/*
* File ClusterTree.java
*
* Copyright (C) 2010 Remco Bouckaert remco@cs.auckland.ac.nz
*
* This file is part of BEAST2.
* 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 beast.base.evolution.tree;


import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.*;

import beast.base.core.Description;
import beast.base.core.Input;
import beast.base.evolution.alignment.Alignment;
import beast.base.evolution.distance.Distance;
import beast.base.evolution.distance.JukesCantorDistance;
import beast.base.inference.StateNode;
import beast.base.inference.StateNodeInitialiser;
import beast.base.inference.parameter.RealParameter;





/**
 * Adapted from Weka's HierarchicalClustering class *
 */
@Description("Create initial beast.tree by hierarchical clustering, either through one of the classic link methods " +
        "or by neighbor joining. The following link methods are supported: " +
        "<br/>o single link, " +
        "<br/>o complete link, " +
        "<br/>o UPGMA=average link, " +
        "<br/>o mean link, " +
        "<br/>o centroid, " +
        "<br/>o Ward and " +
        "<br/>o adjusted complete link " +
        "<br/>o neighborjoining " +
        "<br/>o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining")
public class ClusterTree extends Tree implements StateNodeInitialiser {

    public enum Type {single, average, complete, upgma, mean, centroid, ward, adjcomplete, neighborjoining, neighborjoining2}


    double EPSILON = 1e-10;

    final public Input<Type> clusterTypeInput = new Input<>("clusterType", "type of clustering algorithm used for generating initial beast.tree. " +
            "Should be one of " + Arrays.toString(Type.values()) + " (default " + Type.average + ")", Type.average, Type.values());
    final public Input<Alignment> dataInput = new Input<>("taxa", "alignment data used for calculating distances for clustering");

    final public Input<Distance> distanceInput = new Input<>("distance", "method for calculating distance between two sequences (default Jukes Cantor)");

    final public Input<RealParameter> clockRateInput = new Input<>("clock.rate",
            "the clock rate parameter, used to divide all divergence times by, to convert from substitutions to times. (default 1.0)",
            new RealParameter(new Double[] {1.0}));

    /**
     * Whether the distance represent node height (if false) or branch length (if true).
     */
    protected boolean distanceIsBranchLength = false;
    Distance distance;
    List<String> taxaNames;

    /**
     * Holds the Link type used calculate distance between clusters
     */
    Type linkType = Type.single;


    @Override
    public void initAndValidate() {
    	
        RealParameter clockRate = clockRateInput.get();

    	if (dataInput.get() != null) {
    		taxaNames = dataInput.get().getTaxaNames();
    	} else {
    		if (m_taxonset.get() == null) {
    			throw new RuntimeException("At least one of taxa and taxonset input needs to be specified");
    		}
    		taxaNames = m_taxonset.get().asStringList();
    	}
        if (Boolean.valueOf(System.getProperty("beast.resume")) &&
                (isEstimatedInput.get() || (m_initial.get() != null && m_initial.get().isEstimatedInput.get()))) {
            // don't bother creating a cluster tree to save some time, if it is read from file anyway
            // make a caterpillar
            Node left = newNode();
            left.setNr(0);
            left.setID(taxaNames.get(0));
            left.setHeight(0);
            for (int i = 1; i < taxaNames.size(); i++) {
                final Node right = newNode();
                right.setNr(i);
                right.setID(taxaNames.get(i));
                right.setHeight(0);
                final Node parent = newNode();
                parent.setNr(taxaNames.size() + i - 1);
                parent.setHeight(i);
                left.setParent(parent);
                parent.setLeft(left);
                right.setParent(parent);
                parent.setRight(right);
                left = parent;
            }
            root = left;
            leafNodeCount = taxaNames.size();
            nodeCount = leafNodeCount * 2 - 1;
            internalNodeCount = leafNodeCount - 1;
            super.initAndValidate();
            return;
        }

        distance = distanceInput.get();
        if (distance == null) {
            distance = new JukesCantorDistance();
        }
        if (distance instanceof Distance.Base){
        	if (dataInput.get() == null) {
        		// Distance requires an alignment?
        	}
        	((Distance.Base) distance).setPatterns(dataInput.get());
        }

        linkType = clusterTypeInput.get();

        if (linkType == Type.upgma) linkType = Type.average;

        if (linkType == Type.neighborjoining || linkType == Type.neighborjoining2) {
            distanceIsBranchLength = true;
        }
        final Node root = buildClusterer();
        setRoot(root);
        root.labelInternalNodes((getNodeCount() + 1) / 2);
        super.initAndValidate();
        if (linkType == Type.neighborjoining2) {
            // set tip dates to zero
            final Node[] nodes = getNodesAsArray();
            for (int i = 0; i < getLeafNodeCount(); i++) {
                nodes[i].setHeight(0);
            }
            super.initAndValidate();
        }

        if (m_initial.get() != null)
            processTraits(m_initial.get().m_traitList.get());
        else
            processTraits(m_traitList.get());

        if (timeTraitSet != null)
            adjustTreeNodeHeights(root);
        else {
        	// all nodes should be at zero height if no date-trait is available
        	for (int i = 0; i < getLeafNodeCount(); i++) {
        		getNode(i).setHeight(0);
        	}
        }

        //divide all node heights by clock rate to convert from substitutions to time.
        for (Node node : getInternalNodes()) {
            double height = node.getHeight();
            node.setHeight(height/clockRate.getValue());
        }

        initStateNodes();
    }


    public ClusterTree() {
    } // c'tor


    /**
     * class representing node in cluster hierarchy *
     */
    class NodeX {
        NodeX m_left;
        NodeX m_right;
        NodeX m_parent;
        int m_iLeftInstance;
        int m_iRightInstance;
        double m_fLeftLength = 0;
        double m_fRightLength = 0;
        double m_fHeight = 0;

        void setHeight(double height1, double height2) {
            if (height1 < EPSILON) {
                height1 = EPSILON;
            }
            if (height2 < EPSILON) {
                height2 = EPSILON;
            }
            m_fHeight = height1;
            if (m_left == null) {
                m_fLeftLength = height1;
            } else {
                m_fLeftLength = height1 - m_left.m_fHeight;
            }
            if (m_right == null) {
                m_fRightLength = height2;
            } else {
                m_fRightLength = height2 - m_right.m_fHeight;
            }
        }

        void setLength(double length1, double length2) {
            if (length1 < EPSILON) {
                length1 = EPSILON;
            }
            if (length2 < EPSILON) {
                length2 = EPSILON;
            }
            m_fLeftLength = length1;
            m_fRightLength = length2;
            m_fHeight = length1;
            if (m_left != null) {
                m_fHeight += m_left.m_fHeight;
            }
        }

        @Override
		public String toString() {
            final DecimalFormat myFormatter = new DecimalFormat("#.#####", new DecimalFormatSymbols(Locale.US));

            if (m_left == null) {
                if (m_right == null) {
                    return "(" + taxaNames.get(m_iLeftInstance) + ":" + myFormatter.format(m_fLeftLength) + "," +
                            taxaNames.get(m_iRightInstance) + ":" + myFormatter.format(m_fRightLength) + ")";
                } else {
                    return "(" + taxaNames.get(m_iLeftInstance) + ":" + myFormatter.format(m_fLeftLength) + "," +
                            m_right.toString() + ":" + myFormatter.format(m_fRightLength) + ")";
                }
            } else {
                if (m_right == null) {
                    return "(" + m_left.toString() + ":" + myFormatter.format(m_fLeftLength) + "," +
                            taxaNames.get(m_iRightInstance) + ":" + myFormatter.format(m_fRightLength) + ")";
                } else {
                    return "(" + m_left.toString() + ":" + myFormatter.format(m_fLeftLength) + "," + m_right.toString() + ":" + myFormatter.format(m_fRightLength) + ")";
                }
            }
        }

        Node toNode() {
            final Node node = newNode();
            node.setHeight(m_fHeight);
            if (m_left == null) {
                node.setLeft(newNode());
                node.getLeft().setNr(m_iLeftInstance);
                node.getLeft().setID(taxaNames.get(m_iLeftInstance));
                node.getLeft().setHeight(m_fHeight - m_fLeftLength);
                if (m_right == null) {
                    node.setRight(newNode());
                    node.getRight().setNr(m_iRightInstance);
                    node.getRight().setID(taxaNames.get(m_iRightInstance));
                    node.getRight().setHeight(m_fHeight - m_fRightLength);
                } else {
                    node.setRight(m_right.toNode());
                }
            } else {
                node.setLeft(m_left.toNode());
                if (m_right == null) {
                    node.setRight(newNode());
                    node.getRight().setNr(m_iRightInstance);
                    node.getRight().setID(taxaNames.get(m_iRightInstance));
                    node.getRight().setHeight(m_fHeight - m_fRightLength);
                } else {
                    node.setRight(m_right.toNode());
                }
            }
            if (node.getHeight() < node.getLeft().getHeight() + EPSILON) {
                node.setHeight(node.getLeft().getHeight() + EPSILON);
            }
            if (node.getHeight() < node.getRight().getHeight() + EPSILON) {
                node.setHeight(node.getRight().getHeight() + EPSILON);
            }

            node.getRight().setParent(node);
            node.getLeft().setParent(node);
            return node;
        }
    } // class NodeX

    /**
     * used for priority queue for efficient retrieval of pair of clusters to merge*
     */
    class Tuple {
        public Tuple(final double d, final int i, final int j, final int size1, final int size2) {
            m_fDist = d;
            m_iCluster1 = i;
            m_iCluster2 = j;
            m_nClusterSize1 = size1;
            m_nClusterSize2 = size2;
        }

        double m_fDist;
        int m_iCluster1;
        int m_iCluster2;
        int m_nClusterSize1;
        int m_nClusterSize2;
    }

    /**
     * comparator used by priority queue*
     */
    class TupleComparator implements Comparator<Tuple> {
        @Override
		public int compare(final Tuple o1, final Tuple o2) {
            if (o1.m_fDist < o2.m_fDist) {
                return -1;
            } else if (o1.m_fDist == o2.m_fDist) {
                return 0;
            }
            return 1;
        }
    }

    // return distance according to distance metric
    double distance(final int taxon1, final int taxon2) {
        return distance.pairwiseDistance(taxon1, taxon2);
    } // distance

    // 1-norm
    double distance(final double[] pattern1, final double[] pattern2) {
        double dist = 0;
        for (int i = 0; i < dataInput.get().getPatternCount(); i++) {
            dist += dataInput.get().getPatternWeight(i) * Math.abs(pattern1[i] - pattern2[i]);
        }
        return dist / dataInput.get().getSiteCount();
    }


    @SuppressWarnings("unchecked")
    public Node buildClusterer() {
        final int taxonCount = taxaNames.size();
        if (taxonCount == 1) {
            // pathological case
            final Node node = newNode();
            node.setHeight(1);
            node.setNr(0);
            return node;
        }

        // use array of integer vectors to store cluster indices,
        // starting with one cluster per instance
        final List<Integer>[] clusterID = new ArrayList[taxonCount];
        for (int i = 0; i < taxonCount; i++) {
            clusterID[i] = new ArrayList<>();
            clusterID[i].add(i);
        }
        // calculate distance matrix
        final int clusters = taxonCount;

        // used for keeping track of hierarchy
        final NodeX[] clusterNodes = new NodeX[taxonCount];
        if (linkType == Type.neighborjoining || linkType == Type.neighborjoining2) {
            neighborJoining(clusters, clusterID, clusterNodes);
        } else {
            doLinkClustering(clusters, clusterID, clusterNodes);
        }

        // move all clusters in m_nClusterID array
        // & collect hierarchy
        for (int i = 0; i < taxonCount; i++) {
            if (clusterID[i].size() > 0) {
                return clusterNodes[i].toNode();
            }
        }
        return null;
    } // buildClusterer

    /**
     * use neighbor joining algorithm for clustering
     * This is roughly based on the RapidNJ simple implementation and runs at O(n^3)
     * More efficient implementations exist, see RapidNJ (or my GPU implementation :-))
     *
     * @param clusters
     * @param clusterID
     * @param clusterNodes
     */
    void neighborJoining(int clusters, final List<Integer>[] clusterID, final NodeX[] clusterNodes) {
        final int n = taxaNames.size();

        final double[][] dist = new double[clusters][clusters];
        for (int i = 0; i < clusters; i++) {
            dist[i][i] = 0;
            for (int j = i + 1; j < clusters; j++) {
                dist[i][j] = getDistance0(clusterID[i], clusterID[j]);
                dist[j][i] = dist[i][j];
            }
        }

        final double[] separationSums = new double[n];
        final double[] separations = new double[n];
        final int[] nextActive = new int[n];

        //calculate initial separation rows
        for (int i = 0; i < n; i++) {
            double sum = 0;
            for (int j = 0; j < n; j++) {
                sum += dist[i][j];
            }
            separationSums[i] = sum;
            separations[i] = sum / (clusters - 2);
            nextActive[i] = i + 1;
        }

        while (clusters > 2) {
            // find minimum
            int min1 = -1;
            int min2 = -1;
            double min = Double.MAX_VALUE;
            {
                int i = 0;
                while (i < n) {
                    final double sep1 = separations[i];
                    final double[] row = dist[i];
                    int j = nextActive[i];
                    while (j < n) {
                        final double sep2 = separations[j];
                        final double val = row[j] - sep1 - sep2;
                        if (val < min) {
                            // new minimum
                            min1 = i;
                            min2 = j;
                            min = val;
                        }
                        j = nextActive[j];
                    }
                    i = nextActive[i];
                }
            }
            // record distance
            final double minDistance = dist[min1][min2];
            clusters--;
            final double sep1 = separations[min1];
            final double sep2 = separations[min2];
            final double dist1 = (0.5 * minDistance) + (0.5 * (sep1 - sep2));
            final double dist2 = (0.5 * minDistance) + (0.5 * (sep2 - sep1));
            if (clusters > 2) {
                // update separations  & distance
                double newSeparationSum = 0;
                final double mutualDistance = dist[min1][min2];
                final double[] row1 = dist[min1];
                final double[] row2 = dist[min2];
                for (int i = 0; i < n; i++) {
                    if (i == min1 || i == min2 || clusterID[i].size() == 0) {
                        row1[i] = 0;
                    } else {
                        final double val1 = row1[i];
                        final double val2 = row2[i];
                        final double distance = (val1 + val2 - mutualDistance) / 2.0;
                        newSeparationSum += distance;
                        // update the separationsum of cluster i.
                        separationSums[i] += (distance - val1 - val2);
                        separations[i] = separationSums[i] / (clusters - 2);
                        row1[i] = distance;
                        dist[i][min1] = distance;
                    }
                }
                separationSums[min1] = newSeparationSum;
                separations[min1] = newSeparationSum / (clusters - 2);
                separationSums[min2] = 0;
                merge(min1, min2, dist1, dist2, clusterID, clusterNodes);
                int prev = min2;
                // since min1 < min2 we havenActiveRows[0] >= 0, so the next loop should be save
                while (clusterID[prev].size() == 0) {
                    prev--;
                }
                nextActive[prev] = nextActive[min2];
            } else {
                merge(min1, min2, dist1, dist2, clusterID, clusterNodes);
                break;
            }
        }

        for (int i = 0; i < n; i++) {
            if (clusterID[i].size() > 0) {
                for (int j = i + 1; j < n; j++) {
                    if (clusterID[j].size() > 0) {
                        final double dist1 = dist[i][j];
                        if (clusterID[i].size() == 1) {
                            merge(i, j, dist1, 0, clusterID, clusterNodes);
                        } else if (clusterID[j].size() == 1) {
                            merge(i, j, 0, dist1, clusterID, clusterNodes);
                        } else {
                            merge(i, j, dist1 / 2.0, dist1 / 2.0, clusterID, clusterNodes);
                        }
                        break;
                    }
                }
            }
        }
    } // neighborJoining

    /**
     * Perform clustering using a link method
     * This implementation uses a priority queue resulting in a O(n^2 log(n)) algorithm
     *
     * @param clusters    number of clusters
     * @param clusterID
     * @param clusterNodes
     */
    void doLinkClustering(int clusters, final List<Integer>[] clusterID, final NodeX[] clusterNodes) {
        final int instances = taxaNames.size();
        final PriorityQueue<Tuple> queue = new PriorityQueue<>(clusters * clusters / 2, new TupleComparator());
        final double[][] distance0 = new double[clusters][clusters];
        for (int i = 0; i < clusters; i++) {
            distance0[i][i] = 0;
            for (int j = i + 1; j < clusters; j++) {
                distance0[i][j] = getDistance0(clusterID[i], clusterID[j]);
                distance0[j][i] = distance0[i][j];
                queue.add(new Tuple(distance0[i][j], i, j, 1, 1));
            }
        }
        while (clusters > 1) {
            int min1 = -1;
            int min2 = -1;
            // use priority queue to find next best pair to cluster
            Tuple t;
            do {
                t = queue.poll();
            }
            while (t != null && (clusterID[t.m_iCluster1].size() != t.m_nClusterSize1 || clusterID[t.m_iCluster2].size() != t.m_nClusterSize2));
            min1 = t.m_iCluster1;
            min2 = t.m_iCluster2;
            merge(min1, min2, t.m_fDist/2.0, t.m_fDist/2.0, clusterID, clusterNodes);
            // merge  clusters

            // update distances & queue
            for (int i = 0; i < instances; i++) {
                if (i != min1 && clusterID[i].size() != 0) {
                    final int i1 = Math.min(min1, i);
                    final int i2 = Math.max(min1, i);
                    final double distance = getDistance(distance0, clusterID[i1], clusterID[i2]);
                    queue.add(new Tuple(distance, i1, i2, clusterID[i1].size(), clusterID[i2].size()));
                }
            }

            clusters--;
        }
    } // doLinkClustering

    void merge(int min1, int min2, double dist1, double dist2, final List<Integer>[] clusterID, final NodeX[] clusterNodes) {
        if (min1 > min2) {
            final int h = min1;
            min1 = min2;
            min2 = h;
            final double f = dist1;
            dist1 = dist2;
            dist2 = f;
        }
        clusterID[min1].addAll(clusterID[min2]);
        //clusterID[min2].removeAllElements();
        clusterID[min2].removeAll(clusterID[min2]);

        // track hierarchy
        final NodeX node = new NodeX();
        if (clusterNodes[min1] == null) {
            node.m_iLeftInstance = min1;
        } else {
            node.m_left = clusterNodes[min1];
            clusterNodes[min1].m_parent = node;
        }
        if (clusterNodes[min2] == null) {
            node.m_iRightInstance = min2;
        } else {
            node.m_right = clusterNodes[min2];
            clusterNodes[min2].m_parent = node;
        }
        if (distanceIsBranchLength) {
            node.setLength(dist1, dist2);
        } else {
            node.setHeight(dist1, dist2);
        }
        clusterNodes[min1] = node;
    } // merge

    /**
     * calculate distance the first time when setting up the distance matrix *
     */
    double getDistance0(final List<Integer> cluster1, final List<Integer> cluster2) {
        double bestDist = Double.MAX_VALUE;
        switch (linkType) {
            case single:
            case neighborjoining:
            case neighborjoining2:
            case centroid:
            case complete:
            case adjcomplete:
            case average:
            case mean:
                // set up two instances for distance function
                bestDist = distance(cluster1.get(0), cluster2.get(0));
                break;
            case ward: {
                // finds the distance of the change in caused by merging the cluster.
                // The information of a cluster is calculated as the error sum of squares of the
                // centroids of the cluster and its members.
                final double ESS1 = calcESS(cluster1);
                final double ESS2 = calcESS(cluster2);
                final List<Integer> merged = new ArrayList<>();
                merged.addAll(cluster1);
                merged.addAll(cluster2);
                final double ESS = calcESS(merged);
                bestDist = ESS * merged.size() - ESS1 * cluster1.size() - ESS2 * cluster2.size();
            }
            break;
		default:
			break;
        }
        return bestDist;
    } // getDistance0

    /**
     * calculate the distance between two clusters
     *
     * @param cluster1 list of indices of instances in the first cluster
     * @param cluster2 dito for second cluster
     * @return distance between clusters based on link type
     */
    double getDistance(final double[][] distance, final List<Integer> cluster1, final List<Integer> cluster2) {
        double bestDist = Double.MAX_VALUE;
        switch (linkType) {
            case single:
                // find single link distance aka minimum link, which is the closest distance between
                // any item in cluster1 and any item in cluster2
                bestDist = Double.MAX_VALUE;
                for (int i = 0; i < cluster1.size(); i++) {
                    final int i1 = cluster1.get(i);
                    for (int j = 0; j < cluster2.size(); j++) {
                        final int i2 = cluster2.get(j);
                        final double dist = distance[i1][i2];
                        if (bestDist > dist) {
                            bestDist = dist;
                        }
                    }
                }
                break;
            case complete:
            case adjcomplete:
                // find complete link distance aka maximum link, which is the largest distance between
                // any item in cluster1 and any item in cluster2
                bestDist = 0;
                for (int i = 0; i < cluster1.size(); i++) {
                    final int i1 = cluster1.get(i);
                    for (int j = 0; j < cluster2.size(); j++) {
                        final int i2 = cluster2.get(j);
                        final double dist = distance[i1][i2];
                        if (bestDist < dist) {
                            bestDist = dist;
                        }
                    }
                }
                if (linkType == Type.complete) {
                    break;
                }
                // calculate adjustment, which is the largest within cluster distance
                double maxDist = 0;
                for (int i = 0; i < cluster1.size(); i++) {
                    final int i1 = cluster1.get(i);
                    for (int j = i + 1; j < cluster1.size(); j++) {
                        final int i2 = cluster1.get(j);
                        final double dist = distance[i1][i2];
                        if (maxDist < dist) {
                            maxDist = dist;
                        }
                    }
                }
                for (int i = 0; i < cluster2.size(); i++) {
                    final int i1 = cluster2.get(i);
                    for (int j = i + 1; j < cluster2.size(); j++) {
                        final int i2 = cluster2.get(j);
                        final double dist = distance[i1][i2];
                        if (maxDist < dist) {
                            maxDist = dist;
                        }
                    }
                }
                bestDist -= maxDist;
                break;
            case average:
                // finds average distance between the elements of the two clusters
                bestDist = 0;
                for (int i = 0; i < cluster1.size(); i++) {
                    final int i1 = cluster1.get(i);
                    for (int j = 0; j < cluster2.size(); j++) {
                        final int i2 = cluster2.get(j);
                        bestDist += distance[i1][i2];
                    }
                }
                bestDist /= (cluster1.size() * cluster2.size());
                break;
            case mean: {
                // calculates the mean distance of a merged cluster (akak Group-average agglomerative clustering)
                final List<Integer> merged = new ArrayList<>();
                merged.addAll(cluster1);
                merged.addAll(cluster2);
                bestDist = 0;
                for (int i = 0; i < merged.size(); i++) {
                    final int i1 = merged.get(i);
                    for (int j = i + 1; j < merged.size(); j++) {
                        final int i2 = merged.get(j);
                        bestDist += distance[i1][i2];
                    }
                }
                final int n = merged.size();
                bestDist /= (n * (n - 1.0) / 2.0);
            }
            break;
            case centroid:
                // finds the distance of the centroids of the clusters
                final int patterns = dataInput.get().getPatternCount();
                final double[] centroid1 = new double[patterns];
                for (int i = 0; i < cluster1.size(); i++) {
                    final int taxonIndex = cluster1.get(i);
                    for (int j = 0; j < patterns; j++) {
                        centroid1[j] += dataInput.get().getPattern(taxonIndex, j);
                    }
                }
                final double[] centroid2 = new double[patterns];
                for (int i = 0; i < cluster2.size(); i++) {
                    final int taxonIndex = cluster2.get(i);
                    for (int j = 0; j < patterns; j++) {
                        centroid2[j] += dataInput.get().getPattern(taxonIndex, j);
                    }
                }
                for (int j = 0; j < patterns; j++) {
                    centroid1[j] /= cluster1.size();
                    centroid2[j] /= cluster2.size();
                }
                bestDist = distance(centroid1, centroid2);
                break;
            case ward: {
                // finds the distance of the change in caused by merging the cluster.
                // The information of a cluster is calculated as the error sum of squares of the
                // centroids of the cluster and its members.
                final double ESS1 = calcESS(cluster1);
                final double ESS2 = calcESS(cluster2);
                final List<Integer> merged = new ArrayList<>();
                merged.addAll(cluster1);
                merged.addAll(cluster2);
                final double ESS = calcESS(merged);
                bestDist = ESS * merged.size() - ESS1 * cluster1.size() - ESS2 * cluster2.size();
            }
            break;
		default:
			break;
        }
        return bestDist;
    } // getDistance


    /**
     * calculated error sum-of-squares for instances wrt centroid *
     */
    double calcESS(final List<Integer> cluster) {
        final int patterns = dataInput.get().getPatternCount();
        final double[] centroid = new double[patterns];
        for (int i = 0; i < cluster.size(); i++) {
            final int taxonIndex = cluster.get(i);
            for (int j = 0; j < patterns; j++) {
                centroid[j] += dataInput.get().getPattern(taxonIndex, j);
            }
        }
        for (int j = 0; j < patterns; j++) {
            centroid[j] /= cluster.size();
        }
        // set up two instances for distance function
        double eSS = 0;
        for (int i = 0; i < cluster.size(); i++) {
            final double[] instance = new double[patterns];
            final int taxonIndex = cluster.get(i);
            for (int j = 0; j < patterns; j++) {
                instance[j] += dataInput.get().getPattern(taxonIndex, j);
            }
            eSS += distance(centroid, instance);
        }
        return eSS / cluster.size();
    } // calcESS

    @Override
    public void initStateNodes() {
        if (m_initial.get() != null) {
            m_initial.get().assignFromWithoutID(this);
        }
    }

    @Override
    public void getInitialisedStateNodes(final List<StateNode> stateNodes) {
        if (m_initial.get() != null) {
            stateNodes.add(m_initial.get());
        }
    }

} // class ClusterTree
