/*
* IndelModel.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.oldevomodel.indel;
import dr.evolution.util.Units;
import dr.inference.model.AbstractModel;
/**
* This abstract class contains methods that are of general use for
* modelling insertions and deletions.
*
* @version $$
*
* @author Alexei Drummond
*/
public abstract class IndelModel extends AbstractModel implements Units {
public static final String INDEL_MODEL = "indelModel";
//
// Public stuff
//
public IndelModel(String name) {
super(name);
units = Units.Type.GENERATIONS;
}
//
// functions that define an indel model (left for subclass)
//
/**
* Gets the birth rate of insertions of a given length.
*/
public abstract double getBirthRate(int length);
/**
* Gets the death rate of insertions of a given length.
*/
public abstract double getDeathRate(int length);
/**
* Units in which time units are measured.
*/
private Type units;
/**
* sets units of measurement.
*
* @param u units
*/
public void setUnits(Type u)
{
units = u;
}
/**
* returns units of measurement.
*/
public Type getUnits()
{
return units;
}
}