net.sourceforge.cilib.bioinf.sequencealignment
Class MatchFogel

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

All Implemented Interfaces:

ScoringMethod

public class MatchFogel
extends Object
implements ScoringMethod

A scoring function based on the overall score for the number of matched symbols over all columns. Each matching pair of symbols adds 1 point to the fitness value. The number of matches in each column is linearly scaled(such that any column that was fully matched up was doubled). Fitness found in paper from Fogel in his GA for MSA.

Author:

Fabien Zablocki

Constructor Summary

MatchFogel()

Method Summary

double	getScore(ArrayList<String> alignment)
void	setLinearScale(boolean linearScale)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

MatchFogel

public MatchFogel()

Method Detail

setVerbose

public void setVerbose(boolean verbose)

setLinearScale

public void setLinearScale(boolean linearScale)

getScore

public double getScore(ArrayList<String> alignment)

Specified by:

getScore in interface ScoringMethod