/*
* FitnessFunction.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evolution.wrightfisher;
/**
* An abstract class defining a general fitness function on a byte-encoded molecular sequence
*
* @author Alexei Drummond
*/
public abstract class FitnessFunction {
public abstract double getFitness(byte[] sequence);
/**
* @return the relative fitness increase of the new state at given position to the old state.
*/
public abstract double getFitnessFactor(int pos, byte newState, byte oldState);
/**
* @return a tabulation of the fitness of each allele at each site. The maximum fitness at
* eachh site is 1.
*/
public abstract double[][] getFitnessTable();
public abstract void initializeToFittest(byte[] genome);
}