a dot-bracket structure string from the 'rest' array as
 * returned by read_record() and returns it. All occurences of comments within the
 * 'lines' array will be skipped as long as they do not break the structure string.
 * If no structure could be read, this function returns NULL.
 *
 * \see read_record()
 *
 * \param lines   The (multiline) character array to be parsed
 * \param length  The assumed length of the dot-bracket string (passing a value < 1 results in no length limit)
 * \param option  Some options which may be passed to alter the behavior of the function, use 0 for no options
 * \return        The dot-bracket string read from lines or NULL
 */
char *extract_record_rest_structure(const char **lines,
                                    unsigned int length,
                                    unsigned int option);

char *pack_structure(const char *struc);

char *unpack_structure(const char *packed);

short *make_pair_table(const char *structure);

short *make_pair_table_pk(const char *structure);

short *copy_pair_table(const short *pt);

short *alimake_pair_table(const char *structure);

short *make_pair_table_snoop(const char *structure);

int *make_loop_index_pt(short *pt);


int bp_distance(const char *str1,
                const char *str2);

void print_tty_input_seq(void);

void print_tty_input_seq_str(const char *s);

void print_tty_constraint_full(void);

void print_tty_constraint(unsigned int option);

void str_DNA2RNA(char *sequence);

void  str_uppercase(char *sequence);

int   *get_iindx(unsigned int length);

int   *get_indx(unsigned int length);

void getConstraint( char **cstruc,
                    const char **lines,
                    unsigned int option);

void constrain_ptypes(const char *constraint,
                      unsigned int length,
                      char *ptype,
                      int *BP,
                      int min_loop_size,
                      unsigned int idx_type);

unsigned int  *make_referenceBP_array(short *reference_pt,
                                      unsigned int turn);

unsigned int  *compute_BPdifferences( short *pt1,
                                      short *pt2,
                                      unsigned int turn);

#endif