WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / plot_layouts.h

diff --git a/binaries/src/ViennaRNA/H/plot_layouts.h b/binaries/src/ViennaRNA/H/plot_layouts.h
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+/**
+ * \file plot_layouts.h
+ *
+ * \brief Secondary structure plot layout algorithms
+ *
+ *  c Ronny Lorenz
+ *    The ViennaRNA Package
+ */
+#ifndef __VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H__
+#define __VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H__
+
+#include "data_structures.h"
+#include "naview.h"
+
+#ifndef PI
+#define  PI       3.141592654
+#endif
+#define  PIHALF       PI/2.
+
+
+/**
+ *  \brief Definition of Plot type <i>simple</i>
+ *
+ *  This is the plot type definition for several RNA structure plotting functions telling
+ *  them to use <b>Simple</b> plotting algorithm
+ *
+ *  \see rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()
+ */
+#define VRNA_PLOT_TYPE_SIMPLE     0
+
+/**
+ *  \brief Definition of Plot type <i>Naview</i>
+ *
+ *  This is the plot type definition for several RNA structure plotting functions telling
+ *  them to use <b>Naview</b> plotting algorithm
+ *
+ *  \see 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
+
+/**
+ *  \brief Definition of Plot type <i>Circular</i>
+ *
+ *  This is the plot type definition for several RNA structure plotting functions telling
+ *  them to produce a <b>Circular plot</b>
+ *
+ *  \see 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
+
+
+/**
+ *  \brief 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 \e naview program of \ref bruccoleri_88 "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 #VRNA_PLOT_TYPE_SIMPLE, #VRNA_PLOT_TYPE_NAVIEW, #VRNA_PLOT_TYPE_CIRCULAR
+ *
+ */
+extern int rna_plot_type;
+
+/**
+ *  \brief Calculate nucleotide coordinates for secondary structure plot the <i>Simple way</i>
+ *
+ *  \see make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(),
+ *  PS_rna_plot, svg_rna_plot()
+ *
+ *  \param  pair_table  The pair table of the secondary structure
+ *  \param  X           a pointer to an array with enough allocated space to hold the x coordinates
+ *  \param  Y           a pointer to an array with enough allocated space to hold the y coordinates
+ *  \return             length of sequence on success, 0 otherwise
+ */
+int simple_xy_coordinates(short *pair_table,
+                          float *X,
+                          float *Y);
+
+/**
+ *  \brief Calculate nucleotide coordinates for <i>Circular Plot</i>
+ *
+ *  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 \f$P^t\f$ in addition to the actual R<sup>2</sup> coordinates.
+ *  the simplest way to do so may be to compute a radius scaling factor \f$rs\f$ in the interval \f$[0,1]\f$ 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 \f$P^t\f$, i.e. \f$ P^{t}_x[i] = X[i] * rs\f$
+ *  and \f$P^{t}_y[i] = Y[i] * rs\f$.
+ *
+ *  \see make_pair_table(), rna_plot_type, simple_xy_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(),
+ *  PS_rna_plot, svg_rna_plot()
+ *
+ *  \param  pair_table  The pair table of the secondary structure
+ *  \param  x           a pointer to an array with enough allocated space to hold the x coordinates
+ *  \param  y           a pointer to an array with enough allocated space to hold the y coordinates
+ *  \return             length of sequence on success, 0 otherwise
+ */
+int simple_circplot_coordinates(short *pair_table,
+                                float *x,
+                                float *y);
+
+
+#endif