/*
* ColouredExchangeOperator.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.operators;
import dr.evolution.tree.NodeRef;
import dr.evomodel.coalescent.structure.ColourSamplerModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;
import dr.xml.*;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
/**
* Implements branch exchange operations.
* There is a NARROW and WIDE variety.
* The narrow exchange is very similar to a rooted-tree
* nearest-neighbour interchange but with the restriction
* that node height must remain consistent.
* <p/>
* KNOWN BUGS: WIDE operator cannot be used on trees with 4 or less tips!
*/
// Cleaning out untouched stuff. Can be resurrected if needed
@Deprecated
public class ColouredExchangeOperator extends SimpleMCMCOperator {
public static final String NARROW_EXCHANGE = "colouredNarrowExchange";
public static final String WIDE_EXCHANGE = "colouredWideExchange";
public static final int NARROW = 0;
public static final int WIDE = 1;
private static final int MAX_TRIES = 10000;
private int mode = NARROW;
private final TreeModel tree;
private final ColourSamplerModel colouringModel;
public ColouredExchangeOperator(int mode, TreeModel tree, ColourSamplerModel colouringModel, double weight) {
this.mode = mode;
this.tree = tree;
this.colouringModel = colouringModel;
setWeight(weight);
}
public double doOperation() {
double logP = colouringModel.getTreeColouringWithProbability().getLogProbabilityDensity();
int tipCount = tree.getExternalNodeCount();
switch (mode) {
case NARROW:
narrow();
break;
case WIDE:
wide();
break;
}
if (tree.getExternalNodeCount() != tipCount) {
throw new RuntimeException("Lost some tips in " + ((mode == NARROW) ? "NARROW mode." : "WIDE mode."));
}
colouringModel.resample();
double logQ = colouringModel.getTreeColouringWithProbability().getLogProbabilityDensity();
return logP - logQ;
}
/**
* WARNING: Assumes strictly bifurcating tree.
*/
public void narrow() {
NodeRef i = null, iP = null, j = null, jP = null;
int tries = 0;
//Echoose
while (tries < MAX_TRIES) {
i = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
while (tree.getRoot() == i || tree.getParent(i) == tree.getRoot()) {
i = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
}
iP = tree.getParent(i);
jP = tree.getParent(iP);
j = tree.getChild(jP, 0);
if (j == iP) {
j = tree.getChild(jP, 1);
}
if ((tree.getNodeHeight(j) < tree.getNodeHeight(iP)) && (tree.getNodeHeight(i) < tree.getNodeHeight(jP))) {
break;
}
tries += 1;
}
//System.out.println("tries = " + tries);
//Eupdate
if (tries < MAX_TRIES) {
eupdate(i, j, iP, jP);
tree.pushTreeChangedEvent(iP);
tree.pushTreeChangedEvent(jP);
} else throw new RuntimeException("Couldn't find valid narrow move on this tree!!");
}
/**
* WARNING: Assumes strictly bifurcating tree.
*/
public void wide() {
NodeRef i = null, iP = null, j = null, jP = null;
int tries = 0;
//Echoose
while (tries < MAX_TRIES) {
i = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
while (tree.getRoot() == i) {
i = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
}
j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
while (j == i || j == tree.getRoot()) {
j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
}
iP = tree.getParent(i);
jP = tree.getParent(j);
if ((iP != jP) && (i != jP) && (j != iP) &&
(tree.getNodeHeight(j) < tree.getNodeHeight(iP)) &&
(tree.getNodeHeight(i) < tree.getNodeHeight(jP))) {
break;
}
tries += 1;
}
//System.out.println("tries = " + tries);
//Eupdate
if (tries < MAX_TRIES) {
eupdate(i, j, iP, jP);
} else {
throw new RuntimeException("Couldn't find valid wide move on this tree!");
}
}
public int getMode() {
return mode;
}
public String getOperatorName() {
return ((mode == NARROW) ? "Narrow" : "Wide") + " Exchange";
}
public Element createOperatorElement(Document d) {
throw new RuntimeException("not implemented");
}
private void eupdate(NodeRef i, NodeRef j, NodeRef iP, NodeRef jP) {
tree.beginTreeEdit();
tree.removeChild(iP, i);
tree.removeChild(jP, j);
tree.addChild(jP, i);
tree.addChild(iP, j);
tree.endTreeEdit();
}
public double getMinimumAcceptanceLevel() {
if (mode == NARROW) return 0.05;
else return 0.01;
}
public double getMinimumGoodAcceptanceLevel() {
if (mode == NARROW) return 0.05;
else return 0.01;
}
public String getPerformanceSuggestion() {
if (Utils.getAcceptanceProbability(this) < getMinimumAcceptanceLevel()) {
return "";
} else if (Utils.getAcceptanceProbability(this) > getMaximumAcceptanceLevel()) {
return "";
} else {
return "";
}
}
public static XMLObjectParser NARROW_EXCHANGE_PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return NARROW_EXCHANGE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
ColourSamplerModel colourSamplerModel = (ColourSamplerModel) xo.getChild(ColourSamplerModel.class);
double weight = xo.getDoubleAttribute("weight");
return new ColouredExchangeOperator(NARROW, treeModel, colourSamplerModel, weight);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents a narrow exchange operator. " +
"This operator swaps a random subtree with its uncle.";
}
public Class getReturnType() {
return ColouredExchangeOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule("weight"),
new ElementRule(TreeModel.class),
new ElementRule(ColourSamplerModel.class),
};
};
public static XMLObjectParser WIDE_EXCHANGE_PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return WIDE_EXCHANGE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
ColourSamplerModel colourSamplerModel = (ColourSamplerModel) xo.getChild(ColourSamplerModel.class);
double weight = xo.getDoubleAttribute("weight");
return new ColouredExchangeOperator(WIDE, treeModel, colourSamplerModel, weight);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents a wide exchange operator. " +
"This operator swaps two random subtrees.";
}
public Class getReturnType() {
return ColouredExchangeOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule("weight"),
new ElementRule(ColourSamplerModel.class),
new ElementRule(TreeModel.class)
};
};
}