/*
* EvolutionaryProcessDelegate.java
*
* Copyright (c) 2002-2016 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.evomodel.treedatalikelihood;
import beagle.Beagle;
import dr.evomodel.substmodel.SubstitutionModel;
/**
* Implementations of this interface are used to delegate control of substitution
* models along branches of a tree.
*
* @author Marc Suchard
* @author Andrew Rambaut
* @version $Id$
*/
public interface EvolutionaryProcessDelegate {
boolean canReturnComplexDiagonalization();
int getEigenBufferCount();
int getMatrixBufferCount();
int getSubstitutionModelCount();
SubstitutionModel getSubstitutionModel(int index);
int getEigenIndex(int bufferIndex);
int getMatrixIndex(int branchIndex);
double[] getRootStateFrequencies();
void updateSubstitutionModels(Beagle beagle, boolean flipBuffers);
void updateTransitionMatrices(Beagle beagle, int[] branchIndices, double[] edgeLengths, int updateCount, boolean flipBuffers);
void flipTransitionMatrices(int[] branchIndices, int updateCount);
void storeState();
void restoreState();
}