net.sourceforge.cilib.bioinf.sequencealignment
Class BestMatch

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

All Implemented Interfaces:

ScoringMethod

public class BestMatch
extends Object
implements ScoringMethod

A scoring function based on the highest number of matches per column. Each matching pair of symbols adds 1 point to the fitness value. Takes the best value for each column.

Author:

Fabien Zablocki

Constructor Summary

BestMatch()

Method Summary

double	getScore(ArrayList<String> alignment) Get the score of the given alignment.
void	setVerbose(boolean verbose) Set the printing verbosity in this ScoringMethod.

Methods inherited from class java.lang.Object

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

Constructor Detail

BestMatch

public BestMatch()

Method Detail

setVerbose

public void setVerbose(boolean verbose)

Set the printing verbosity in this ScoringMethod. TODO: This should disappear and log4j should be used instead if it is needed.

Parameters:

verbose - The value of the switch.

getScore

public double getScore(ArrayList<String> alignment)

Get the score of the given alignment.

Specified by:

getScore in interface ScoringMethod

Parameters:

alignment - The alignment to evaluate.

Returns:

the alignment score.