H/plot_layouts.h File Reference

Secondary structure plot layout algorithms. More...

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Defines
#define	VRNA_PLOT_TYPE_SIMPLE   0
	Definition of Plot type simple.
#define	VRNA_PLOT_TYPE_NAVIEW   1
	Definition of Plot type Naview.
#define	VRNA_PLOT_TYPE_CIRCULAR   2
	Definition of Plot type Circular.
Functions
int	simple_xy_coordinates (short *pair_table, float *X, float *Y)
	Calculate nucleotide coordinates for secondary structure plot the Simple way.
int	simple_circplot_coordinates (short *pair_table, float *x, float *y)
	Calculate nucleotide coordinates for Circular Plot.
Variables
int	rna_plot_type
	Switch for changing the secondary structure layout algorithm.

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Detailed Description

Secondary structure plot layout algorithms.

c Ronny Lorenz The ViennaRNA Package

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Define 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()

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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_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

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 in addition to the actual R² coordinates. the simplest way to do so may be to compute a radius scaling factor in the interval 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 , i.e. and .

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_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

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