RNAlib-2.4.0
PS_dot.h
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1 #ifndef VIENNA_RNA_PACKAGE_PS_DOT_H
2 #define VIENNA_RNA_PACKAGE_PS_DOT_H
3 
4 
8 #include <ViennaRNA/plot_aln.h>
9 
10 #ifdef VRNA_WARN_DEPRECATED
11 # ifdef __GNUC__
12 # define DEPRECATED(func) func __attribute__ ((deprecated))
13 # else
14 # define DEPRECATED(func) func
15 # endif
16 #else
17 # define DEPRECATED(func) func
18 #endif
19 
20 /* make this interface backward compatible with RNAlib < 2.2.0 */
21 #define VRNA_BACKWARD_COMPAT
22 
35 #define VRNA_PLOT_PROBABILITIES_BP 1U
36 #define VRNA_PLOT_PROBABILITIES_ACC 2U
37 
38 #define VRNA_PLOT_PROBABILITIES_UD 4U
39 #define VRNA_PLOT_PROBABILITIES_UD_LIN 8U
40 
41 #define VRNA_PLOT_PROBABILITIES_SD 16U
42 
43 #define VRNA_PLOT_PROBABILITIES_SC_MOTIF 32U
44 #define VRNA_PLOT_PROBABILITIES_SC_UP 64U
45 #define VRNA_PLOT_PROBABILITIES_SC_BP 128U
46 
47 #define VRNA_PLOT_PROBABILITIES_DEFAULT ( VRNA_PLOT_PROBABILITIES_BP \
48  | VRNA_PLOT_PROBABILITIES_SD \
49  | VRNA_PLOT_PROBABILITIES_SC_MOTIF \
50  | VRNA_PLOT_PROBABILITIES_UD_LIN )
51 typedef struct {
52  char *comment;
53  char *title;
54 
55  vrna_data_lin_t **top;
56  char **top_title;
57 
58  vrna_data_lin_t **bottom;
59  char **bottom_title;
60 
61  vrna_data_lin_t **left;
62  char **left_title;
63 
64  vrna_data_lin_t **right;
65  char **right_title;
67 
68 
69 int
70 vrna_plot_dp_EPS( const char *filename,
71  const char *sequence,
72  vrna_ep_t *upper,
73  vrna_ep_t *lower,
74  vrna_dotplot_auxdata_t *auxdata,
75  unsigned int options);
76 
77 int PS_color_dot_plot(char *string,
78  cpair *pi,
79  char *filename);
80 
81 int PS_color_dot_plot_turn( char *seq,
82  cpair *pi,
83  char *filename,
84  int winSize);
85 
105 int PS_dot_plot_list( char *seq,
106  char *filename,
107  plist *pl,
108  plist *mf,
109  char *comment);
110 
111 int vrna_plot_dp_PS_list( char *seq,
112  int cp,
113  char *wastlfile,
114  plist *pl,
115  plist *mf,
116  char *comment);
117 
118 int PS_dot_plot_turn( char *seq,
119  plist *pl,
120  char *filename,
121  int winSize);
122 
123 #ifdef VRNA_BACKWARD_COMPAT
124 
140 DEPRECATED(int PS_dot_plot( char *string,
141  char *file));
142 
143 #endif
144 
149 #endif
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:69
Definition: PS_dot.h:51
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:199
int PS_dot_plot(char *string, char *file)
Produce postscript dot-plot.
Various data structures and pre-processor macros.
Various utility- and helper-functions for secondary structure parsing, converting, etc.
Various functions for plotting Sequence / Structure Alignments.
Various functions for plotting RNA secondary structures.
Definition: data_structures.h:210
int PS_dot_plot_list(char *seq, char *filename, plist *pl, plist *mf, char *comment)
Produce a postscript dot-plot from two pair lists.