Demo Suffix Array - SeqAn API Documentation

# Page Demo Suffix Array

Example for how to create a suffix array and use it as a dictionary.

Given a sequence $s$, a suffix array is an array containing start positions of all suffices of $s$ in lexicographical order. A suffix array can simply be used to find all occurrences of an arbitrary substring $t$ in $s$ in O(|t|*log(|s|)).

SeqAn contains various suffix array construction algorithms like the Skew algorithm (J. Karkkainen and P. Sanders, "Simple Linear Work Suffix Array Construction", 2003), a more efficient modification of the Skew algorithm (difference cover of 7), external memory Skew algorithms, the prefix-doubling algorithm (U. Manber and G. Myers, "Suffix arrays: A new method for online string searching", 1993), the algorithm of Larsson and Sadakane (N.J. Larsson and K. Sadakane, "Faster Suffix Sorting", 1999), and a quicksort based algorithm.

The following example constructs a suffix array using the modified Skew algorithm and searches the interval of suffices beginning with $t="l"$. The start positions of these suffices are the occurrences of $t$, which are outputted at last. This is only an example for createSuffixArray and similar functions. For an index based substring search better use the more generic Finder class (see @Demo.Index Finder@ demo).

    ///A tutorial about suffix arrays.
    #include <iostream>
    #include <seqan/index.h>

    using namespace seqan2;

    int main()
    {
        String<char> text = "hello world!";
        String<char> pattern = "l";
        String<unsigned> sa;

    //Build a suffix array using the Skew7 algorithm.
        resize(sa, length(text));
        createSuffixArray(sa, text, Skew7());

    //Search the interval of suffices beginning with the pattern.
        Pair<unsigned> hitRange;
        hitRange = equalRangeSA(text, sa, pattern);

    //Output the suffix indices, i.e. the occurrences of the pattern.
        for (unsigned i = hitRange.i1; i < hitRange.i2; ++i)
            std::cout << sa[i] << " ";
        std::cout << std::endl;

        return 0;
    }

Demo: demos/dox/index/sufarray.cpp

    weese@tanne:~/seqan$ cd demos
    weese@tanne:~/seqan/demos$ make index_sufarray
    weese@tanne:~/seqan/demos$ ./index_sufarray
    9 2 3

#### Dox Sources

    @page DemoSuffixArray Demo Suffix Array

    @brief Example for how to create a suffix array and use it as a dictionary.

    Given a sequence $s$, a suffix array is an array containing start positions
    of all suffices of $s$ in lexicographical order. A suffix array can simply be
    used to find all occurrences of an arbitrary substring $t$ in $s$ in
    O(|t|*log(|s|)).

    SeqAn contains various suffix array construction algorithms like the Skew
    algorithm (J. Karkkainen and P. Sanders, "Simple Linear Work Suffix Array
    Construction", 2003), a more efficient modification of the Skew algorithm
    (difference cover of 7), external memory Skew algorithms, the prefix-doubling
    algorithm (U. Manber and G. Myers, "Suffix arrays: A new method for online
    string searching", 1993), the algorithm of Larsson and Sadakane (N.J. Larsson
    and K. Sadakane, "Faster Suffix Sorting", 1999), and a quicksort based
    algorithm.

    The following example constructs a suffix array using the modified Skew
    algorithm and searches the interval of suffices beginning with $t="l"$. The
    start positions of these suffices are the occurrences of $t$, which are
    outputted at last. This is only an example for @link createSuffixArray
    @endlink and similar functions. For an index based substring search better
    use the more generic @link Finder @endlink class (see @Demo.Index Finder@
    demo).

    @include demos/dox/index/sufarray.cpp

    @code{.console}
    weese@tanne:~/seqan$ cd demos
    weese@tanne:~/seqan/demos$ make index_sufarray
    weese@tanne:~/seqan/demos$ ./index_sufarray
    9 2 3
    @endcode