int PS_rna_plot ( char *string,
char *structure,
char *file)
Produce a secondary structure graph in PostScript and write it to 'filename'.
int PS_rna_plot_a (
char *string,
char *structure,
char *file,
char *pre,
char *post)
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
int gmlRNA (char *string,
char *structure,
char *ssfile,
char option)
Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.
int ssv_rna_plot (char *string,
char *structure,
char *ssfile)
Produce a secondary structure graph in SStructView format.
int svg_rna_plot (char *string,
char *structure,
char *ssfile)
Produce a secondary structure plot in SVG format and write it to a file.
int xrna_plot ( char *string,
char *structure,
char *ssfile)
Produce a secondary structure plot for further editing in XRNA.
int rna_plot_type
Switch for changing the secondary structure layout algorithm.
Two low-level functions provide direct access to the graph lauyouting algorithms:
int simple_xy_coordinates ( short *pair_table,
float *X,
float *Y)
Calculate nucleotide coordinates for secondary structure plot the Simple way.
int naview_xy_coordinates ( short *pair_table,
float *X,
float *Y)
int PS_color_dot_plot ( char *string,
cpair *pi,
char *filename)
int PS_color_dot_plot_turn (char *seq,
cpair *pi,
char *filename,
int winSize)
int PS_dot_plot_list (char *seq,
char *filename,
plist *pl,
plist *mf,
char *comment)
Produce a postscript dot-plot from two pair lists.
int PS_dot_plot_turn (char *seq,
struct plist *pl,
char *filename,
int winSize)
int PS_color_aln (
const char *structure,
const char *filename,
const char *seqs[],
const char *names[])
Several functions provide useful applications to RNA sequences
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.
void str_DNA2RNA(char *sequence);
Convert a DNA input sequence to RNA alphabet.
void str_uppercase(char *sequence);
Convert an input sequence to uppercase.
char *pack_structure (const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
char *unpack_structure (const char *packed)
Unpack secondary structure previously packed with pack_structure().
short *make_pair_table (const char *structure)
Create a pair table of a secondary structure.
short *copy_pair_table (const short *pt)
Get an exact copy of a pair table.
void print_tty_input_seq (void)
Print a line to stdout that asks for an input sequence.
void print_tty_constraint_full (void)
Print structure constraint characters to stdout (full constraint support).
void print_tty_constraint (unsigned int option)
Print structure constraint characters to stdout.
int *get_iindx (unsigned int length)
Get an index mapper array (iindx) for accessing the energy matrices, e.g.
int *get_indx (unsigned int length)
Get an index mapper array (indx) for accessing the energy matrices, e.g.
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.
char *get_line(FILE *fp);
Read a line of arbitrary length from a stream.
unsigned int read_record(
char **header,
char **sequence,
char ***rest,
unsigned int options);
Get a data record from stdin.
char *time_stamp (void)
Get a timestamp.
void warn_user (const char message[])
Print a warning message.
void nrerror (const char message[])
Die with an error message.
void init_rand (void)
Make random number seeds.
unsigned short xsubi[3];
Current 48 bit random number.
double urn (void)
get a random number from [0..1]
int int_urn (int from, int to)
Generates a pseudo random integer in a specified range.
void *space (unsigned size)
Allocate space safely.
void *xrealloc ( void *p,
unsigned size)
Reallocate space safely.
1.6.1