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1 package edu.unc.genomics.visualization;
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2
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3 import java.io.Serializable;
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4 import java.util.Collection;
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5
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6 import org.apache.commons.math.stat.clustering.Clusterable;
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7
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8 /**
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9 * @author timpalpant
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10 * Holds a row of data for the KMeans program
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11 */
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12 class KMeansRow implements Clusterable<KMeansRow>, Serializable {
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13
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14 private static final long serialVersionUID = -323598431692368500L;
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15
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16 private final String id;
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17 /** Point coordinates. */
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18 private final float[] point;
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19
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20 /**
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21 * Build an instance wrapping an float array.
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22 * <p>The wrapped array is referenced, it is <em>not</em> copied.</p>
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23 * @param point the n-dimensional point in integer space
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24 */
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25 public KMeansRow(final String id, final float[] point) {
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26 this.point = point;
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27 this.id = id;
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28 }
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29
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30 /**
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31 * Get the n-dimensional point in float space.
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32 * @return a reference (not a copy!) to the wrapped array
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33 */
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34 public float[] getPoint() {
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35 return point;
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36 }
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37
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38 /** {@inheritDoc} */
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39 public double distanceFrom(final KMeansRow p) {
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40 double sumSquares = 0;
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41 float[] otherPoint = p.getPoint();
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42 for (int i = 0; i < point.length; i++) {
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43 sumSquares += Math.pow(point[i]-otherPoint[i], 2);
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44 }
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45 return Math.sqrt(sumSquares);
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46 }
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47
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48 /** {@inheritDoc} */
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49 public KMeansRow centroidOf(final Collection<KMeansRow> points) {
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50 float[] centroid = new float[getPoint().length];
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51 for (KMeansRow p : points) {
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52 for (int i = 0; i < centroid.length; i++) {
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53 centroid[i] += p.getPoint()[i];
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54 }
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55 }
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56 for (int i = 0; i < centroid.length; i++) {
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57 centroid[i] /= points.size();
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58 }
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59 return new KMeansRow(id, centroid);
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60 }
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61
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62 /** {@inheritDoc} */
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63 @Override
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64 public boolean equals(final Object other) {
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65 if (!(other instanceof KMeansRow)) {
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66 return false;
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67 }
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68 final float[] otherPoint = ((KMeansRow) other).getPoint();
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69 if (point.length != otherPoint.length) {
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70 return false;
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71 }
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72 for (int i = 0; i < point.length; i++) {
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73 if (point[i] != otherPoint[i]) {
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74 return false;
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75 }
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76 }
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77 return true;
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78 }
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79
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80 /** {@inheritDoc} */
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81 @Override
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82 public int hashCode() {
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83 int hashCode = 0;
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84 for (Float i : point) {
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85 hashCode += i.hashCode() * 13 + 7;
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86 }
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87 return hashCode;
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88 }
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89
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90 /**
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91 * {@inheritDoc}
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92 * @since 2.1
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93 */
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94 @Override
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95 public String toString() {
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96 final StringBuilder buff = new StringBuilder(id);
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97 for (float value : getPoint()) {
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98 buff.append("\t").append(value);
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99 }
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100 return buff.toString();
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101 }
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102
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103 /**
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104 * @return the id
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105 */
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106 public String getId() {
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107 return id;
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108 }
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109
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110 }
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