net.sourceforge.cilib.bioinf.sequencealignment
Class GapFogel

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

All Implemented Interfaces:

GapPenaltiesMethod

public class GapFogel
extends Object
implements GapPenaltiesMethod

Method that calculates a gap score by linearly or not scale the number of gaps over all columns. Found in paper from Fogel in his GA for MSA

Author:

Fabien Zablocki

Constructor Summary

GapFogel()

Method Summary

double	getPenalty(ArrayList<String> alignmentList)
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

GapFogel

public GapFogel()

Method Detail

setLinearScale

public void setLinearScale(boolean linearScale)

setVerbose

public void setVerbose(boolean verbose)

getPenalty

public double getPenalty(ArrayList<String> alignmentList)

Specified by:

getPenalty in interface GapPenaltiesMethod