Package org.snpeff.align

Class NeedlemanWunsch

java.lang.Object

org.snpeff.align.NeedlemanWunsch

Direct Known Subclasses:

SmithWaterman, VcfRefAltAlign

public class NeedlemanWunsch
extends java.lang.Object

Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
NeedlemanWunsch(java.lang.String a, java.lang.String b)

Method Summary

Modifier and Type	Method	Description
java.lang.String	align()
java.lang.String	getAlignment()
int	getAlignmentScore()
int	getOffset()
void	setDeletion(int deletion)
void	setMatch(int match)
void	setMissMatch(int missMatch)
void	setUseSpace(boolean useSpace)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

NeedlemanWunsch

public NeedlemanWunsch(java.lang.String a,
                       java.lang.String b)

Method Detail

align

public java.lang.String align()

getAlignment

public java.lang.String getAlignment()

getAlignmentScore

public int getAlignmentScore()

getOffset

public int getOffset()

setDeletion

public void setDeletion(int deletion)

setMatch

public void setMatch(int match)

setMissMatch

public void setMissMatch(int missMatch)

setUseSpace

public void setUseSpace(boolean useSpace)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object