1 #ifndef VIENNA_RNA_PACKAGE_PLOT_UTILS_H
2 #define VIENNA_RNA_PACKAGE_PLOT_UTILS_H
3 
4 /**
5  *  @file     ViennaRNA/plotting/utils.h
6  *  @ingroup  utils, plotting_utils
7  *  @brief    Various utilities to assist in plotting secondary structures and consensus structures
8  */
9 
10 #include <ViennaRNA/datastructures/basic.h>
11 #include <ViennaRNA/model.h>
12 #include <ViennaRNA/utils/structures.h>
13 
14 /**
15  *  @addtogroup  plotting_utils
16  *  @{
17  *  @brief  Functions for Creating Secondary Structure Plots, Dot-Plots, and More
18  *  @}
19  */
20 
21 
22 /**
23  *  @addtogroup  annotation_utils
24  *  @{
25  *  @brief  Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others
26  */
27 
28 /**
29  *  @brief  Produce covariance annotation for an alignment given a secondary structure
30  *
31  */
32 char **
33 vrna_annotate_covar_db(const char   **alignment,
34                        const char   *structure,
35                        vrna_md_t    *md_p);
36 
37 
38 char **
39 vrna_annotate_covar_db_extended(const char   **alignment,
40                                 const char   *structure,
41                                 vrna_md_t    *md_p,
42                                 unsigned int options);
43 
44 
45 /**
46  *  @brief  Produce covariance annotation for an alignment given a set of base pairs
47  *
48  */
49 vrna_cpair_t *
50 vrna_annotate_covar_pairs(const char  **alignment,
51                           vrna_ep_t   *pl,
52                           vrna_ep_t   *mfel,
53                           double      threshold,
54                           vrna_md_t   *md);
55 
56 
57 /**
58  * @}
59  */
60 
61 #endif
62