de.bioforscher.singa.sequence.algorithms.alignment

Class NeedlemanWunschAlignment

java.lang.Object

de.bioforscher.singa.sequence.algorithms.alignment.NeedlemanWunschAlignment

public class NeedlemanWunschAlignment
extends Object

Author:

cl

Constructor Summary

Constructors

Constructor and Description
NeedlemanWunschAlignment(SubstitutionMatrix substitutionMatrix, ProteinSequence firstSequence, ProteinSequence secondSequence)

Method Summary

Modifier and Type	Method and Description
ProteinSequence	getAlignedFirstSequence()
ProteinSequence	getAlignedSecondSequence()
int	getGapCost()
DynamicProgrammingGraph	getGraph()
double	getScore()
void	setGapCost(int gapCost)

Methods inherited from class java.lang.Object

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

Constructor Detail

NeedlemanWunschAlignment

public NeedlemanWunschAlignment(SubstitutionMatrix substitutionMatrix,
                                ProteinSequence firstSequence,
                                ProteinSequence secondSequence)

Method Detail

getGraph

public DynamicProgrammingGraph getGraph()

getGapCost

public int getGapCost()

setGapCost

public void setGapCost(int gapCost)

getScore

public double getScore()

getAlignedFirstSequence

public ProteinSequence getAlignedFirstSequence()

getAlignedSecondSequence

public ProteinSequence getAlignedSecondSequence()