1#ifndef __VIENNA_RNA_PACKAGE_UTILS_H__
2#define __VIENNA_RNA_PACKAGE_UTILS_H__
12#define VRNA_INPUT_ERROR 1U
16#define VRNA_INPUT_QUIT 2U
20#define VRNA_INPUT_MISC 4U
28#define VRNA_INPUT_FASTA_HEADER 8U
34#define VRNA_INPUT_SEQUENCE 16U
40#define VRNA_INPUT_CONSTRAINT 32U
46#define VRNA_INPUT_NO_TRUNCATION 256U
51#define VRNA_INPUT_NO_REST 512U
56#define VRNA_INPUT_NO_SPAN 1024U
61#define VRNA_INPUT_NOSKIP_BLANK_LINES 2048U
66#define VRNA_INPUT_BLANK_LINE 4096U
71#define VRNA_INPUT_NOSKIP_COMMENTS 128U
76#define VRNA_INPUT_COMMENT 8192U
84#define VRNA_CONSTRAINT_PIPE 1U
88#define VRNA_CONSTRAINT_DOT 2U
92#define VRNA_CONSTRAINT_X 4U
96#define VRNA_CONSTRAINT_ANG_BRACK 8U
100#define VRNA_CONSTRAINT_RND_BRACK 16U
104#define VRNA_CONSTRAINT_MULTILINE 32U
108#define VRNA_CONSTRAINT_NO_HEADER 64U
112#define VRNA_CONSTRAINT_ALL 128U
116#define VRNA_CONSTRAINT_G 256U
128#define VRNA_OPTION_MULTILINE 32U
134#define MIN2(A, B) ((A) < (B) ? (A) : (B))
138#define MAX2(A, B) ((A) > (B) ? (A) : (B))
142#define MIN3(A, B, C) (MIN2( (MIN2((A),(B))) ,(C)))
146#define MAX3(A, B, C) (MAX2( (MAX2((A),(B))) ,(C)))
152#define XSTR(s) STR(s)
158#ifndef FILENAME_MAX_LENGTH
165#define FILENAME_MAX_LENGTH 80
172#define FILENAME_ID_LENGTH 42
179char *strdup(
const char *s);
185#define space(S) calloc(1,(S))
240extern unsigned short xsubi[3];
259void filecopy(FILE *from, FILE *to);
316int skip_comment_lines(
char **line);
339 unsigned int options);
341unsigned int get_multi_input_line(
char **
string,
342 unsigned int options);
399 unsigned int options);
416char *extract_record_rest_structure(
const char **lines,
418 unsigned int option);
455short *make_pair_table_pk(
const char *structure);
494int bp_distance(
const char *str1,
586void getConstraint(
char **cstruc,
588 unsigned int option);
606 unsigned int idx_type);
608unsigned int *make_referenceBP_array(
short *reference_pt,
611unsigned int *compute_BPdifferences(
short *pt1,
int * get_iindx(unsigned int length)
Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...
void nrerror(const char message[])
Die with an error message.
void str_uppercase(char *sequence)
Convert an input sequence to uppercase.
short * copy_pair_table(const short *pt)
Get an exact copy of a pair table.
char * unpack_structure(const char *packed)
Unpack secondary structure previously packed with pack_structure()
void constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type)
Insert constraining pair types according to constraint structure string.
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
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.
short * alimake_pair_table(const char *structure)
void * space(unsigned size)
Allocate space safely.
void * xrealloc(void *p, unsigned size)
Reallocate space safely.
void init_rand(void)
Make random number seeds.
unsigned int get_input_line(char **string, unsigned int options)
int hamming_bound(const char *s1, const char *s2, int n)
Calculate hamming distance between two sequences up to a specified length.
char * pack_structure(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
char * get_line(FILE *fp)
Read a line of arbitrary length from a stream.
double urn(void)
get a random number from [0..1]
short * make_pair_table(const char *structure)
Create a pair table of a secondary structure.
short * make_pair_table_snoop(const char *structure)
int * make_loop_index_pt(short *pt)
Compute the "base pair" distance between two secondary structures s1 and s2.
void str_DNA2RNA(char *sequence)
Convert a DNA input sequence to RNA alphabet.
char * random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
int hamming(const char *s1, const char *s2)
Calculate hamming distance between two sequences.
int * get_indx(unsigned int length)
Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.
void print_tty_input_seq_str(const char *s)
Print a line with a user defined string and a ruler to stdout.
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)
void warn_user(const char message[])
Print a warning message.
unsigned short xsubi[3]
Current 48 bit random number.
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)