/*
* Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
*
* 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.app.beauti.options;
import dr.app.beauti.types.OperatorType;
import dr.app.beauti.types.PriorType;
import dr.app.beauti.types.StartingTreeType;
import dr.app.beauti.types.TreePriorType;
import dr.evolution.datatype.DataType;
import dr.evolution.datatype.PloidyType;
import dr.evolution.tree.Tree;
import java.util.List;
/**
* @author Andrew Rambaut
* @author Walter Xie
* @version $Id$
*/
public class PartitionTreeModel extends PartitionOptions {
private PartitionTreePrior treePrior;
private StartingTreeType startingTreeType = StartingTreeType.RANDOM;
private Tree userStartingTree = null;
private boolean isNewick = true;
private boolean fixedTree = false;
// private double initialRootHeight = 1.0;
//TODO if use EBSP and *BEAST, validate Ploidy of every PD is same for each tree that the PD(s) belongs to
// BeastGenerator.checkOptions()
private PloidyType ploidyType = PloidyType.AUTOSOMAL_NUCLEAR;
public PartitionTreeModel(BeautiOptions options, AbstractPartitionData partition) {
super(options, partition.getName());
}
/**
* A copy constructor
*
* @param options the beauti options
* @param name the name of the new model
* @param source the source model
*/
public PartitionTreeModel(BeautiOptions options, String name, PartitionTreeModel source) {
super(options, name);
treePrior = source.treePrior;
startingTreeType = source.startingTreeType;
userStartingTree = source.userStartingTree;
isNewick = source.isNewick;
fixedTree = source.fixedTree;
// initialRootHeight = source.initialRootHeight;
ploidyType = source.ploidyType;
}
protected void initModelParametersAndOpererators() {
createParameter("tree", "The tree");
createParameter("treeModel.internalNodeHeights", "internal node heights of the tree (except the root)");
createParameter("treeModel.allInternalNodeHeights", "internal node heights of the tree");
createParameterTree(this, "treeModel.rootHeight", "root height of the tree", true, 1.0);
//TODO treeBitMove should move to PartitionClockModelTreeModelLink, after Alexei finish
createOperator("treeBitMove", "Tree", "Swaps the rates and change locations of local clocks", "tree",
OperatorType.TREE_BIT_MOVE, -1.0, treeWeights);
createScaleOperator("treeModel.rootHeight", demoTuning, demoWeights);
createOperator("uniformHeights", "Internal node heights", "Draws new internal node heights uniformally",
"treeModel.internalNodeHeights", OperatorType.UNIFORM, -1, branchWeights);
createOperator("subtreeSlide", "Tree", "Performs the subtree-slide rearrangement of the tree", "tree",
OperatorType.SUBTREE_SLIDE, 1.0, treeWeights);
createOperator("narrowExchange", "Tree", "Performs local rearrangements of the tree", "tree",
OperatorType.NARROW_EXCHANGE, -1, treeWeights);
createOperator("wideExchange", "Tree", "Performs global rearrangements of the tree", "tree",
OperatorType.WIDE_EXCHANGE, -1, demoWeights);
createOperator("wilsonBalding", "Tree", "Performs the Wilson-Balding rearrangement of the tree", "tree",
OperatorType.WILSON_BALDING, -1, demoWeights);
//=============== microsat ======================
createParameter("treeModel.microsatellite.internalNodesParameter", "Microsatellite sampler tree internal node parameter");
createOperator("microsatInternalNodesParameter", "Microsat tree internal node",
"Random integer walk on microsatellite sampler tree internal node parameter",
"treeModel.microsatellite.internalNodesParameter", OperatorType.RANDOM_WALK_INT, 1.0, branchWeights);
}
/**
* return a list of parameters that are required
*
* @param parameters the parameter list
*/
public void selectParameters(List<Parameter> parameters) {
setAvgRootAndRate();
getParameter("tree");
getParameter("treeModel.internalNodeHeights");
getParameter("treeModel.allInternalNodeHeights");
Parameter rootHeightParameter = getParameter("treeModel.rootHeight");
if (rootHeightParameter.priorType == PriorType.NONE_TREE_PRIOR || !rootHeightParameter.isPriorEdited()) {
rootHeightParameter.initial = getInitialRootHeight();
rootHeightParameter.truncationLower = options.maximumTipHeight;
rootHeightParameter.uniformLower = options.maximumTipHeight;
rootHeightParameter.isTruncated = true;
}
if (options.useStarBEAST) {
rootHeightParameter.isCalibratedYule = treePrior.getNodeHeightPrior() == TreePriorType.SPECIES_YULE_CALIBRATION;
} else {
rootHeightParameter.isCalibratedYule = treePrior.getNodeHeightPrior() == TreePriorType.YULE_CALIBRATION;
parameters.add(rootHeightParameter);
}
if (getDataType().getType() == DataType.MICRO_SAT) {
getParameter("treeModel.microsatellite.internalNodesParameter");
}
}
/**
* return a list of operators that are required
*
* @param operators the operator list
*/
public void selectOperators(List<Operator> operators) {
setAvgRootAndRate();
// if not a fixed tree then sample tree space
if (!fixedTree) {
Operator subtreeSlideOp = getOperator("subtreeSlide");
if (!subtreeSlideOp.tuningEdited) {
subtreeSlideOp.tuning = getInitialRootHeight() / 10.0;
}
operators.add(subtreeSlideOp);
operators.add(getOperator("narrowExchange"));
operators.add(getOperator("wideExchange"));
operators.add(getOperator("wilsonBalding"));
}
operators.add(getOperator("treeModel.rootHeight"));
operators.add(getOperator("uniformHeights"));
if (getDataType().getType() == DataType.MICRO_SAT) {
operators.add(getOperator("microsatInternalNodesParameter"));
}
}
/////////////////////////////////////////////////////////////
public PartitionTreePrior getPartitionTreePrior() {
return treePrior;
}
public void setPartitionTreePrior(PartitionTreePrior treePrior) {
this.treePrior = treePrior;
}
public StartingTreeType getStartingTreeType() {
return startingTreeType;
}
public void setStartingTreeType(StartingTreeType startingTreeType) {
this.startingTreeType = startingTreeType;
}
public Tree getUserStartingTree() {
return userStartingTree;
}
public void setUserStartingTree(Tree userStartingTree) {
this.userStartingTree = userStartingTree;
}
public boolean isNewick() {
return isNewick;
}
public void setNewick(boolean newick) {
isNewick = newick;
}
public void setPloidyType(PloidyType ploidyType) {
this.ploidyType = ploidyType;
}
public PloidyType getPloidyType() {
return ploidyType;
}
public double getInitialRootHeight() {
return getAvgRootAndRate()[0];
}
// public void setInitialRootHeight(double initialRootHeight) {
// this.initialRootHeight = initialRootHeight;
// }
// private void calculateInitialRootHeightPerTree() {
// initialRootHeight = options.clockModelOptions
// .calculateInitialRootHeightAndRate(options.getDataPartitions(this)) [0];
// }
public String getPrefix() {
String prefix = "";
if (options.getPartitionTreeModels().size() > 1) { //|| options.isSpeciesAnalysis()
// There is more than one active partition model
prefix += getName() + ".";
}
return prefix;
}
public int getDimension() { // n-1
return options.getTaxonCount(options.getDataPartitions(this)) - 1;
}
}