RNAlib-2.4.14
probabilities.h
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1 #ifndef VIENNA_RNA_PACKAGE_PLOT_PROBABILITIES_H
2 #define VIENNA_RNA_PACKAGE_PLOT_PROBABILITIES_H
3 
4 
5 #include <ViennaRNA/datastructures/basic.h>
6 #include <ViennaRNA/utils/structures.h>
7 
8 #ifdef VRNA_WARN_DEPRECATED
9 # if defined(__clang__)
10 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
11 # elif defined(__GNUC__)
12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13 # else
14 # define DEPRECATED(func, msg) func
15 # endif
16 #else
17 # define DEPRECATED(func, msg) func
18 #endif
19 
32 #define VRNA_PLOT_PROBABILITIES_BP 1U
33 #define VRNA_PLOT_PROBABILITIES_ACC 2U
34 
35 #define VRNA_PLOT_PROBABILITIES_UD 4U
36 #define VRNA_PLOT_PROBABILITIES_UD_LIN 8U
37 
38 #define VRNA_PLOT_PROBABILITIES_SD 16U
39 
40 #define VRNA_PLOT_PROBABILITIES_SC_MOTIF 32U
41 #define VRNA_PLOT_PROBABILITIES_SC_UP 64U
42 #define VRNA_PLOT_PROBABILITIES_SC_BP 128U
43 
44 #define VRNA_PLOT_PROBABILITIES_DEFAULT (VRNA_PLOT_PROBABILITIES_BP \
45  | VRNA_PLOT_PROBABILITIES_SD \
46  | VRNA_PLOT_PROBABILITIES_SC_MOTIF \
47  | VRNA_PLOT_PROBABILITIES_UD_LIN)
48 typedef struct {
49  char *comment;
50  char *title;
51 
52  vrna_data_lin_t **top;
53  char **top_title;
54 
55  vrna_data_lin_t **bottom;
56  char **bottom_title;
57 
58  vrna_data_lin_t **left;
59  char **left_title;
60 
61  vrna_data_lin_t **right;
62  char **right_title;
63 } vrna_dotplot_auxdata_t;
64 
65 
66 int
67 vrna_plot_dp_EPS(const char *filename,
68  const char *sequence,
69  vrna_ep_t *upper,
70  vrna_ep_t *lower,
71  vrna_dotplot_auxdata_t *auxdata,
72  unsigned int options);
73 
74 
75 int
76 vrna_plot_dp_PS_list(char *seq,
77  int cp,
78  char *wastlfile,
79  plist *pl,
80  plist *mf,
81  char *comment);
82 
83 
84 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
85 
86 int
87 PS_color_dot_plot(char *string,
88  cpair *pi,
89  char *filename);
90 
91 
92 int
93 PS_color_dot_plot_turn(char *seq,
94  cpair *pi,
95  char *filename,
96  int winSize);
97 
98 
99 int
100 PS_dot_plot_turn(char *seq,
101  plist *pl,
102  char *filename,
103  int winSize);
104 
105 
125 int PS_dot_plot_list(char *seq,
126  char *filename,
127  plist *pl,
128  plist *mf,
129  char *comment);
130 
131 
147 DEPRECATED(int PS_dot_plot(char *string,
148  char *file),
149  "Use vrna_plot_dp_EPS() instead");
150 
151 #endif
152 
157 #endif
vrna_cpair_s
this datastructure is used as input parameter in functions of PS_dot.c
Definition: basic.h:112
vrna_dotplot_auxdata_t
Definition: probabilities.h:48
PS_dot_plot
int PS_dot_plot(char *string, char *file)
Produce postscript dot-plot.
basic.h
Various data structures and pre-processor macros.
vrna_data_linear_s
Definition: basic.h:124
PS_dot_plot_list
int PS_dot_plot_list(char *seq, char *filename, plist *pl, plist *mf, char *comment)
Produce a postscript dot-plot from two pair lists.
structures.h
Various utility- and helper-functions for secondary structure parsing, converting, etc.
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453