1/** 2 3@page plots Plotting 4 5@tableofcontents 6 7Create Plots of Secondary Structures, Feature Motifs, and Sequence Alignments 8 9@section utils_ss Producing secondary structure graphs 10 11@verbatim 12int PS_rna_plot ( char *string, 13 char *structure, 14 char *file) 15@endverbatim 16@copybrief PS_rna_plot() 17 18@verbatim 19int PS_rna_plot_a ( 20 char *string, 21 char *structure, 22 char *file, 23 char *pre, 24 char *post) 25@endverbatim 26@copybrief PS_rna_plot_a() 27 28@verbatim 29int gmlRNA (char *string, 30 char *structure, 31 char *ssfile, 32 char option) 33@endverbatim 34@copybrief gmlRNA() 35 36@verbatim 37int ssv_rna_plot (char *string, 38 char *structure, 39 char *ssfile) 40@endverbatim 41@copybrief ssv_rna_plot() 42 43@verbatim 44int svg_rna_plot (char *string, 45 char *structure, 46 char *ssfile) 47@endverbatim 48@copybrief svg_rna_plot() 49 50@verbatim 51int xrna_plot ( char *string, 52 char *structure, 53 char *ssfile) 54@endverbatim 55@copybrief xrna_plot() 56 57@verbatim 58int rna_plot_type 59@endverbatim 60@copybrief rna_plot_type 61 62Two low-level functions provide direct access to the graph lauyouting 63algorithms: 64 65@verbatim 66int simple_xy_coordinates ( short *pair_table, 67 float *X, 68 float *Y) 69@endverbatim 70@copybrief simple_xy_coordinates() 71 72@verbatim 73int naview_xy_coordinates ( short *pair_table, 74 float *X, 75 float *Y) 76@endverbatim 77@copybrief naview_xy_coordinates() 78 79@see PS_dot.h and naview.h for more detailed descriptions. 80 81@htmlonly 82<hr> 83<a href="#toc">Table of Contents</a> 84<hr> 85@endhtmlonly 86 87@section utils_dot Producing (colored) dot plots for base pair probabilities 88 89@verbatim 90int PS_color_dot_plot ( char *string, 91 cpair *pi, 92 char *filename) 93@endverbatim 94@copybrief PS_color_dot_plot() 95 96@verbatim 97int PS_color_dot_plot_turn (char *seq, 98 cpair *pi, 99 char *filename, 100 int winSize) 101@endverbatim 102@copybrief PS_color_dot_plot_turn() 103 104@verbatim 105int PS_dot_plot_list (char *seq, 106 char *filename, 107 plist *pl, 108 plist *mf, 109 char *comment) 110@endverbatim 111@copybrief PS_dot_plot_list() 112 113@verbatim 114int PS_dot_plot_turn (char *seq, 115 struct plist *pl, 116 char *filename, 117 int winSize) 118@endverbatim 119@copybrief PS_dot_plot_turn() 120 121@see PS_dot.h for more detailed descriptions. 122 123@section utils_aln Producing (colored) alignments 124 125@verbatim 126int PS_color_aln ( 127 const char *structure, 128 const char *filename, 129 const char *seqs[], 130 const char *names[]) 131@endverbatim 132@copybrief PS_color_aln() 133 134 */ 135