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 Sequences 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