Search Algorithms — ViennaRNA Package

# Search Algorithms

Implementations of various search algorithms to detect strings of objects within other strings of objects.

  Functions

  const unsigned int *vrna_search_BMH_num(const unsigned int *needle, size_t needle_size, const unsigned int *haystack, size_t haystack_size, size_t start, size_t *badchars, unsigned char cyclic)

    Search for a string of elements in a larger string of elements using the Boyer-Moore-Horspool algorithm.

        #include <ViennaRNA/search/BoyerMoore.h>

    To speed-up subsequent searches with this function, the Bad Character Table should be precomputed and passed as argument `badchars`.

    See also

    vrna_search_BM_BCT_num(), vrna_search_BMH()

    Parameters:

      - needle – The pattern of object representations to search for

      - needle_size – The size (length) of the pattern provided in `needle`

      - haystack – The string of objects the search will be performed on

      - haystack_size – The size (length) of the `haystack` string

      - start – The position within `haystack` where to start the search

      - badchars – A pre-computed Bad Character Table obtained from vrna_search_BM_BCT_num() (If NULL, a Bad Character Table will be generated automatically)

      - cyclic – Allow for cyclic matches if non-zero, stop search at end of haystack otherwise

    Returns:

      A pointer to the first occurence of `needle` within `haystack` after position `start`

  const char *vrna_search_BMH(const char *needle, size_t needle_size, const char *haystack, size_t haystack_size, size_t start, size_t *badchars, unsigned char cyclic)

    Search for an ASCII pattern within a larger ASCII string using the Boyer-Moore-Horspool algorithm.

        #include <ViennaRNA/search/BoyerMoore.h>

    To speed-up subsequent searches with this function, the Bad Character Table should be precomputed and passed as argument `badchars`. Furthermore, both, the lengths of `needle` and the length of `haystack` should be pre-computed and must be passed along with each call.

    See also

    vrna_search_BM_BCT(), vrna_search_BMH_num()

    Parameters:

      - needle – The NULL-terminated ASCII pattern to search for

      - needle_size – The size (length) of the pattern provided in `needle`

      - haystack – The NULL-terminated ASCII string of the search will be performed on

      - haystack_size – The size (length) of the `haystack` string

      - start – The position within `haystack` where to start the search

      - badchars – A pre-computed Bad Character Table obtained from vrna_search_BM_BCT() (If NULL, a Bad Character Table will be generated automatically)

      - cyclic – Allow for cyclic matches if non-zero, stop search at end of haystack otherwise

    Returns:

      A pointer to the first occurence of `needle` within `haystack` after position `start`

  size_t *vrna_search_BM_BCT_num(const unsigned int *pattern, size_t pattern_size, unsigned int num_max)

    Retrieve a Boyer-Moore Bad Character Table for a pattern of elements represented by natural numbers.

        #include <ViennaRNA/search/BoyerMoore.h>

    See also

    vrna_search_BMH_num(), vrna_search_BM_BCT()

    Note

    We store the maximum number representation of an element `num_max` at position `0`. So the actual bad character table `T` starts at `T`[1] for an element represented by number `0`.

    Parameters:

      - pattern – The pattern of element representations used in the subsequent search

      - pattern_size – The size (length) of the pattern provided in `pattern`

      - num_max – The maximum number representation of an element, i.e. the size of the alphabet

    Returns:

      A Bad Character Table for use in our Boyer-Moore search algorithm implementation(s)

  size_t *vrna_search_BM_BCT(const char *pattern)

    Retrieve a Boyer-Moore Bad Character Table for a NULL-terminated pattern of ASCII characters.

        #include <ViennaRNA/search/BoyerMoore.h>

    See also

    vrna_search_BMH(), vrna_search_BM_BCT_num()

    Note

    We store the maximum number representation of an element, i.e. `127` at position `0`. So the actual bad character table `T` starts at `T`[1] for an element represented by ASCII code `0`.

    Parameters:

      - pattern – The NULL-terminated pattern of ASCII characters used in the subsequent search

    Returns:

      A Bad Character Table for use in our Boyer-Moore search algorithm implementation(s)