RNAlib-2.1.9
Macros | Functions | Variables
plot_layouts.h File Reference

Secondary structure plot layout algorithms. More...

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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 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...
 

Variables

int rna_plot_type
 Switch for changing the secondary structure layout algorithm. More...
 

Detailed Description

Secondary structure plot layout algorithms.

c Ronny Lorenz The ViennaRNA Package

Macro Definition Documentation

#define VRNA_PLOT_TYPE_SIMPLE   0

Definition of Plot type simple

This is the plot type definition for several RNA structure plotting functions telling them to use Simple plotting algorithm

See Also
rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()
#define VRNA_PLOT_TYPE_NAVIEW   1

Definition of Plot type Naview

This is the plot type definition for several RNA structure plotting functions telling them to use Naview plotting algorithm

See Also
rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()
#define VRNA_PLOT_TYPE_CIRCULAR   2

Definition of Plot type Circular

This is the plot type definition for several RNA structure plotting functions telling them to produce a Circular plot

See Also
rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()

Function Documentation

int simple_xy_coordinates ( short *  pair_table,
float *  X,
float *  Y 
)

Calculate nucleotide coordinates for secondary structure plot the Simple way

See Also
make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(), PS_rna_plot, svg_rna_plot()
Parameters
pair_tableThe pair table of the secondary structure
Xa pointer to an array with enough allocated space to hold the x coordinates
Ya pointer to an array with enough allocated space to hold the y coordinates
Returns
length of sequence on success, 0 otherwise
int simple_circplot_coordinates ( short *  pair_table,
float *  x,
float *  y 
)

Calculate nucleotide coordinates for Circular Plot

This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.

Note
In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate a second tangential point $P^t$ in addition to the actual R2 coordinates. the simplest way to do so may be to compute a radius scaling factor $rs$ in the interval $[0,1]$ that weights the proportion of base pair span to the actual length of the sequence. This scaling factor can then be used to calculate the coordinates for $P^t$, i.e. $ P^{t}_x[i] = X[i] * rs$ and $P^{t}_y[i] = Y[i] * rs$.
See Also
make_pair_table(), rna_plot_type, simple_xy_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(), PS_rna_plot, svg_rna_plot()
Parameters
pair_tableThe pair table of the secondary structure
xa pointer to an array with enough allocated space to hold the x coordinates
ya pointer to an array with enough allocated space to hold the y coordinates
Returns
length of sequence on success, 0 otherwise

Variable Documentation

int rna_plot_type

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).

Note
To provide thread safety please do not rely on this global variable in future implementations but pass a plot type flag directly to the function that decides which layout algorithm it may use!
See Also
VRNA_PLOT_TYPE_SIMPLE, VRNA_PLOT_TYPE_NAVIEW, VRNA_PLOT_TYPE_CIRCULAR