net.sourceforge.cilib.bioinf.sequencealignment
Class BinaryAlignmentCreator

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

public class BinaryAlignmentCreator
extends Object

This class is responsible for creating an output alignment by populating the input alignment with gaps at positions given by the discretization of the particles positions. Works with 4 bits encoding in conjonction with BinaryMSAProblem.

Author:

Fabien Zablocki

Constructor Summary

BinaryAlignmentCreator()

Method Summary

ArrayList<String>	getAlignment()
double	getFitness(Collection<String> alignment, Vector solution, int[] gapsArray)
ScoringMethod	getTheMethod()
void	setAlignment(ArrayList<String> align)
void	setJustEvaluate(boolean justEvaluate)
void	setScoringMethod(ScoringMethod theMethod)

Methods inherited from class java.lang.Object

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

Constructor Detail

BinaryAlignmentCreator

public BinaryAlignmentCreator()

Method Detail

getFitness

public double getFitness(Collection<String> alignment,
                         Vector solution,
                         int[] gapsArray)

setScoringMethod

public void setScoringMethod(ScoringMethod theMethod)

getTheMethod

public ScoringMethod getTheMethod()

getAlignment

public ArrayList<String> getAlignment()

setAlignment

public void setAlignment(ArrayList<String> align)

setJustEvaluate

public void setJustEvaluate(boolean justEvaluate)