/*
* Genome.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;
/**
* @author rambaut
* Date: Apr 19, 2005
* Time: 8:55:11 PM
*/
public interface Genome {
Genome replicate(Mutator mutator, FitnessFunction fitnessFunction);
byte[] getSequence();
int hammingDistance(Genome other);
String getDNASequenceString();
String getAminoAcidSequenceString();
Genome getParent();
double getFitness();
void mark();
void unmark();
int getMarks();
Mutation[] getMutations();
int getGenomeLength();
}