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.visualization;
39
40 import ffx.numerics.clustering.Cluster;
41 import ffx.numerics.clustering.ClusteringAlgorithm;
42 import ffx.numerics.clustering.CompleteLinkageStrategy;
43 import ffx.numerics.clustering.LinkageStrategy;
44 import ffx.numerics.clustering.PDistClusteringAlgorithm;
45
46 import javax.swing.JFrame;
47 import javax.swing.JPanel;
48 import javax.swing.WindowConstants;
49 import java.awt.BorderLayout;
50 import java.awt.Color;
51 import java.awt.Frame;
52
53 /**
54 * Simple Swing JFrame that hosts a DendrogramPanel to visualize a clustering
55 * result. Provides a demo main method to render example dendrograms.
56 *
57 * @author Lars Behnke, 2013
58 * @author Michael J. Schnieders
59 * @since 1.0
60 */
61 public class DendrogramFrame extends JFrame {
62
63 /**
64 * Creates a frame displaying a dendrogram for the provided clustering result.
65 *
66 * @param cluster the root Cluster to visualize
67 */
68 public DendrogramFrame(Cluster cluster) {
69 setSize(500, 400);
70 setLocation(100, 200);
71 setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
72
73 JPanel content = new JPanel();
74 DendrogramPanel dp = new DendrogramPanel();
75
76 setContentPane(content);
77 content.setBackground(Color.red);
78 content.setLayout(new BorderLayout());
79 content.add(dp, BorderLayout.CENTER);
80 dp.setBackground(Color.WHITE);
81 dp.setLineColor(Color.BLACK);
82 dp.setScaleValueDecimals(0);
83 dp.setScaleValueInterval(1);
84 dp.setShowDistances(false);
85
86 dp.setModel(cluster);
87 setVisible(true);
88 }
89
90 /**
91 * Demo entry point that creates two frames with example dendrograms.
92 *
93 * @param args CLI arguments (unused)
94 */
95 public static void main(String[] args) {
96 LinkageStrategy strategy = new CompleteLinkageStrategy();
97 Frame f1 = new DendrogramFrame(createSampleCluster(strategy));
98 f1.setSize(500, 400);
99 f1.setLocation(100, 200);
100 Frame f2 = new DendrogramFrame(createSampleCluster2(strategy));
101 f2.setSize(500, 400);
102 f2.setLocation(600, 200);
103 }
104
105 /**
106 * Creates a small sample Cluster for demonstration purposes.
107 *
108 * @param strategy the LinkageStrategy used by the clustering algorithm
109 * @return a sample root Cluster
110 */
111 private static Cluster createSampleCluster(LinkageStrategy strategy) {
112 double[][] distances = new double[][]{
113 {1, 9, 7, 11, 14, 4, 3, 8, 10, 9, 2, 8, 6, 13, 10}
114 };
115 String[] names = new String[]{"O1", "O2", "O3", "O4", "O5", "O6"};
116 ClusteringAlgorithm alg = new PDistClusteringAlgorithm();
117 Cluster cluster = alg.performClustering(distances, names, strategy);
118 cluster.toConsole(0);
119 return cluster;
120 }
121
122 /**
123 * Creates a second sample Cluster for demonstration purposes.
124 *
125 * @param strategy the LinkageStrategy used by the clustering algorithm
126 * @return a sample root Cluster
127 */
128 private static Cluster createSampleCluster2(LinkageStrategy strategy) {
129 double[][] distances = new double[][]{
130 {1, 9, 7, 11, 14, 12, 4, 3, 8, 10, 12, 9, 2, 8, 9, 6, 13, 11, 10, 7, 2}
131 };
132 String[] names = new String[]{"O1", "O2", "O3", "O4", "O5", "O6", "07"};
133 ClusteringAlgorithm alg = new PDistClusteringAlgorithm();
134 Cluster cluster = alg.performClustering(distances, names, strategy);
135 cluster.toConsole(0);
136 return cluster;
137 }
138 }