- - - - - - -

RNAlib-2.1.2 -

- - -

Main Page
Related Pages

+ + +

Utilities - Odds and Ends

Miscellaneous Utilities

-Producing secondary structure graphs

int PS_rna_plot ( char *string, +

+Producing secondary structure graphs

+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 (
+

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,
+

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,
+

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,
+

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,
+

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.

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, +

+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,
+

Calculate nucleotide coordinates for secondary structure plot the Simple way.

+int naview_xy_coordinates ( short *pair_table,
                             float *X,
                             float *Y)
-

See also:: PS_dot.h and naview.h for more detailed descriptions.

See also:: PS_dot.h and naview.h for more detailed descriptions.

Table of Contents

-Producing (colored) dot plots for base pair probabilities

int PS_color_dot_plot ( char *string,
+
+Producing (colored) dot plots for base pair probabilities
++int PS_color_dot_plot ( char *string,
                         cpair *pi,
                         char *filename)
-
 int PS_color_dot_plot_turn (char *seq,
+
 
++int PS_color_dot_plot_turn (char *seq,
                             cpair *pi,
                             char *filename,
                             int winSize)
-
 int PS_dot_plot_list (char *seq,
+
 
++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,
+
 Produce a postscript dot-plot from two pair lists. 
++int PS_dot_plot_turn (char *seq,
                       struct plist *pl,
                       char *filename,
                       int winSize)
-
 See also:
PS_dot.h for more detailed descriptions.
-
-Producing (colored) alignments
-int PS_color_aln (
+
 
+See also:
PS_dot.h for more detailed descriptions.
+
+Producing (colored) alignments
++int PS_color_aln (
             const char *structure,
             const char *filename,
             const char *seqs[],
             const char *names[])
-  
+

Table of Contents

-RNA sequence related utilities

+RNA sequence related utilities

Several functions provide useful applications to RNA sequences

char  *random_string (int l,
++char  *random_string (int l,
                       const char symbols[])
-
 Create a random string using characters from a specified symbol set. 
-int   hamming ( const char *s1,
+
 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. 
+

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.

Table of Contents

-RNA secondary structure related utilities

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.

+RNA secondary structure related utilities

+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.

Table of Contents

-Miscellaneous Utilities

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. (constraint support is specified by option parameter)

int   *get_iindx (unsigned int length)
-

Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions.

int   *get_indx (unsigned int length)
-

Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.

void constrain_ptypes (
+
+Miscellaneous Utilities
++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. (constraint support is specified by option parameter). 
++int   *get_iindx (unsigned int length)
+
 Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions. 
++int   *get_indx (unsigned int length)
+
 Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions. 
++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(
+
 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,
+
 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. 
-See also:
utils.h for a complete overview and detailed description of the utility functions
+