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