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## de.jstacs.algorithms.alignment
Class Alignment

    java.lang.Object
      de.jstacs.algorithms.alignment.Alignment

    public class Alignment

extends Object

Class for computing optimal alignments using Needleman-Wunsch algorithm of for affine gap costs Gotohs algorithm. The class also provides the possibility of specifying the number of off-diagonals. In this case, the current implementation helps to reduce the runtime but not the memory consumption.

Author:
  Jan Grau, Jens Keilwagen
See Also:
  `AffineCosts`

Nested Class Summary
`static class` | `Alignment.AlignmentType`

Constructor Summary
`Alignment(Alignment.AlignmentType type, Costs costs)` Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs`.
`Alignment(Alignment.AlignmentType type, Costs costs, int offDiagonal)` Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs` and a banded version of the alignment algorithm.

Method Summary
`PairwiseStringAlignment` | `getAlignment(Sequence s1, int startS1, int endS1, Sequence s2, int startS2, int endS2)` Computes and returns the alignment of `s1` and `s2` (`Alignment(AlignmentType, Costs)`).
`PairwiseStringAlignment` | `getAlignment(Sequence s1, Sequence s2)` Computes and returns the alignment of `s1` and `s2` (`Alignment(AlignmentType, Costs)`).

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### Alignment

    public Alignment(Alignment.AlignmentType type,
                     Costs costs)

  Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs`.

  Parameters:
    `type` - the type of the alignment
    `costs` - the costs

### Alignment

    public Alignment(Alignment.AlignmentType type,
                     Costs costs,
                     int offDiagonal)

  Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs` and a banded version of the alignment algorithm. If the alignment is performed for `Sequence`s of different length, the number of secondary diagonals must be at least as large as the difference of the lengths.

  Parameters:
    `type` - the type of the alignment
    `costs` - the costs
    `offDiagonal` - the number of secondary diagonals at both sides of the diagonal

Method Detail

### getAlignment

    public PairwiseStringAlignment getAlignment(Sequence s1,
                                                Sequence s2)

  Computes and returns the alignment of `s1` and `s2` (`Alignment(AlignmentType, Costs)`).

  Parameters:
    `s1` - the first sequence
    `s2` - the second sequence
  Returns:
    the alignment

### getAlignment

    public PairwiseStringAlignment getAlignment(Sequence s1,
                                                int startS1,
                                                int endS1,
                                                Sequence s2,
                                                int startS2,
                                                int endS2)

  Computes and returns the alignment of `s1` and `s2` (`Alignment(AlignmentType, Costs)`).

  Parameters:
    `s1` - the first sequence
    `startS1` - the start position in the first sequence
    `endS1` - the end position in the first sequence
    `s2` - the second sequence
    `startS2` - the start position in the second sequence
    `endS2` - the end position in the second sequence
  Returns:
    the alignment

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