/*
* SiteModel.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.sitemodel;
import dr.oldevomodel.substmodel.FrequencyModel;
import dr.oldevomodel.substmodel.SubstitutionModel;
/**
* SiteModel - Specifies how rates and substitution models vary across sites.
*
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id: SiteModel.java,v 1.77 2005/05/24 20:25:58 rambaut Exp $
*/
public interface SiteModel extends SiteRateModel {
public static final String SITE_MODEL = "siteModel";
/**
* Get this site model's substitution model
*
* @return the substitution model
*/
SubstitutionModel getSubstitutionModel();
/**
* Specifies whether SiteModel should integrate over the different categories at
* each site. If true, the SiteModel will calculate the likelihood of each site
* for each category. If false it will assume that there is each site can have a
* different category.
*
* @return the boolean
*/
boolean integrateAcrossCategories(); // TODO Consider moving into SiteRateModel
/**
* Get the category of a particular site. If integrateAcrossCategories is true.
* then throws an IllegalArgumentException.
*
* @param site the index of the site
* @return the index of the category
*/
int getCategoryOfSite(int site); // TODO Consider moving into SiteRateModel
/**
* Get the frequencyModel for this SiteModel.
*
* @return the frequencyModel.
*/
FrequencyModel getFrequencyModel();
}