Deprecated Interface for Multiple Sequence Alignment Utilities — ViennaRNA Package

# Deprecated Interface for Multiple Sequence Alignment Utilities

  Typedefs

  typedef struct vrna_pinfo_s pair_info

    Old typename of vrna_pinfo_s.

        #include <ViennaRNA/sequences/alignments.h>

    Deprecated:

      Use vrna_pinfo_t instead!

  Functions

  int read_clustal(FILE *clust, char *AlignedSeqs[], char *names[])

        #include <ViennaRNA/sequences/alignments.h>

  char *consensus(const char *AS[])

        #include <ViennaRNA/sequences/alignments.h>

  char *consens_mis(const char *AS[])

        #include <ViennaRNA/sequences/alignments.h>

  char *get_ungapped_sequence(const char *seq)

        #include <ViennaRNA/sequences/alignments.h>

  int get_mpi(char *Alseq[], int n_seq, int length, int *mini)

    Get the mean pairwise identity in steps from ?to?(ident).

        #include <ViennaRNA/sequences/alignments.h>

    Deprecated:

      Use vrna_aln_mpi() as a replacement

    Parameters:

      - Alseq

      - n_seq – The number of sequences in the alignment

      - length – The length of the alignment

      - mini

    Returns:

      The mean pairwise identity

  void encode_ali_sequence(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)

    Get arrays with encoded sequence of the alignment.

        #include <ViennaRNA/sequences/alignments.h>

    this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)

    Parameters:

      - sequence – The gapped sequence from the alignment

      - S – pointer to an array that holds encoded sequence

      - s5 – pointer to an array that holds the next base 5’ of alignment position i

      - s3 – pointer to an array that holds the next base 3’ of alignment position i

      - ss

      - as

      - circ – assume the molecules to be circular instead of linear (circ=0)

  void alloc_sequence_arrays(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)

    Allocate memory for sequence array used to deal with aligned sequences.

        #include <ViennaRNA/sequences/alignments.h>

    Note that these arrays will also be initialized according to the sequence alignment given

    See also

    free_sequence_arrays()

    Parameters:

      - sequences – The aligned sequences

      - S – A pointer to the array of encoded sequences

      - S5 – A pointer to the array that contains the next 5’ nucleotide of a sequence position

      - S3 – A pointer to the array that contains the next 3’ nucleotide of a sequence position

      - a2s – A pointer to the array that contains the alignment to sequence position mapping

      - Ss – A pointer to the array that contains the ungapped sequence

      - circ – assume the molecules to be circular instead of linear (circ=0)

  void free_sequence_arrays(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)

    Free the memory of the sequence arrays used to deal with aligned sequences.

        #include <ViennaRNA/sequences/alignments.h>

    This function frees the memory previously allocated with alloc_sequence_arrays()

    See also

    alloc_sequence_arrays()

    Parameters:

      - n_seq – The number of aligned sequences

      - S – A pointer to the array of encoded sequences

      - S5 – A pointer to the array that contains the next 5’ nucleotide of a sequence position

      - S3 – A pointer to the array that contains the next 3’ nucleotide of a sequence position

      - a2s – A pointer to the array that contains the alignment to sequence position mapping

      - Ss – A pointer to the array that contains the ungapped sequence