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
|
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.fastq;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
import java.lang.reflect.Modifier;
import junit.framework.TestCase;
/**
* Unit test for Fastq.
*/
public final class FastqTest
extends TestCase
{
public void testImmutable()
{
Class<Fastq> cls = Fastq.class;
assertTrue(Modifier.isPublic(cls.getModifiers()));
assertTrue(Modifier.isFinal(cls.getModifiers()));
Field[] fields = cls.getDeclaredFields();
for (Field field : fields)
{
assertTrue(Modifier.isPrivate(field.getModifiers()));
assertTrue(Modifier.isFinal(field.getModifiers()) ||
(Modifier.isVolatile(field.getModifiers()) && Modifier.isTransient(field.getModifiers())));
}
}
public void testConstructor()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertNotNull(fastq);
try
{
new Fastq(null, "sequence", "quality_", FastqVariant.FASTQ_SANGER);
fail("ctr(null description) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
new Fastq("description", null, "quality_", FastqVariant.FASTQ_SANGER);
fail("ctr(null sequence) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
new Fastq("description", "sequence", null, FastqVariant.FASTQ_SANGER);
fail("ctr(null quality) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
new Fastq("description", "sequence", "quality_", null);
fail("ctr(null variant) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testDescription()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertTrue(fastq.getDescription() != null);
assertEquals("description", fastq.getDescription());
}
public void testSequence()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertTrue(fastq.getSequence() != null);
assertEquals("sequence", fastq.getSequence());
}
public void testQuality()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertTrue(fastq.getQuality() != null);
assertEquals("quality_", fastq.getQuality());
}
public void testVariant()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertTrue(fastq.getVariant() != null);
assertEquals(FastqVariant.FASTQ_SANGER, fastq.getVariant());
}
public void testEquals()
{
Fastq fastq0 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
Fastq fastq1 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertFalse(fastq0.equals(null));
assertFalse(fastq1.equals(null));
assertFalse(fastq0.equals(new Object()));
assertFalse(fastq1.equals(new Object()));
assertTrue(fastq0.equals(fastq0));
assertTrue(fastq1.equals(fastq1));
assertFalse(fastq0 == fastq1);
assertFalse(fastq0.equals(fastq1));
assertFalse(fastq1.equals(fastq0));
}
public void testHashCode()
{
Fastq fastq0 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
Fastq fastq1 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
assertEquals(fastq0.hashCode(), fastq0.hashCode());
assertEquals(fastq1.hashCode(), fastq1.hashCode());
if (fastq0.equals(fastq1))
{
assertEquals(fastq0.hashCode(), fastq1.hashCode());
assertEquals(fastq1.hashCode(), fastq0.hashCode());
}
if (fastq1.equals(fastq0))
{
assertEquals(fastq0.hashCode(), fastq1.hashCode());
assertEquals(fastq1.hashCode(), fastq0.hashCode());
}
}
}
|
