chainSeedsGlobally - SeqAn API Documentation

# fn() chainSeedsGlobally
Global chaining of seeds.

Defined in | <seqan/seeds.h>
Signature | `void chainSeedsGlobally(target, seedSet, tag);`

## Parameters

`target` | A container to append the seeds to.
`seedSet` | The SeedSet object to get the seeds from.
`tag` | The tag to select the algorithm with (currently only SparseChaining is supported).

## Detailed Description

Chaining of seeds between two sequences can be performed using sparse chaining as defined in (Gusfield, 1997).

### Example

The following example demonstrates how to use the `chainSeedsGlobally()` function. First, a SeedSet is built and filled with SimpleSeed object. Then, a String of SimpleSeed objects is defined and filled using the `chainSeedsGlobally()` function.

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

    using namespace seqan;

    int main()
    {
        // Build SeedSet.
        SeedSet<Seed<Simple>, Unordered> seedSet;
        addSeed(seedSet, Seed<Simple>(0, 93, 281, 342), Single());
        addSeed(seedSet, Seed<Simple>(3, 237, 127, 364), Single());
        addSeed(seedSet, Seed<Simple>(3, 284, 86, 368), Single());
        addSeed(seedSet, Seed<Simple>(5, 146, 239, 374), Single());
        addSeed(seedSet, Seed<Simple>(299, 352, 405, 460), Single());

        // Perform sparse chaining, uses time O(n log n).
        String<Seed<Simple> > chain;
        chainSeedsGlobally(chain, seedSet, SparseChaining());

        // Print results to stdout.
        for (unsigned i = 0; i < length(chain); ++i)
            std::cout << "Seed(" << beginPositionH(chain[i]) << ", "
                      << beginPositionV(chain[i]) << ", " << endPositionH(chain[i])
                      << ", " << endPositionV(chain[i]) << ")\n";

        return 0;
    }

Demo: demos/dox/seeds/seeds_chaining.cpp

The output is as follows. Only the first and last seeds are written to `std::cout`.

    Seed(0, 93, 281, 342)
    Seed(299, 352, 405, 460)

### References

- Dan Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, January 1997.

## Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### Dox Sources

    /*!
     * @fn chainSeedsGlobally
     *
     * @headerfile <seqan/seeds.h>
     *
     * @brief Global chaining of seeds.
     *
     * @signature void chainSeedsGlobally(target, seedSet, tag);
     *
     * @param[out] target A @link ContainerConcept container @endlink to append the
     *                    seeds to.
     * @param[in] seedSet The @link SeedSet @endlink object to get the seeds from.
     * @param[in] tag The tag to select the algorithm with (currently only @link
     *                GlobalChainingTags#SparseChaining SparseChaining @endlink is
     *                supported).
     *
     * Chaining of seeds between two sequences can be performed using sparse
     * chaining as defined in (Gusfield, 1997).
     *
     * @section Example
     *
     * The following example demonstrates how to use the
     * <tt>chainSeedsGlobally()</tt> function. First, a @link SeedSet @endlink is
     * built and filled with @link SimpleSeed @endlink object. Then, a @link String
     * @endlink of @link SimpleSeed @endlink objects is defined and filled using the
     * <tt>chainSeedsGlobally()</tt> function.
     *
     * @include demos/dox/seeds/seeds_chaining.cpp
     *
     * The output is as follows. Only the first and last seeds are written to
     * <tt>std::cout</tt>.
     *
     * @include demos/dox/seeds/seeds_chaining.cpp.stdout
     *
     * @section References
     *
     * <ul> <li>Dan Gusfield. Algorithms on Strings, Trees, and Sequences: Computer
     * Science and Computational Biology. Cambridge University Press, January
     * 1997.</li> </ul>
     */