info.bioinfweb.commons.bio.alignment.pairwise

Class NeedlemanWunschAligner

java.lang.Object

info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner

All Implemented Interfaces:

PairwiseAligner

public class NeedlemanWunschAligner
extends java.lang.Object
implements PairwiseAligner

Performs a global Needleman Wunsch pairwise alignment. This class is based on the implementation of Daniel Himmelein available here in the version from 7.11.2012 under the terms of Apache License 2.0.

Author:

Daniel Himmelein, Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	GAP_SCORE
static int	MATCH_SCORE
static int	MISMATCH_SCORE

Constructor Summary

Constructors

Constructor and Description
NeedlemanWunschAligner()

Method Summary

Modifier and Type	Method and Description
java.lang.CharSequence[]	align(java.lang.CharSequence seqA, java.lang.CharSequence seqB)
char	getGapChar()
int	getScore()
void	setGapChar(char gapChar)

Methods inherited from class java.lang.Object

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

Field Detail

MATCH_SCORE

public static int MATCH_SCORE

MISMATCH_SCORE

public static int MISMATCH_SCORE

GAP_SCORE

public static int GAP_SCORE

Constructor Detail

NeedlemanWunschAligner

public NeedlemanWunschAligner()

Method Detail

getGapChar

public char getGapChar()

setGapChar

public void setGapChar(char gapChar)

getScore

public int getScore()

align

public java.lang.CharSequence[] align(java.lang.CharSequence seqA,
                                      java.lang.CharSequence seqB)

Specified by:

align in interface PairwiseAligner