net.sourceforge.cilib.bioinf.sequencealignment
Class GapFourFour

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

All Implemented Interfaces:

GapPenaltiesMethod

public class GapFourFour
extends Object
implements GapPenaltiesMethod

Method that penalises gaps. Penalisation is done according to the following formula: gap groups*4 + total amount of gaps*0.4

Author:

Fabien Zablocki

Constructor Summary

GapFourFour()

Method Summary

ArrayList<String>	getFinalAlignment()
double	getPenalty(ArrayList<String> alignment)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

GapFourFour

public GapFourFour()

Method Detail

setVerbose

public void setVerbose(boolean verbose)

getFinalAlignment

public ArrayList<String> getFinalAlignment()

getPenalty

public double getPenalty(ArrayList<String> alignment)

Specified by:

getPenalty in interface GapPenaltiesMethod