/*
* ContinuousRateTransformation.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.continuous;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
/**
* Created by msuchard on 9/14/16.
*/
public interface ContinuousRateTransformation {
double getNormalization();
class Default implements ContinuousRateTransformation {
private final Tree tree;
private final boolean scaleByTime;
private final boolean useTreeLength;
public Default(Tree tree, boolean scaleByTime, boolean useTreeLength) {
this.tree = tree;
this.scaleByTime = scaleByTime;
this.useTreeLength = useTreeLength;
}
@Override
public double getNormalization() {
if (!scaleByTime) {
return 1.0;
} else {
return (useTreeLength ?
(1.0 / getTreeLength()) :
(1.0 / tree.getNodeHeight(tree.getRoot()))
);
}
}
private double getTreeLength() {
double treeLength = 0;
for (int i = 0; i < tree.getNodeCount(); i++) {
NodeRef node = tree.getNode(i);
if (!tree.isRoot(node)) {
treeLength += tree.getBranchLength(node);
}
}
return treeLength;
}
}
}
// TODO I suspect this class should be a Model and store/restore treeLength