net.maizegenetics.taxa.tree.TreeClusters Maven / Gradle / Ivy

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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
There is a newer version: 5.2.94
package net.maizegenetics.taxa.tree;

import java.util.Arrays;

import net.maizegenetics.taxa.Taxon;

/**
 * @author Peter Bradbury 2/23/2010 For a Tree and a given number of clusters,
 * this class finds the members of those clusters.
 */
public class TreeClusters {

    Tree theTree;
    int nTaxa;
    double[] sortedHeight;
    int nNodes;

    public TreeClusters(Tree theTree) {
        this.theTree = theTree;
        nTaxa = theTree.getExternalNodeCount();
        nNodes = theTree.getInternalNodeCount();
        sortedHeight = new double[nNodes];
        for (int n = 0; n < nNodes; n++) {
            sortedHeight[n] = theTree.getInternalNode(n).getNodeHeight();
        }
        Arrays.sort(sortedHeight);
    }

    /**
     * For a given number of groups this function returns the group membership
     * for each taxon.
     *
     * @param numberOfGroups the number of groups desired
     * @return an array of integers indicating the group of each taxon
     */
    public int[] getGroups(int numberOfGroups) {
        int[] groups = new int[nTaxa];
        if (numberOfGroups == 1) {
            for (int t = 0; t < nTaxa; t++) {
                groups[t] = 0;
            }
        } else if (numberOfGroups == nTaxa) {
            for (int t = 0; t < nTaxa; t++) {
                groups[t] = t;
            }
        } else {
            double maxHeight = sortedHeight[nNodes - numberOfGroups];
            for (int t = 0; t < nTaxa; t++) {
                groups[t] = -1;
            }
            int group = 0;
            for (int t = 0; t < nTaxa; t++) {
                if (groups[t] == -1) {
                    Node aNode = theTree.getExternalNode(t);
                    while (aNode.getParent() != null && aNode.getParent().getNodeHeight() <= maxHeight) {
                        aNode = aNode.getParent();
                    }
                    setNodeToGroup(aNode, group, groups);
                    group++;
                }
            }
        }
        return groups;
    }

    /**
     * This function returns taxa group membership when the tree is cut at the
     * designated height.
     *
     * @param height the height at which the tree is cut
     * @return the group membership of each taxon
     */
    public int[] getGroups(double height) {
        int[] groups = new int[nTaxa];
        double maxHeight = sortedHeight[nNodes - 1];
        if (maxHeight < height) { //all individuals are in a single group
            for (int t = 0; t < nTaxa; t++) {
                groups[t] = 0;
            }
        } else {
            for (int t = 0; t < nTaxa; t++) {
                groups[t] = -1;
            }
            int group = 0;
            for (int t = 0; t < nTaxa; t++) {
                if (groups[t] == -1) {
                    Node aNode = theTree.getExternalNode(t);
                    while (aNode.getParent() != null && aNode.getParent().getNodeHeight() <= height) {
                        aNode = aNode.getParent();
                    }
                    setNodeToGroup(aNode, group, groups);
                    group++;
                }
            }
        }

        return groups;
    }

    public void setNodeToGroup(Node aNode, int group, int[] groups) {
        if (aNode.isLeaf()) {
            Taxon nodeId = aNode.getIdentifier();
            int index = theTree.whichIdNumber(nodeId);
            groups[index] = group;
        }
        int nChildren = aNode.getChildCount();
        for (int c = 0; c < nChildren; c++) {
            setNodeToGroup(aNode.getChild(c), group, groups);
        }
    }

}