RankedForest.java

/*
 * RankedForest.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.evolution.tree;

import java.util.*;

/**
 * @author Alexei Drummond
 */
public interface RankedForest {

    public List<RankedNode> getNodes();

    public int getSize();

    public int rank();

    public boolean compatibleRank(List<BitSet> constraints);

    public Set<BitSet> clades();

    public int constraintsSatisfied();

    public boolean isClear();


    public class Default implements RankedForest {

        List<RankedNode> nodes;
        boolean clear;

        public Default(int size, boolean clear) {
            nodes = new ArrayList<RankedNode>(size);
            for (int i = size - 1; i >= 0; i--) {
                nodes.add(new RankedNode(i, size));
            }
            this.clear = clear;
        }

        public int getSize() {
            return nodes.get(0).n;
        }

        public int rank() {
            return nodes.get(0).rank;
        }

        public boolean compatibleRank(List<BitSet> constraints) {
            return true;
        }

        public Set<BitSet> clades() {
            return Collections.emptySet();

        }

        public int constraintsSatisfied() {
            return 0;
        }

        public boolean isClear() {
            return clear;
        }

        public List<RankedNode> getNodes() {
            return nodes;
        }
    }

    public class Parent implements RankedForest {

        RankedForest child;
        RankedNode parent;
        List<RankedNode> nodes;
        HashSet<BitSet> clades;
        int constraintsSatisfied = 0;
        boolean clear;

        public Parent(RankedForest child, RankedNode parent, List<BitSet> constraints) {
            this.child = child;
            this.parent = parent;
            nodes = new ArrayList<RankedNode>();
            nodes.add(parent);
            nodes.addAll(child.getNodes());
            nodes.remove(parent.child1);
            nodes.remove(parent.child2);

            clades = new HashSet<BitSet>();
            clades.addAll(child.clades());
            clades.add(parent.cladeBits);

            if (!clear) {
                constraintsSatisfied = child.constraintsSatisfied();
                //System.out.println(parent.cladeBits);
                if (constraints.contains(parent.cladeBits)) {
                    //System.out.println("Found " + parent.cladeBits + " in constraints!");
                    constraintsSatisfied += 1;
                }
                clear = (constraintsSatisfied == constraints.size());
            }

            //System.out.println("making parent wih rank " + parent.rank);
        }

        public List<RankedNode> getNodes() {
            return nodes;
        }

        public int getSize() {
            return nodes.get(0).n;
        }

        public int rank() {
            return nodes.get(0).rank;
        }

        public boolean compatibleRank(List<BitSet> constraints) {

            if (constraints.size() == 1) return true;

            int rank = 0;
            for (BitSet constraint : constraints) {
                int newRank = getRank(constraint);
                if (newRank < rank) return false;
                rank = newRank;
            }
            if (rank != Integer.MAX_VALUE) clear = true;
            return true;
        }

        public Set<BitSet> clades() {
            return clades;
        }

        public int constraintsSatisfied() {
            return constraintsSatisfied;
        }

        public boolean isClear() {
            return clear;
        }

        private int getRank(BitSet constraint) {
            //if (constraint.cardinality() > parent.rank) return Integer.MAX_VALUE;

            if (parent.cladeBits.equals(constraint)) {
                return parent.rank;
            } else {
                if (child instanceof Parent) {
                    return ((Parent) child).getRank(constraint);
                }
                return Integer.MAX_VALUE;
            }
        }

        //public String toString() {}
    }
}