<commit_before>/*
 * MutableTree.java
 *
 * Copyright (C) 2002-2006 <NAME> and <NAME>
 *
 * 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.evolution.tree;

import dr.evolution.util.MutableTaxonList;

/**
 * Interface for a phylogenetic or genealogical tree.
 *
 * @version $Id: MutableTree.java,v 1.22 2006/07/28 11:27:32 rambaut Exp $
 *
 * @author <NAME>
 * @author <NAME>
 */
public interface MutableTree extends Tree, MutableTaxonList {

    public class InvalidTreeException extends Exception {
		/**
		 *
		 */
		private static final long serialVersionUID = 1955744780140327882L;

		public InvalidTreeException(String message) { super(message); }
	}

    // return true if tree already in edit mode
    boolean beginTreeEdit();

    void endTreeEdit();

	/**
	 * Add child to the children of parent.
	 * @throws IllegalArgumentException If child is already a child of parent
	 */
	void addChild(NodeRef parent, NodeRef child);

	/**
	 * Removes child from the children of parent.
	 * @throws IllegalArgumentException If child is not a child of parent
	 */
	void removeChild(NodeRef parent, NodeRef child);

    /**
     *  Replace child with another
     * @param node
     * @param child  of node to replace
     * @param newChild replacment child
     */
    void replaceChild(NodeRef node, NodeRef child, NodeRef newChild);

    /**
	 * Will throw an exception if any nodes have this node as their children.
	 */
	void setRoot(NodeRef root);


	/**
	 * set the height of the ith node in the tree (where the first n are internal).
	 */
	void setNodeHeight(NodeRef node, double height);

	/**
	 * set the rate of the ith node in the tree (where the first n are internal).
	 */
	void setNodeRate(NodeRef node, double height);

	/**
	 * set the length of the branch above the ith node in the tree (where the first n are internal).
	 */
	void setBranchLength(NodeRef node, double length);

	/**
	 * Sets an named attribute for a given node.
	 * @param node the node whose attribute is being set.
	 * @param name the name of the attribute.
	 * @param value the new value of the attribute.
	 */
	public void setNodeAttribute(NodeRef node, String name, Object value);

	/**
	 * Adds a listener to this tree.
	 */
	void addMutableTreeListener(MutableTreeListener listener);

	public class Utils {

		public static int order(MutableTree tree, NodeRef node) {

			if (tree.isExternal(node)) {
				return node.getNumber();
			} else {
				NodeRef child1 = tree.getChild(node, 0);
				NodeRef child2 = tree.getChild(node, 1);

				int num1 = order(tree, child1);
				int num2 = order(tree, child2);

				if (num1 > num2) {
					// swap child order
					tree.removeChild(node, child1);
					tree.removeChild(node, child2);
					tree.addChild(node, child2);
					tree.addChild(node, child1);
				}
				return Math.min(num1, num2);
			}
		}

		/**
		 * Multiples all node heights by the given scale.
		 */
		public static void scaleNodeHeights(MutableTree tree, double scale) {
			for (int i = 0; i < tree.getExternalNodeCount(); i++) {
				NodeRef node = tree.getExternalNode(i);
				tree.setNodeHeight(node, tree.getNodeHeight(node)*scale);
			}

			for (int i = 0; i < tree.getInternalNodeCount(); i++) {
				NodeRef node = tree.getInternalNode(i);
				tree.setNodeHeight(node, tree.getNodeHeight(node)*scale);
			}
		}

		/**
		 * This method makes sure all internal nodes are at least as tall as their children.
		 * Following this method call there will be no negative branches, but some node heights may
		 * have changed
		 */
		public static void correctHeightsForTips(MutableTree tree) {
			correctHeightsForTips(tree, tree.getRoot());
		}

		/**
		 * This method makes sure all internal nodes from the given node down are at least as tall
		 * as their children.
		 * Following this method call there will be no negative branches, but some node heights may
		 * have changed
		 */
        private static void correctHeightsForTips(MutableTree tree, NodeRef node) {

            if( !tree.isExternal(node) ) {
                // pre-order recursion
                for(int i = 0; i < tree.getChildCount(node); i++) {
                    correctHeightsForTips(tree, tree.getChild(node, i));
                }
            }

            if( !tree.isRoot(node) ) {
                final double parentHeight = tree.getNodeHeight(tree.getParent(node));

                if( parentHeight <= tree.getNodeHeight(node) ) {
                    // set the parent height to be slightly above this node's height
                    // picks
                    double height = tree.getNodeHeight(node);
                    height += tree.getNodeHeight(tree.getRoot()) * (Math.random() * 0.001);
                    tree.setNodeHeight(tree.getParent(node), height);
                }
            }
        }
	}
}<commit_msg>Fixed starting state bug (was using Math.double random variable)<commit_after>/*
 * MutableTree.java
 *
 * Copyright (C) 2002-2006 <NAME> and <NAME>
 *
 * 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.evolution.tree;

import dr.evolution.util.MutableTaxonList;
import dr.math.MathUtils;

/**
 * Interface for a phylogenetic or genealogical tree.
 *
 * @version $Id: MutableTree.java,v 1.22 2006/07/28 11:27:32 rambaut Exp $
 *
 * @author <NAME>
 * @author <NAME>
 */
public interface MutableTree extends Tree, MutableTaxonList {

    public class InvalidTreeException extends Exception {
		/**
		 *
		 */
		private static final long serialVersionUID = 1955744780140327882L;

		public InvalidTreeException(String message) { super(message); }
	}

    // return true if tree already in edit mode
    boolean beginTreeEdit();

    void endTreeEdit();

	/**
	 * Add child to the children of parent.
	 * @throws IllegalArgumentException If child is already a child of parent
	 */
	void addChild(NodeRef parent, NodeRef child);

	/**
	 * Removes child from the children of parent.
	 * @throws IllegalArgumentException If child is not a child of parent
	 */
	void removeChild(NodeRef parent, NodeRef child);

    /**
     *  Replace child with another
     * @param node
     * @param child  of node to replace
     * @param newChild replacment child
     */
    void replaceChild(NodeRef node, NodeRef child, NodeRef newChild);

    /**
	 * Will throw an exception if any nodes have this node as their children.
	 */
	void setRoot(NodeRef root);


	/**
	 * set the height of the ith node in the tree (where the first n are internal).
	 */
	void setNodeHeight(NodeRef node, double height);

	/**
	 * set the rate of the ith node in the tree (where the first n are internal).
	 */
	void setNodeRate(NodeRef node, double height);

	/**
	 * set the length of the branch above the ith node in the tree (where the first n are internal).
	 */
	void setBranchLength(NodeRef node, double length);

	/**
	 * Sets an named attribute for a given node.
	 * @param node the node whose attribute is being set.
	 * @param name the name of the attribute.
	 * @param value the new value of the attribute.
	 */
	public void setNodeAttribute(NodeRef node, String name, Object value);

	/**
	 * Adds a listener to this tree.
	 */
	void addMutableTreeListener(MutableTreeListener listener);

	public class Utils {

		public static int order(MutableTree tree, NodeRef node) {

			if (tree.isExternal(node)) {
				return node.getNumber();
			} else {
				NodeRef child1 = tree.getChild(node, 0);
				NodeRef child2 = tree.getChild(node, 1);

				int num1 = order(tree, child1);
				int num2 = order(tree, child2);

				if (num1 > num2) {
					// swap child order
					tree.removeChild(node, child1);
					tree.removeChild(node, child2);
					tree.addChild(node, child2);
					tree.addChild(node, child1);
				}
				return Math.min(num1, num2);
			}
		}

		/**
		 * Multiples all node heights by the given scale.
		 */
		public static void scaleNodeHeights(MutableTree tree, double scale) {
			for (int i = 0; i < tree.getExternalNodeCount(); i++) {
				NodeRef node = tree.getExternalNode(i);
				tree.setNodeHeight(node, tree.getNodeHeight(node)*scale);
			}

			for (int i = 0; i < tree.getInternalNodeCount(); i++) {
				NodeRef node = tree.getInternalNode(i);
				tree.setNodeHeight(node, tree.getNodeHeight(node)*scale);
			}
		}

		/**
		 * This method makes sure all internal nodes are at least as tall as their children.
		 * Following this method call there will be no negative branches, but some node heights may
		 * have changed
		 */
		public static void correctHeightsForTips(MutableTree tree) {
			correctHeightsForTips(tree, tree.getRoot());
		}

		/**
		 * This method makes sure all internal nodes from the given node down are at least as tall
		 * as their children.
		 * Following this method call there will be no negative branches, but some node heights may
		 * have changed
		 */
        private static void correctHeightsForTips(MutableTree tree, NodeRef node) {

            if( !tree.isExternal(node) ) {
                // pre-order recursion
                for(int i = 0; i < tree.getChildCount(node); i++) {
                    correctHeightsForTips(tree, tree.getChild(node, i));
                }
            }

            if( !tree.isRoot(node) ) {
                final double parentHeight = tree.getNodeHeight(tree.getParent(node));

                if( parentHeight <= tree.getNodeHeight(node) ) {
                    // set the parent height to be slightly above this node's height
                    // picks
                    double height = tree.getNodeHeight(node);
                    height += tree.getNodeHeight(tree.getRoot()) * (MathUtils.nextDouble() * 0.001);                  
                    tree.setNodeHeight(tree.getParent(node), height);
                }
            }
        }
	}
}
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