de.jstacs.algorithms
Class Alignment

java.lang.Object
  extended by 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
          The 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, costs 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, 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, Costs)).

Returns:
the alignment