alignments.h

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#ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H
#define VIENNA_RNA_PACKAGE_ALN_UTIL_H

#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

typedef struct vrna_pinfo_s vrna_pinfo_t;


#define VRNA_ALN_DEFAULT      0U


#define VRNA_ALN_RNA          1U


#define VRNA_ALN_DNA          2U


#define VRNA_ALN_UPPERCASE    4U


#define VRNA_ALN_LOWERCASE    8U

#define VRNA_MEASURE_SHANNON_ENTROPY  1U

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

/* the following typedefs are for backward compatibility only */

typedef struct vrna_pinfo_s pair_info;

#endif

#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/model.h>

struct vrna_pinfo_s {
  unsigned  i;      
  unsigned  j;      
  float     p;      
  float     ent;    
  short     bp[8];  
  char      comp;   
};


int
vrna_aln_mpi(const char **alignment);


vrna_pinfo_t *
vrna_aln_pinfo(vrna_fold_compound_t *vc,
               const char           *structure,
               double               threshold);


int *
vrna_aln_pscore(const char  **alignment,
                vrna_md_t   *md);


char **
vrna_aln_slice(const char   **alignment,
               unsigned int i,
               unsigned int j);


void
vrna_aln_free(char **alignment);


char **
vrna_aln_uppercase(const char **alignment);


char **
vrna_aln_toRNA(const char **alignment);


char **
vrna_aln_copy(const char    **alignment,
              unsigned int  options);


float *
vrna_aln_conservation_struct(const char       **alignment,
                             const char       *structure,
                             const vrna_md_t  *md);


float *
vrna_aln_conservation_col(const char      **alignment,
                          const vrna_md_t *md_p,
                          unsigned int    options);


char *
vrna_aln_consensus_sequence(const char      **alignment,
                            const vrna_md_t *md_p);

char *
vrna_aln_consensus_mis(const char       **alignment,
                       const vrna_md_t  *md_p);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#include <stdio.h>
DEPRECATED(int read_clustal(FILE  *clust,
                            char  *AlignedSeqs[],
                            char  *names[]),
          "Use vrna_file_msa_read() and vrna_file_msa_read_record() instead");


DEPRECATED(char *consensus(const char *AS[]),
          "Use vrna_aln_consensus_sequence() instead!");


DEPRECATED(char *consens_mis(const char *AS[]),
          "Use vrna_aln_consensus_mis() instead!");


DEPRECATED(char *get_ungapped_sequence(const char *seq),
          "Use vrna_seq_ungapped() instead!");


DEPRECATED(int get_mpi(char *Alseq[],
                       int  n_seq,
                       int  length,
                       int  *mini),
          "Use vrna_aln_mpi() instead");

/*
 #############################################################
 # some helper functions that might be useful in the library #
 #############################################################
 */

DEPRECATED(void encode_ali_sequence(const char      *sequence,
                                    short           *S,
                                    short           *s5,
                                    short           *s3,
                                    char            *ss,
                                    unsigned short  *as,
                                    int             circ),
          "This function is obsolete");


DEPRECATED(void  alloc_sequence_arrays(const char     **sequences,
                                       short          ***S,
                                       short          ***S5,
                                       short          ***S3,
                                       unsigned short ***a2s,
                                       char           ***Ss,
                                       int            circ),
          "This function is obsolete");


DEPRECATED(void  free_sequence_arrays(unsigned int    n_seq,
                                      short           ***S,
                                      short           ***S5,
                                      short           ***S3,
                                      unsigned short  ***a2s,
                                      char            ***Ss),
          "This fucntion is obsolete");

#endif

#endif