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 import java.util.List;
41
42 /**
43 * Defines algorithms that produce hierarchical clusters from distance data.
44 *
45 * @author Lars Behnke, 2013
46 * @author Michael J. Schnieders
47 * @since 1.0
48 */
49 public interface ClusteringAlgorithm {
50
51 /**
52 * Performs hierarchical agglomerative clustering on a square distance matrix.
53 *
54 * @param distances an N x N symmetric matrix of pairwise distances (upper triangle used)
55 * @param clusterNames an array of N names corresponding to rows/columns of distances
56 * @param linkageStrategy the linkage criterion used to update inter-cluster distances
57 * @return the root Cluster of the resulting hierarchy (dendrogram)
58 */
59 Cluster performClustering(double[][] distances, String[] clusterNames,
60 LinkageStrategy linkageStrategy);
61
62 /**
63 * Performs hierarchical clustering when each initial element has an associated weight.
64 *
65 * @param distances an N x N symmetric matrix of pairwise distances
66 * @param clusterNames an array of N names corresponding to the input elements
67 * @param weights an array of N non-negative weights for the input elements
68 * @param linkageStrategy the linkage criterion used to update inter-cluster distances
69 * @return the root Cluster of the resulting hierarchy (dendrogram)
70 */
71 Cluster performWeightedClustering(double[][] distances, String[] clusterNames,
72 double[] weights, LinkageStrategy linkageStrategy);
73
74 /**
75 * Performs a flat clustering by agglomerating until the next linkage distance would exceed
76 * the provided threshold, and returns the list of clusters at that cut.
77 *
78 * @param distances an N x N symmetric matrix of pairwise distances
79 * @param clusterNames an array of N names corresponding to the input elements
80 * @param linkageStrategy the linkage criterion used to update inter-cluster distances
81 * @param threshold the maximum allowed inter-cluster linkage distance for merging
82 * @return list of clusters obtained at the specified threshold
83 */
84 List<Cluster> performFlatClustering(double[][] distances,
85 String[] clusterNames, LinkageStrategy linkageStrategy, Double threshold);
86 }