net.sourceforge.cilib.bioinf.sequencealignment
Class PAM250SoP

java.lang.Object
  net.sourceforge.cilib.bioinf.sequencealignment.PAM250SoP

All Implemented Interfaces:

ScoringMethod

public class PAM250SoP
extends Object
implements ScoringMethod

This class implements the Sum Of Pairs scoring function that uses PAM250 substitutions matrices that give scores for proteins in a biologically meaningful manner. SoP routine has been optimized for speed.

Author:

Fabien Zablocki

Constructor Summary

PAM250SoP()

Method Summary

double	getScore(ArrayList<String> alignment)
void	setVerbose(boolean verbose)
void	setWeight(boolean weight)

Methods inherited from class java.lang.Object

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

Constructor Detail

PAM250SoP

public PAM250SoP()

Method Detail

setVerbose

public void setVerbose(boolean verbose)

setWeight

public void setWeight(boolean weight)

getScore

public double getScore(ArrayList<String> alignment)

Specified by:

getScore in interface ScoringMethod