1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025.
6 //
7 // This file is part of Force Field X.
8 //
9 // Force Field X is free software; you can redistribute it and/or modify it
10 // under the terms of the GNU General Public License version 3 as published by
11 // the Free Software Foundation.
12 //
13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16 // details.
17 //
18 // You should have received a copy of the GNU General Public License along with
19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20 // Place, Suite 330, Boston, MA 02111-1307 USA
21 //
22 // Linking this library statically or dynamically with other modules is making a
23 // combined work based on this library. Thus, the terms and conditions of the
24 // GNU General Public License cover the whole combination.
25 //
26 // As a special exception, the copyright holders of this library give you
27 // permission to link this library with independent modules to produce an
28 // executable, regardless of the license terms of these independent modules, and
29 // to copy and distribute the resulting executable under terms of your choice,
30 // provided that you also meet, for each linked independent module, the terms
31 // and conditions of the license of that module. An independent module is a
32 // module which is not derived from or based on this library. If you modify this
33 // library, you may extend this exception to your version of the library, but
34 // you are not obligated to do so. If you do not wish to do so, delete this
35 // exception statement from your version.
36 //
37 // ******************************************************************************
38 package ffx.numerics.clustering;
39
40 /**
41 * Simple value object storing a distance and an optional weight used during
42 * linkage computations; comparable by distance and cloneable.
43 *
44 * @author Lars Behnke, 2013
45 * @author Michael J. Schnieders
46 * @since 1.0
47 */
48 public class Distance implements Comparable<Distance>, Cloneable {
49
50 private Double distance;
51 private Double weight;
52
53 /**
54 * Creates a Distance with value 0 and weight 1.
55 */
56 public Distance() {
57 this(0.0);
58 }
59
60 /**
61 * Creates a Distance with the given value and unit weight.
62 *
63 * @param distance the distance value
64 */
65 public Distance(Double distance) {
66 this(distance, 1.0);
67 }
68
69 /**
70 * Creates a Distance with the given value and weight.
71 *
72 * @param distance the distance value
73 * @param weight the weight associated with this distance
74 */
75 public Distance(Double distance, Double weight) {
76 this.distance = distance;
77 this.weight = weight;
78 }
79
80 /**
81 * Gets the distance value.
82 *
83 * @return the distance value (may be null)
84 */
85 public Double getDistance() {
86 return distance;
87 }
88
89 /**
90 * Sets the distance value.
91 *
92 * @param distance the distance value to set
93 */
94 public void setDistance(Double distance) {
95 this.distance = distance;
96 }
97
98 /**
99 * Gets the weight.
100 *
101 * @return the weight
102 */
103 public Double getWeight() {
104 return weight;
105 }
106
107 /**
108 * Sets the weight.
109 *
110 * @param weight the weight to set
111 */
112 public void setWeight(Double weight) {
113 this.weight = weight;
114 }
115
116 /**
117 * Checks whether the distance value is NaN or undefined.
118 *
119 * @return true if the distance is null or NaN; false otherwise
120 */
121 public boolean isNaN() {
122 return distance == null || distance.isNaN();
123 }
124
125 /**
126 * Compares by distance value, with null other treated as greater (this < other).
127 *
128 * @param distance the other Distance to compare to
129 * @return negative, zero, or positive per Comparable contract
130 */
131 @Override
132 public int compareTo(Distance distance) {
133 return distance == null ? 1 : getDistance().compareTo(distance.getDistance());
134 }
135
136 /**
137 * Returns a string containing distance and weight values.
138 *
139 * @return formatted string representation
140 */
141 @Override
142 public String toString() {
143 return String.format("distance : %.2f, weight : %.2f", distance, weight);
144 }
145
146 /**
147 * Creates a clone of this Distance.
148 *
149 * @return a clone of this Distance
150 */
151 @Override
152 public Distance clone() {
153 try {
154 Distance clone = (Distance) super.clone();
155 clone.distance = distance;
156 clone.weight = weight;
157 return clone;
158 } catch (CloneNotSupportedException e) {
159 throw new AssertionError();
160 }
161 }
162 }