de.jstacs.algorithms
Class Alignment

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

public class Alignment
extends Object

Class for gapped global alignments using the extended Needleman-Wunsch algorithm.

Author:

Jan Grau

Nested Class Summary

static interface	Alignment.Costs General interface for the costs of an alignment.
static class	Alignment.SimpleCosts Class for simple costs with costs mismatch for a mismatch, costs start to start a new gap, elong to elongate a gap by one position, and costs of 0 for a match
static class	Alignment.StringAlignment Class for the representation of an alignment of two strings.

Constructor Summary

Alignment(Sequence s1, Sequence s2, Alignment.Costs costs)
Creates a new Alignment.StringAlignment instance that aligns the sequences s1 and s2 using the costs defined in costs.

Method Summary

Alignment.StringAlignment

getAlignment() Computes and returns the alignment of s1 and s2 (Alignment(Sequence, Sequence, de.jstacs.algorithms.Alignment.Costs))

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Alignment

public Alignment(Sequence s1,
                 Sequence s2,
                 Alignment.Costs costs)

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

Parameters:

s1 - the first sequence

s2 - the second sequence

costs - the costs

Method Detail

getAlignment

public Alignment.StringAlignment getAlignment()

Computes and returns the alignment of s1 and s2 (Alignment(Sequence, Sequence, de.jstacs.algorithms.Alignment.Costs))

Returns:

the alignment