net.sourceforge.cilib.bioinf.sequencealignment
Class GapOpeningAndExtensionPenalty

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

All Implemented Interfaces:

GapPenaltiesMethod

public class GapOpeningAndExtensionPenalty
extends Object
implements GapPenaltiesMethod

Method that penalises indels as gap groups. Penalty for k contiguous indels (1 gap group) = Gop + (k-1)Gep where Gop is GapOpeningPenalty and Gep is GapExtensionPenalty

Author:

Fabien Zablocki

Constructor Summary

GapOpeningAndExtensionPenalty()

Method Summary

double	getPenalty(ArrayList<String> alignment)
void	setGapExtensionPenalty(double gapExtensionPenalty)
void	setGapOpeningPenalty(double gapOpeningPenalty)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

GapOpeningAndExtensionPenalty

public GapOpeningAndExtensionPenalty()

Method Detail

setVerbose

public void setVerbose(boolean verbose)

setGapExtensionPenalty

public void setGapExtensionPenalty(double gapExtensionPenalty)

setGapOpeningPenalty

public void setGapOpeningPenalty(double gapOpeningPenalty)

getPenalty

public double getPenalty(ArrayList<String> alignment)

Specified by:

getPenalty in interface GapPenaltiesMethod