/*
* SingleScalarTreeTransform.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.evomodel.tree;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
/**
* @author Marc A. Suchard
*/
public class SingleScalarTreeTransform extends TreeTransform {
public SingleScalarTreeTransform(Parameter scale) {
super("singleScalarTreeTransform");
scale.addBounds(new Parameter.DefaultBounds(1.0, 0.0, 1));
this.scale = scale;
addVariable(scale);
}
public double transform(Tree tree, NodeRef node, double originalHeight) {
if (tree.isExternal(node)) {
return originalHeight;
}
final double rootHeight = tree.getNodeHeight(tree.getRoot());
return rootHeight - getScaleForNode(tree, node) * (rootHeight - originalHeight);
}
protected double getScaleForNode(Tree tree, NodeRef node) {
return scale.getParameterValue(0);
}
public String getInfo() {
return "Linear transform by " + scale.getId();
}
protected void handleVariableChangedEvent(Variable variable, int index, Variable.ChangeType type) {
fireModelChanged(scale);
}
private final Parameter scale;
}