distancematrix.java

著名的开源仿真软件yale

package edu.udo.cs.yale.operator.clusterer.upgma;

public class DistanceMatrix implements Matrix {

    private double distance[][];
    private String name[];

    /** Copy constructor */
    private DistanceMatrix(DistanceMatrix matrix) {
	this.distance = new double[matrix.distance.length][];
	for (int i = 0; i < this.distance.length; i++) {
	    this.distance[i] = new double[i];
	    for (int j = 0; j < i; j++) {
		this.distance[i][j] = matrix.distance[i][j];
	    }
	}
	this.name = new String[matrix.name.length];
	for (int i = 0; i < this.name.length; i++) {
	    this.name[i] = matrix.name[i];
	}
    }

    public DistanceMatrix(int n) {
	distance = new double[n][];
	for (int i = 0; i < n; i++) {
	    distance[i] = new double[i];
	}
	name = new String[n];
    }

    public String getName(int i) {
	return name[i];
    }

    public void setName(int i, String name) {
	this.name[i] = name;
    }

    public int getDimension() {
	return distance.length;
    }

    public double getDistance(int i, int j) {
	if (i == j) return 0;
	if (j < i) return getDistance(j, i);
	return distance[j][i];
    }

    public void setDistance(int i, int j, double d) {
	if (d < 0.0) throw new IllegalArgumentException("Distances must be > 0");
	if (i == j) {
	    if (d != 0.0) throw new IllegalArgumentException("d("+i+","+i+") = "+d+" != 0");
	    else return;
	}
	if (j < i) { setDistance(j, i, d); return; }
	distance[j][i] = d;
    }

    /** Throws an IllegalArgumentException if the matrix is no distance measure.  */
    public void verify() {
	for (int i = 0; i < distance.length; i++) {
	    for (int j = 0; j < i; j++) {
		for (int k = 0; k < distance.length; k++) {
		    if (getDistance(i,j) + getDistance(j,k) < getDistance(i,k)) {
			throw new IllegalArgumentException("Matrix violates triangle inequality ("+i+","+j+","+k+")");
		    }
		}
	    }
	}
    }

    public DistanceMatrix copy() {
	return new DistanceMatrix(this);
    }

    public String toString() {
	String str = "";
	for (int i = 0; i < distance.length; i++) {
	    if (i != 0) str += "\n";
	    for (int j = 0; j < distance.length; j++) {
		if (j != 0) str += "\t";
		str += getDistance(i,j);
	    }
	}
	return str;
    }


    public double getValue(int i, int j) { return getDistance(i,j); }
    public void setValue(int i, int j, double v) { setDistance(i,j,v); }
    public boolean isFixed(int i, int j) { return (i <= j);  }
    public String getLabel(int i) { return name[i].toString(); }
}