plot_structure.h

#ifndef VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H
#define VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H

#include <ViennaRNA/model.h>
#include <ViennaRNA/plot_layouts.h>

#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
#  define DEPRECATED(func) func __attribute__ ((deprecated))
# else
#  define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif

/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT

/**
 *  @file plot_structure.h
 *  @ingroup   plotting_utils
 *  @brief Various functions for plotting RNA secondary structures
 */

/**
 *  @{
 *  @ingroup   plotting_utils
 */

/* write PostScript drawing of structure to file with annotation */
int PS_rna_plot_snoop_a(char *string,
                        char *structure,
                        char *ssfile,
                        int *relative_access,
                        const char *seqs[]);

/**
 *  @brief 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.
 *
 *  @param seq        The RNA sequence
 *  @param structure  The secondary structure in dot-bracket notation
 *  @param file       The filename of the postscript output
 *  @param md_p       Model parameters used to generate a commandline option string in the output (Maybe NULL)
 *  @return           1 on success, 0 otherwise
 */
int vrna_file_PS_rnaplot( const char *seq,
                          const char *structure,
                          const char *file,
                          vrna_md_t  *md_p);

/**
 *  @brief 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.
 *
 *  @param seq     The RNA sequence
 *  @param structure  The secondary structure in dot-bracket notation
 *  @param file       The filename of the postscript output
 *  @param pre        PostScript code to appear before the secondary structure plot
 *  @param post       PostScript code to appear after the secondary structure plot
 *  @param md_p       Model parameters used to generate a commandline option string in the output (Maybe NULL)
 *  @return           1 on success, 0 otherwise
 */
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);

/**
 *  @brief 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
 *  @a 'X' or @a 'x' the resulting file will coordinates for an initial layout of the graph.
 *
 *  @param  string    The RNA sequence
 *  @param  structure The secondary structure in dot-bracket notation
 *  @param  ssfile    The filename of the gml output
 *  @param  option    The option flag
 *  @return           1 on success, 0 otherwise
 */
int gmlRNA( char *string,
            char *structure,
            char *ssfile,
            char option);

/**
 *  @brief  Produce a secondary structure graph in SStructView format
 *
 *  Write coord file for SStructView
 *
 *  @param  string    The RNA sequence
 *  @param  structure The secondary structure in dot-bracket notation
 *  @param  ssfile    The filename of the ssv output
 *  @return           1 on success, 0 otherwise
 */
int ssv_rna_plot( char *string,
                  char *structure,
                  char *ssfile);

/**
 *  @brief Produce a secondary structure plot in SVG format and write it to a file
 *
 *  @param string     The RNA sequence
 *  @param structure  The secondary structure in dot-bracket notation
 *  @param ssfile     The filename of the svg output
 *  @return           1 on success, 0 otherwise
 */
int svg_rna_plot( char *string,
                  char *structure,
                  char *ssfile);

/**
 *  @brief Produce a secondary structure plot for further editing in XRNA
 *
 *  @param string     The RNA sequence
 *  @param structure  The secondary structure in dot-bracket notation
 *  @param ssfile     The filename of the xrna output
 *  @return           1 on success, 0 otherwise
 */
int xrna_plot(char *string,
              char *structure,
              char *ssfile);

#ifdef VRNA_BACKWARD_COMPAT

/**
 *  @brief Produce a secondary structure graph in PostScript and write it to 'filename'.
 *
 *  @deprecated   Use vrna_file_PS_rnaplot() instead!
 */
DEPRECATED(int PS_rna_plot(char *string, char *structure, char *file));

/**
 *  @brief Produce a secondary structure graph in PostScript including additional
 *  annotation macros and write it to 'filename'
 *
 *  @deprecated   Use vrna_file_PS_rnaplot_a() instead!
 */
DEPRECATED(int PS_rna_plot_a(char *string, char *structure, char *file, char *pre, char *post));

/**
 *  @brief Produce a secondary structure graph in PostScript including additional
 *  annotation macros and write it to 'filename' (detect and draw g-quadruplexes)
 *
 *  @deprecated   Use vrna_file_PS_rnaplot_a() instead!
 */
DEPRECATED(int PS_rna_plot_a_gquad(char *string, char *structure, char *ssfile, char *pre, char *post));

#endif

/**
 * @}
 */

#endif