RNAlib-2.2.7
|
Files | |
file | naview.h |
file | plot_aln.h |
Various functions for plotting Sequence / Structure Alignments. | |
file | plot_layouts.h |
Secondary structure plot layout algorithms. | |
file | plot_structure.h |
Various functions for plotting RNA secondary structures. | |
file | PS_dot.h |
Various functions for plotting RNA secondary structures, dot-plots and other visualizations. | |
Data Structures | |
struct | COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE More... | |
Macros | |
#define | VRNA_PLOT_TYPE_SIMPLE 0 |
Definition of Plot type simple More... | |
#define | VRNA_PLOT_TYPE_NAVIEW 1 |
Definition of Plot type Naview More... | |
#define | VRNA_PLOT_TYPE_CIRCULAR 2 |
Definition of Plot type Circular More... | |
Functions | |
int | PS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[]) |
Produce PostScript sequence alignment color-annotated by consensus structure. | |
int | aliPS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[]) |
int | simple_xy_coordinates (short *pair_table, float *X, float *Y) |
Calculate nucleotide coordinates for secondary structure plot the Simple way More... | |
int | simple_circplot_coordinates (short *pair_table, float *x, float *y) |
Calculate nucleotide coordinates for Circular Plot More... | |
int | vrna_file_PS_rnaplot (const char *seq, const char *structure, const char *file, vrna_md_t *md_p) |
Produce a secondary structure graph in PostScript and write it to 'filename'. More... | |
int | vrna_file_PS_rnaplot_a (const char *seq, const char *structure, const char *file, const char *pre, const char *post, vrna_md_t *md_p) |
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'. More... | |
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. More... | |
int | ssv_rna_plot (char *string, char *structure, char *ssfile) |
Produce a secondary structure graph in SStructView format. More... | |
int | svg_rna_plot (char *string, char *structure, char *ssfile) |
Produce a secondary structure plot in SVG format and write it to a file. More... | |
int | xrna_plot (char *string, char *structure, char *ssfile) |
Produce a secondary structure plot for further editing in XRNA. More... | |
int | PS_rna_plot (char *string, char *structure, char *file) |
Produce a secondary structure graph in PostScript and write it to 'filename'. More... | |
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'. More... | |
int | PS_rna_plot_a_gquad (char *string, char *structure, char *ssfile, char *pre, char *post) |
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename' (detect and draw g-quadruplexes) More... | |
int | PS_dot_plot_list (char *seq, char *filename, plist *pl, plist *mf, char *comment) |
Produce a postscript dot-plot from two pair lists. More... | |
int | PS_dot_plot (char *string, char *file) |
Produce postscript dot-plot. More... | |
Variables | |
int | rna_plot_type |
Switch for changing the secondary structure layout algorithm. More... | |
struct COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE
#define VRNA_PLOT_TYPE_SIMPLE 0 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type simple
This is the plot type definition for several RNA structure plotting functions telling them to use Simple plotting algorithm
#define VRNA_PLOT_TYPE_NAVIEW 1 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type Naview
This is the plot type definition for several RNA structure plotting functions telling them to use Naview plotting algorithm
#define VRNA_PLOT_TYPE_CIRCULAR 2 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type Circular
This is the plot type definition for several RNA structure plotting functions telling them to produce a Circular plot
int aliPS_color_aln | ( | const char * | structure, |
const char * | filename, | ||
const char * | seqs[], | ||
const char * | names[] | ||
) |
#include <ViennaRNA/plot_aln.h>
PS_color_aln for duplexes
int simple_xy_coordinates | ( | short * | pair_table, |
float * | X, | ||
float * | Y | ||
) |
#include <ViennaRNA/plot_layouts.h>
Calculate nucleotide coordinates for secondary structure plot the Simple way
pair_table | The pair table of the secondary structure |
X | a pointer to an array with enough allocated space to hold the x coordinates |
Y | a pointer to an array with enough allocated space to hold the y coordinates |
int simple_circplot_coordinates | ( | short * | pair_table, |
float * | x, | ||
float * | y | ||
) |
#include <ViennaRNA/plot_layouts.h>
Calculate nucleotide coordinates for Circular Plot
This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.
pair_table | The pair table of the secondary structure |
x | a pointer to an array with enough allocated space to hold the x coordinates |
y | a pointer to an array with enough allocated space to hold the y coordinates |
int vrna_file_PS_rnaplot | ( | const char * | seq, |
const char * | structure, | ||
const char * | file, | ||
vrna_md_t * | md_p | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in PostScript and write it to 'filename'.
Note that this function has changed from previous versions and now expects the structure to be plotted in dot-bracket notation as an argument. It does not make use of the global base_pair array anymore.
seq | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
file | The filename of the postscript output |
md_p | Model parameters used to generate a commandline option string in the output (Maybe NULL) |
int vrna_file_PS_rnaplot_a | ( | const char * | seq, |
const char * | structure, | ||
const char * | file, | ||
const char * | pre, | ||
const char * | post, | ||
vrna_md_t * | md_p | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
Same as vrna_file_PS_rnaplot() but adds extra PostScript macros for various annotations (see generated PS code). The 'pre' and 'post' variables contain PostScript code that is verbatim copied in the resulting PS file just before and after the structure plot. If both arguments ('pre' and 'post') are NULL, no additional macros will be printed into the PostScript.
seq | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
file | The filename of the postscript output |
pre | PostScript code to appear before the secondary structure plot |
post | PostScript code to appear after the secondary structure plot |
md_p | Model parameters used to generate a commandline option string in the output (Maybe NULL) |
int gmlRNA | ( | char * | string, |
char * | structure, | ||
char * | ssfile, | ||
char | option | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.
If 'option' is an uppercase letter the RNA sequence is used to label nodes, if 'option' equals 'X' or 'x' the resulting file will coordinates for an initial layout of the graph.
string | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
ssfile | The filename of the gml output |
option | The option flag |
int ssv_rna_plot | ( | char * | string, |
char * | structure, | ||
char * | ssfile | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in SStructView format.
Write coord file for SStructView
string | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
ssfile | The filename of the ssv output |
int svg_rna_plot | ( | char * | string, |
char * | structure, | ||
char * | ssfile | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure plot in SVG format and write it to a file.
string | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
ssfile | The filename of the svg output |
int xrna_plot | ( | char * | string, |
char * | structure, | ||
char * | ssfile | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure plot for further editing in XRNA.
string | The RNA sequence |
structure | The secondary structure in dot-bracket notation |
ssfile | The filename of the xrna output |
int PS_rna_plot | ( | char * | string, |
char * | structure, | ||
char * | file | ||
) |
#include <ViennaRNA/plot_structure.h>
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 | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
int PS_rna_plot_a_gquad | ( | char * | string, |
char * | structure, | ||
char * | ssfile, | ||
char * | pre, | ||
char * | post | ||
) |
#include <ViennaRNA/plot_structure.h>
Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename' (detect and draw g-quadruplexes)
#include <ViennaRNA/PS_dot.h>
Produce a postscript dot-plot from two pair lists.
This function reads two plist structures (e.g. base pair probabilities and a secondary structure) as produced by assign_plist_from_pr() and assign_plist_from_db() and produces a postscript "dot plot" that is written to 'filename'.
Using base pair probabilities in the first and mfe structure in the second plist, the resulting "dot plot" represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy structure.
seq | The RNA sequence |
filename | A filename for the postscript output |
pl | The base pair probability pairlist |
mf | The mfe secondary structure pairlist |
comment | A comment |
int PS_dot_plot | ( | char * | string, |
char * | file | ||
) |
#include <ViennaRNA/PS_dot.h>
Produce postscript dot-plot.
Wrapper to PS_dot_plot_list
Reads base pair probabilities produced by pf_fold() from the global array pr and the pair list base_pair produced by fold() and produces a postscript "dot plot" that is written to 'filename'. The "dot plot" represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy
int rna_plot_type |
#include <ViennaRNA/plot_layouts.h>
Switch for changing the secondary structure layout algorithm.
Current possibility are 0 for a simple radial drawing or 1 for the modified radial drawing taken from the naview program of Bruccoleri & Heinrich (1988).