#ifndef __VIENNA_RNA_PACKAGE_PS_DOT_H__ #define __VIENNA_RNA_PACKAGE_PS_DOT_H__ #include "data_structures.h" #include "plot_layouts.h" #ifdef __GNUC__ #define DEPRECATED(func) func __attribute__ ((deprecated)) #else #define DEPRECATED(func) func #endif /** * \file PS_dot.h * \brief Various functions for plotting RNA secondary structures, dot-plots and other * visualizations */ /* 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 string The RNA sequence * \param structure The secondary structure in dot-bracket notation * \param file The filename of the postscript output * \return 1 on success, 0 otherwise */ 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' * * Same as PS_rna_plot() 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 string 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 * \return 1 on success, 0 otherwise */ int PS_rna_plot_a(char *string, char *structure, char *file, char *pre, char *post); /** * \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); int PS_color_dot_plot(char *string, cpair *pi, char *filename); int PS_color_dot_plot_turn( char *seq, cpair *pi, char *filename, int winSize); /** * \brief 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'.\n * 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. * * \see assign_plist_from_pr(), assign_plist_from_db() * * \param seq The RNA sequence * \param filename A filename for the postscript output * \param pl The base pair probability pairlist * \param mf The mfe secondary structure pairlist * \param comment A comment * \return 1 if postscript was successfully written, 0 otherwise */ int PS_dot_plot_list( char *seq, char *filename, plist *pl, plist *mf, char *comment); int PS_dot_plot_turn( char *seq, struct plist *pl, char *filename, int winSize); int PS_color_aln( const char *structure, const char *filename, const char *seqs[], const char *names[]); /** * PS_color_aln for duplexes */ int aliPS_color_aln(const char *structure, const char *filename, const char *seqs[], const char *names[]); /** * Wrapper to PS_dot_plot_list * * \brief Produce postscript dot-plot * * 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 * \note DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE * * \deprecated This function is deprecated and will be removed soon! Use \ref PS_dot_plot_list() instead! */ DEPRECATED(int PS_dot_plot( char *string, char *file)); #endif