net.sourceforge.cilib.bioinf.sequencealignment
Class AlignmentCreator

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

public class AlignmentCreator
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 Real and Integers positions.

Author:

Fabien Zablocki, gpampara

Constructor Summary

AlignmentCreator()

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

AlignmentCreator

public AlignmentCreator()

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)