# fn() bandedChainAlignment
Computes the best global pairwise alignment between two sequences given a non-empty seed chain.

Defined in | <seqan/seeds.h>
Signature | `TValue bandedChainAlignment(align, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]); TValue bandedChainAlignment(gapsH, gapsV, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]); TValue bandedChainAlignment(frags, strings, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]); TValue bandedChainAlignment(alignmentGraph, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);`

## Parameters

`align` | An Align object that stores the alignment. The number of rows must be 2 and the sequences must have already been set. `row(align, 0)` is the horizontal sequence in the alignment matrix, `row(align, 1)` is the vertical sequence.
`gapsH` | Horizontal gapped sequence in alignment matrix. Type: Gaps.
`gapsV` | Vertical gapped sequence in alignment matrix. Type: Gaps.
`frags` | String of Fragment objects. The sequence with id `0` is the horizontal one, the sequence with id `1` is the vertical one.
`strings` | A StringSet containing two sequences.
`alignmentGraph` | AlignmentGraph object to store the alignment in. The underlying StringSet must be an DependentStringSet. Types: AlignmentGraph.
`seedChain` | The container holding the seeds. Note that the seeds have to be in montonic non-decreasing order and the container has to implement a forward-iterator. Type: SeedSet.
`scoringScheme1` | The scoring scheme used for the alignment. If `scoringScheme2` is specified, then `scoringScheme1` is used for the regions around the seeds and `scoringScheme2` for the gap regions between two consecutive seeds. Types: Score
`scoringScheme2` | The optional scoring scheme for the gap regions between two anchors. Types: Score
`k` | Optional extension of the band around the seeds. At the moment only band extensions greater or equal `1` are allowed. Type: nolink:`int`. Default: 15.
`alignConfig` | The AlignConfig to use for the alignment.

## Return Values

`TValue` | An integer with the alignment score, as given by the Value metafunction of the Score type. If the seed chain is empty then the smallest value of the score type is used to return the minimal value of the selected score type and no alignment is computed.

## Detailed Description

There exist multiple overloads for this function with four configuration dimensions.

First, you can select whether begin and end gaps are free in either sequence using `alignConfig`.

Second, you can select the type of the target storing the alignment. This can be either an Align object, two Gaps objects, a AlignmentGraph, or a string of Fragment objects. Align objects provide an interface to tabular alignments with the restriction of all rows having the same type. Using two Gaps objects has the advantage that you can align sequences with different types, for example DnaString and Dna5String. Alignment Graphs provide a graph-based representation of segment-based colinear alignments. Using Fragment strings is useful for collecting many pairwise alignments, for example in the construction of Alignment Graphs for multiple-sequence alignments (MSA).

Third, you can optionally give a second scoring scheme to fill the gaps between two consecutive seeds. Note that based on the specified scores either an affine or linear gap cost function is used. This only depends on whether for one of the scoring schemes the scores for gap opening and gap extension differ or not. If only one scoring scheme is defined the complete region is computed with the same scoring scheme.

Fourth, you can optinally select a proper band extension for the bands around the seeds. At the moment only band extensions of at least `1` are allowed. The default value is `15` and is based on the default values for the LAGAN-algorithm described by Brudno et al., 2003.

The examples below show some common use cases.

### Examples

Banded chain alignment of two sequences using an Align object and using only one scoring scheme and no free end-gaps.

    Dna5String seqH = "CGAATCCATCCCACACA";
    Dna5String seqV = "GGCGATNNNCATGGCACA";

    String<Seed<Simple> > seedChain;
    appendValue(seedChain, Seed<Simple>(2, 0, 6, 5));
    appendValue(seedChain, Seed<Simple>(9, 6, 12, 9));
    appendValue(seedChain, Seed<Simple>(14, 11, 16, 17));

    Align<Dna5String, ArrayGaps> alignment;
    resize(rows(alignment), 2);
    assignSource(row(alignment, 0), seqH);
    assignSource(row(alignment, 1), seqV);

    Score<int, Simple> scoringScheme(2, -1, -2);

    int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);

Banded chain alignment of two sequences using two Gaps objects, an unordered seed set to hold the seeds, two different scoring schemes for the gaps between the seeds and the seeds and free end-gaps.

    DnaString seqH = "CGAATCCATCCCACACA";
    Dna5String seqV = "GGCGATNNNCATGGCACA";

    SeedSet<Simple, Unordered> seedChain;
    addSeed(seedChain, Seed<Simple>(2, 0, 6, 5), Single());
    addSeed(seedChain, Seed<Simple>(9, 6, 12, 9), Single());
    addSeed(seedChain, Seed<Simple>(14, 11, 16, 17), Single());

    Gaps<DnaString, ArrayGaps> gapsH(seqH);
    Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);

    Score<int, Simple> scoringSchemeSeed(2, -1, -2);
    Score<int, Simple> scoringSchemeGap(5, -3, -1, -5);
    AlignConfig<true, true, true, true> alignConfig;

    int result = globalAlignment(gapsH, gapsV, scoringSchemeSeed, scoringSchemeGap, alignConfig, 2);

### Tutorial

Also see the Seed-and-Extend Tutorial

### Reference

- Brudno M, Do CB, Cooper GM, et al.: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA. Genome Research 2003, 13: 721-731.

## Data Races

Thread safety unknown!

#### Dox Sources

    /*!
     * @fn bandedChainAlignment
     *
     * @headerfile <seqan/seeds.h>
     *
     * @brief Computes the best global pairwise alignment between two sequences
     *        given a non-empty seed chain.
     *
     * @signature TValue bandedChainAlignment(align, seedChain, scoringScheme1[,
     *            scoringScheme2] [, alignConfig] [, k]);
     * @signature TValue bandedChainAlignment(gapsH, gapsV, seedChain,
     *            scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
     * @signature TValue bandedChainAlignment(frags, strings, seedChain,
     *            scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
     * @signature TValue bandedChainAlignment(alignmentGraph, seedChain,
     *            scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
     *
     * @param[in,out] align An @link Align @endlink object that stores the
     *                      alignment. The number of rows must be 2 and the
     *                      sequences must have already been set. <tt>row(align,
     *                      0)</tt> is the horizontal sequence in the alignment
     *                      matrix, <tt>row(align, 1)</tt> is the vertical sequence.
     * @param[in,out] gapsH Horizontal gapped sequence in alignment matrix. Type:
     *                      @link Gaps @endlink.
     * @param[in,out] gapsV Vertical gapped sequence in alignment matrix. Type:
     *                      @link Gaps @endlink.
     * @param[out] frags @link String @endlink of @link Fragment @endlink objects.
     *                   The sequence with id <tt>0</tt> is the horizontal one, the
     *                   sequence with id <tt>1</tt> is the vertical one.
     * @param[in] strings A @link StringSet @endlink containing two sequences.
     * @param[in,out] alignmentGraph  @link AlignmentGraph @endlink object to store
     *                               the alignment in. The underlying @link
     *                               StringSet @endlink must be an @link
     *                               DependentStringSet @endlink. Types:
     *                               AlignmentGraph.
     * @param[in] seedChain The container holding the @link Seed seeds @endlink.
     *                      Note that the @link Seed seeds @endlink have to be in
     *                      montonic non-decreasing order and the container has to
     *                      implement a forward-iterator. Type: @link SeedSet
     *                      @endlink.
     * @param[in] scoringScheme1  The scoring scheme used for the alignment. If
     *                           <tt>scoringScheme2</tt> is specified, then
     *                           <tt>scoringScheme1</tt> is used for the regions
     *                           around the seeds and <tt>scoringScheme2</tt> for
     *                           the gap regions between two consecutive seeds.
     *                           Types: Score
     * @param[in] scoringScheme2  The optional scoring scheme for the gap regions
     *                           between two anchors. Types: Score
     * @param[in] k Optional extension of the band around the seeds. At the moment
     *              only band extensions greater or equal <tt>1</tt> are allowed.
     *              Type: nolink:<tt>int</tt>. Default: 15.
     * @param[in] alignConfig  The @link AlignConfig @endlink to use for the
     *                        alignment.
     *
     * @return TValue An integer with the alignment score, as given by the @link
     *                Score#Value @endlink metafunction of the @link Score @endlink
     *                type. If the seed chain is empty then the @link
     *                OrderedAlphabetConcept#MinValue smallest value of the score
     *                type @endlink is used to return the minimal value of the
     *                selected score type and no alignment is computed.
     *
     * There exist multiple overloads for this function with four configuration
     * dimensions.
     *
     * First, you can select whether begin and end gaps are free in either sequence
     * using <tt>alignConfig</tt>.
     *
     * Second, you can select the type of the target storing the alignment. This can
     * be either an @link Align @endlink object, two @link Gaps @endlink objects, a
     * @link AlignmentGraph @endlink, or a string of @link Fragment @endlink
     * objects. @link Align @endlink objects provide an interface to tabular
     * alignments with the restriction of all rows having the same type. Using two
     * @link Gaps @endlink objects has the advantage that you can align sequences
     * with different types, for example @link DnaString @endlink and @link
     * Dna5String @endlink. @link AlignmentGraph Alignment Graphs @endlink provide a
     * graph-based representation of segment-based colinear alignments. Using @link
     * Fragment @endlink strings is useful for collecting many pairwise alignments,
     * for example in the construction of @link AlignmentGraph Alignment Graphs
     * @endlink for multiple-sequence alignments (MSA).
     *
     * Third, you can optionally give a second scoring scheme to fill the gaps
     * between two consecutive seeds. Note that based on the specified scores either
     * an affine or linear gap cost function is used. This only depends on whether
     * for one of the scoring schemes the scores for gap opening and gap extension
     * differ or not. If only one scoring scheme is defined the complete region is
     * computed with the same scoring scheme.
     *
     * Fourth, you can optinally select a proper band extension for the bands around
     * the seeds. At the moment only band extensions of at least <tt>1</tt> are
     * allowed. The default value is <tt>15</tt> and is based on the default values
     * for the LAGAN-algorithm described by Brudno et al., 2003.
     *
     * The examples below show some common use cases.
     *
     * @section Examples
     *
     * Banded chain alignment of two sequences using an @link Align @endlink object
     * and using only one scoring scheme and no free end-gaps.
     *
     * @code{.cpp}
     * Dna5String seqH = "CGAATCCATCCCACACA";
     * Dna5String seqV = "GGCGATNNNCATGGCACA";
     *
     * String<Seed<Simple> > seedChain;
     * appendValue(seedChain, Seed<Simple>(2, 0, 6, 5));
     * appendValue(seedChain, Seed<Simple>(9, 6, 12, 9));
     * appendValue(seedChain, Seed<Simple>(14, 11, 16, 17));
     *
     * Align<Dna5String, ArrayGaps> alignment;
     * resize(rows(alignment), 2);
     * assignSource(row(alignment, 0), seqH);
     * assignSource(row(alignment, 1), seqV);
     *
     * Score<int, Simple> scoringScheme(2, -1, -2);
     *
     * int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
     * @endcode
     *
     *
     * Banded chain alignment of two sequences using two @link Gaps @endlink
     * objects, an unordered seed set to hold the seeds, two different scoring
     * schemes for the gaps between the seeds and the seeds and free end-gaps.
     *
     * @code{.cpp}
     * DnaString seqH = "CGAATCCATCCCACACA";
     * Dna5String seqV = "GGCGATNNNCATGGCACA";
     *
     * SeedSet<Simple, Unordered> seedChain;
     * addSeed(seedChain, Seed<Simple>(2, 0, 6, 5), Single());
     * addSeed(seedChain, Seed<Simple>(9, 6, 12, 9), Single());
     * addSeed(seedChain, Seed<Simple>(14, 11, 16, 17), Single());
     *
     * Gaps<DnaString, ArrayGaps> gapsH(seqH);
     * Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
     *
     * Score<int, Simple> scoringSchemeSeed(2, -1, -2);
     * Score<int, Simple> scoringSchemeGap(5, -3, -1, -5);
     * AlignConfig<true, true, true, true> alignConfig;
     *
     * int result = globalAlignment(gapsH, gapsV, scoringSchemeSeed, scoringSchemeGap, alignConfig, 2);
     * @endcode
     *
     *
     * @section Tutorial
     *
     * Also see the <a
     * href="http://seqan.readthedocs.org/en/develop/Tutorial/SeedAndExtend.html
     * ">Seed-and-Extend Tutorial</a>
     *
     * @section Reference
     *
     * <ul> <li>Brudno M, Do CB, Cooper GM, et al.: LAGAN and Multi-LAGAN: Efficient
     * Tools for Large-Scale Multiple Alignment of Genomic DNA. Genome Research
     * 2003, 13: 721-731.</li> </ul>
     */