Maximal Repeats - SeqAn API Documentation

# Page Maximal Repeats

Example for using the MaxRepeatsIterator.

Given a sequences, a repeat is a substring that occurs at at least 2 different positions. A maximal repeat is a repeat that cannot be extended to the left or to right to a longer repeat. The following example demonstrates how to iterate over all maximal repeats and output them.

    #include <iostream>
    #include <seqan/index.h>

    using namespace seqan;

Snippet from: demos/dox/index/maxrepeats.cpp

We begin with a @Class.String@ to store our sequence. Then we create an @Class.Index@ of this StringSet.

Afterwards we initialize a string with the sequence and build an index over it

    int main()
    {

        String<char> myString = "How many wood would a woodchuck chuck.";

        typedef Index<String<char> > TMyIndex;
        TMyIndex myIndex(myString);

Snippet from: demos/dox/index/maxrepeats.cpp

To find maximal repeats, we use SeqAn's MaxRepeatsIterator and set the minimum repeat length to 3.

        typedef Iterator<TMyIndex, MaxRepeats>::Type TMaxRepeatIterator;
        TMaxRepeatIterator myRepeatIterator(myIndex, 3);

        while (!atEnd(myRepeatIterator))
        {
            Iterator<TMaxRepeatIterator>::Type myRepeatPair(myRepeatIterator);
            while (!atEnd(myRepeatPair))
            {
                std::cout << *myRepeatPair << ", ";
                ++myRepeatPair;
            }

            std::cout << repLength(myRepeatIterator) << "   ";
            std::cout << "\t\"" << representative(myRepeatIterator) << '\"' << std::endl;

            ++myRepeatIterator;
        }

        return 0;
    }

Snippet from: demos/dox/index/maxrepeats.cpp

A repeat can be represented by its length and positions it occurs at. $myRepeatIterator$ iterates over all repeat strings. Please note that in contrast to supermaximal repeats, given a maximal repeat string, not all pairs of its occurrences are maximal repeats. So we need an iterator to iterate over all maximal pairs of this repeat string. The @Spec.MaxRepeats Iterator@ can be seen as a container and be iterated for itself.

    weese@tanne:~/seqan$ cd ../build
    weese@tanne:~/build$ make demo_index_maxrepeats
    weese@tanne:~/build$ ./bin/demo_index_maxrepeats
    < 8 , 21 >, 5           " wood"
    < 21 , 13 >, < 8 , 13 >, 3      " wo"
    < 26 , 32 >, 5          "chuck"
    weese@tanne:~/seqan/demos$

#### Dox Sources

    @page DemoMaximalRepeats Maximal Repeats

    @brief Example for using the @link MaxRepeatsIterator @endlink.

    Given a sequences, a repeat is a substring that occurs at at least 2
    different positions. A maximal repeat is a repeat that cannot be extended to
    the left or to right to a longer repeat. The following example demonstrates
    how to iterate over all maximal repeats and output them.

    @snippet demos/dox/index/maxrepeats.cpp includes

    We begin with a @Class.String@ to store our sequence. Then we create an
    @Class.Index@ of this @link StringSet @endlink.

    Afterwards we initialize a string with the sequence and build an index over
    it

    @snippet demos/dox/index/maxrepeats.cpp init

    To find maximal repeats, we use SeqAn's @link MaxRepeatsIterator @endlink and
    set the minimum repeat length to 3.

    @snippet demos/dox/index/maxrepeats.cpp iteration

    A repeat can be represented by its length and positions it occurs at.
    $myRepeatIterator$ iterates over all repeat strings. Please note that in
    contrast to supermaximal repeats, given a maximal repeat string, not all
    pairs of its occurrences are maximal repeats. So we need an iterator to
    iterate over all maximal pairs of this repeat string. The @Spec.MaxRepeats
    Iterator@ can be seen as a container and be iterated for itself.

    @code{.console}
    weese@tanne:~/seqan$ cd ../build
    weese@tanne:~/build$ make demo_index_maxrepeats
    weese@tanne:~/build$ ./bin/demo_index_maxrepeats
    < 8 , 21 >, 5           " wood"
    < 21 , 13 >, < 8 , 13 >, 3      " wo"
    < 26 , 32 >, 5          "chuck"
    weese@tanne:~/seqan/demos$
    @endcode