/*
* TreeParameterModel.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.evolution.tree.TreeDoubleTraitProvider;
import dr.evolution.tree.TreeTrait;
import dr.inference.model.AbstractModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
/**
* This class maintains a parameter of length equal to the number of nodes in the tree.
* It can optionally include the root node. If the root node is not included then this
* class will track tree changes that change the root node number and swap the parameter
* values so that the parameter values stay with their node when changes to the tree
* topology occur.
*
* @author Alexei Drummond
*/
public class TreeParameterModel extends AbstractModel implements TreeTrait<Double>, TreeDoubleTraitProvider {
protected final TreeModel tree;
// The tree parameter;
private final Parameter parameter;
// the index of the root node.
private final Parameter rootNodeNumber;
private boolean includeRoot = false;
private Intent intent;
/**
* This class constructs a tree parameter, and will set the dimension of the parameter
* to match the appropriate number of nodes if necessary.
*
* @param tree the tree that this parameter corresponds to
* @param parameter the parameter to keep in sync with tree topology moves.
* @param includeRoot tree if the parameter includes a value associated with the root node.
*/
public TreeParameterModel(TreeModel tree, Parameter parameter, boolean includeRoot) {
this(tree, parameter, includeRoot, Intent.NODE);
}
/**
* This class constructs a tree parameter, and will set the dimension of the parameter
* to match the appropriate number of nodes if necessary.
*
* @param tree the tree that this parameter corresponds to
* @param parameter the parameter to keep in sync with tree topology moves.
* @param includeRoot tree if the parameter includes a value associated with the root node.
*/
public TreeParameterModel(TreeModel tree, Parameter parameter, boolean includeRoot, Intent intent) {
super("treeParameterModel");
this.tree = tree;
this.parameter = parameter;
this.includeRoot = includeRoot;
this.intent = intent;
int dim = parameter.getDimension();
int treeSize = getParameterSize();
if (dim != treeSize) {
// System.err.println("WARNING: setting dimension of parameter to match tree branch count ("
// + dim + " != " + treeSize + ")"); // http://code.google.com/p/beast-mcmc/issues/detail?id=385
parameter.setDimension(treeSize);
}
addModel(tree);
addVariable(parameter);
rootNodeNumber = new Parameter.Default(parameter.getId() + ".rootNodeNumber");
rootNodeNumber.setParameterValue(0, tree.getRoot().getNumber());
addVariable(rootNodeNumber);
}
public int getParameterSize() {
int treeSize = tree.getNodeCount();
if (!includeRoot) {
treeSize -= 1;
}
return treeSize;
}
public void handleModelChangedEvent(Model model, Object object, int index) {
if (model == tree) {
handleRootMove();
}
}
protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
int nodeNumber = getNodeNumberFromParameterIndex(index);
assert (tree.getNode(nodeNumber).getNumber() == nodeNumber);
fireModelChanged(variable, nodeNumber);
}
protected void storeState() {
//rootNodeNumber.storeParameterValues();
}
protected void restoreState() {
//rootNodeNumber.restoreParameterValues();
}
protected void acceptState() {
}
public double getNodeDoubleValue(Tree tree, NodeRef node) {
return getNodeValue(tree, node);
}
public double getNodeValue(Tree tree, NodeRef node) {
assert (!tree.isRoot(node) || includeRoot) : "root node doesn't have a parameter value!";
assert !includeRoot || tree.getRoot().getNumber() == rootNodeNumber.getValue(0).intValue() :
"INTERNAL ERROR! node with number " + rootNodeNumber + " should be the root node.";
int nodeNumber = node.getNumber();
int index = getParameterIndexFromNodeNumber(nodeNumber);
return parameter.getParameterValue(index);
}
public void setNodeValue(Tree tree, NodeRef node, double value) {
assert (!tree.isRoot(node) && !includeRoot) : "root node doesn't have a parameter value!";
assert tree.getRoot().getNumber() == rootNodeNumber.getValue(0).intValue() :
"INTERNAL ERROR! node with number " + rootNodeNumber + " should be the root node.";
int nodeNumber = node.getNumber();
int index = getParameterIndexFromNodeNumber(nodeNumber);
parameter.setParameterValue(index, value);
}
public int getNodeNumberFromParameterIndex(int parameterIndex) {
if (!includeRoot && parameterIndex >= tree.getRoot().getNumber()) return parameterIndex + 1;
return parameterIndex;
}
public int getParameterIndexFromNodeNumber(int nodeNumber) {
if (!includeRoot && nodeNumber > tree.getRoot().getNumber()) return nodeNumber - 1;
return nodeNumber;
}
private void handleRootMove() {
if (!includeRoot) {
final int oldRootNodeNumber = rootNodeNumber.getValue(0).intValue();
final int newRootNodeNumber = tree.getRoot().getNumber();
if (oldRootNodeNumber != newRootNodeNumber) {
if (oldRootNodeNumber > newRootNodeNumber) {
final double oldValue = parameter.getParameterValue(newRootNodeNumber);
final int end = Math.min(parameter.getDimension() - 1, oldRootNodeNumber);
for (int i = newRootNodeNumber; i < end; i++) {
parameter.setParameterValue(i, parameter.getParameterValue(i + 1));
}
parameter.setParameterValue(end, oldValue);
} else if (oldRootNodeNumber < newRootNodeNumber) {
final int end = Math.min(parameter.getDimension() - 1, newRootNodeNumber);
final double oldValue = parameter.getParameterValue(end);
for (int i = end; i > oldRootNodeNumber; i--) {
parameter.setParameterValue(i, parameter.getParameterValue(i - 1));
}
parameter.setParameterValue(oldRootNodeNumber, oldValue);
}
rootNodeNumber.setParameterValue(0, newRootNodeNumber);
}
}
}
/**
* @return the tree model that this parameter is synchronized with
*/
public TreeModel getTreeModel() {
return tree;
}
public String[] getNodeAttributeLabel() {
return new String[]{};
}
public String[] getAttributeForNode(Tree tree, NodeRef node) {
return new String[]{};
}
public String getTraitName() {
return parameter.getId();
}
public Intent getIntent() {
return intent;
}
public Class getTraitClass() {
return Double.class;
}
public boolean getLoggable() {
return true;
}
public Double getTrait(Tree tree, NodeRef node) {
return getNodeValue(tree, node);
}
public String getTraitString(Tree tree, NodeRef node) {
return Double.toString(getNodeValue(tree, node));
}
}