File: Test03.java

package info (click to toggle)
libpj-java 0.0~20150107%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye
  • size: 13,396 kB
  • sloc: java: 99,543; ansic: 987; sh: 153; xml: 26; makefile: 10; sed: 4
file content (163 lines) | stat: -rw-r--r-- 4,823 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
//*****************************************************************************
//
// File:    Test03.java
// Package: edu.rit.compbio.phyl.test
// Unit:    Class edu.rit.compbio.phyl.test.Test03
//
// This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights
// reserved. For further information, contact the author, Alan Kaminsky, at
// ark@cs.rit.edu.
//
// This Java source file is part of the Parallel Java Library ("PJ"). PJ is free
// software; you can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation; either
// version 3 of the License, or (at your option) any later version.
//
// PJ is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
// A PARTICULAR PURPOSE. See the GNU General Public License for more details.
//
// Linking this library statically or dynamically with other modules is making a
// combined work based on this library. Thus, the terms and conditions of the
// GNU General Public License cover the whole combination.
//
// As a special exception, the copyright holders of this library give you
// permission to link this library with independent modules to produce an
// executable, regardless of the license terms of these independent modules, and
// to copy and distribute the resulting executable under terms of your choice,
// provided that you also meet, for each linked independent module, the terms
// and conditions of the license of that module. An independent module is a
// module which is not derived from or based on this library. If you modify this
// library, you may extend this exception to your version of the library, but
// you are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
// may also obtain a copy of the GNU General Public License on the World Wide
// Web at http://www.gnu.org/licenses/gpl.html.
//
//******************************************************************************

package edu.rit.compbio.phyl.test;

import edu.rit.compbio.phyl.DnaSequence;
import edu.rit.compbio.phyl.DnaSequenceTree;

/**
 * Class Test03 is a unit test program for class {@linkplain
 * edu.rit.compbio.phyl.DnaSequenceTree}. It generates all possible rooted
 * bifurcated trees with a given number of tip nodes and prints each tree on the
 * standard output in Newick Standard format.
 * <P>
 * Usage: java edu.rit.compbio.phyl.test.Test03 <I>N</I>
 * <BR><I>N</I> = Number of tip nodes
 *
 * @author  Alan Kaminsky
 * @version 14-Jul-2008
 */
public class Test03
	{

// Prevent construction.

	private Test03()
		{
		}

// Global variables.

	static int N;
	static DnaSequenceTree[] treestack;
	static DnaSequence[] seqstack;

// Main program.

	/**
	 * Unit test main program.
	 */
	public static void main
		(String[] args)
		throws Exception
		{
		if (args.length != 1) usage();
		N = Integer.parseInt (args[0]);
		treestack = new DnaSequenceTree [N];
		for (int i = 0; i < N; ++ i)
			{
			treestack[i] = new DnaSequenceTree (2*i+1);
			}
		seqstack = new DnaSequence [N];
		for (int i = 0; i < N; ++ i)
			{
			seqstack[i] = new DnaSequence (0, 0, nameForLevel (i));
			}
		treestack[0].add (0, seqstack[0]);
		generateTrees (0);
		}

// Hidden operations.

	/**
	 * Generate all trees with one more tip node than the tree at the given
	 * stack level.
	 *
	 * @param  level  Stack level.
	 */
	private static void generateTrees
		(int level)
		{
		DnaSequenceTree tree = treestack[level];
		if (level == N-1)
			{
			System.out.println (tree);
			}
		else
			{
			DnaSequenceTree nexttree = treestack[level+1];
			int len = tree.length();
			for (int i = 0; i < len; ++ i)
				{
				nexttree.copy (tree);
				nexttree.add (i, seqstack[level+1]);
				generateTrees (level+1);
				}
			}
		}

	/**
	 * Returns the DNA sequence name determined by the given level. Level 0 =
	 * <TT>"A"</TT>, level 1 = <TT>"B"</TT>, and so on.
	 *
	 * @param  level  Level.
	 *
	 * @return  DNA sequence name.
	 */
	private static String nameForLevel
		(int level)
		{
		StringBuilder buf = new StringBuilder();
		int v = level + 1;
		while (v > 0)
			{
			buf.insert (0, v2c[v%27]);
			v /= 27;
			}
		return buf.toString();
		}

	private static final char[] v2c = new char[]
		{' ', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
		 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q',
		 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'};

	/**
	 * Print a usage message and exit.
	 */
	private static void usage()
		{
		System.err.println ("Usage: java edu.rit.compbio.phyl.test.Test03 <N>");
		System.err.println ("<N> = Number of tip nodes");
		System.exit (1);
		}

	}