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
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
|
/*
* 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.io.ByteArrayOutputStream;
import java.io.File;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import junit.framework.TestCase;
/**
* Abstract unit test for implementations of FastqWriter.
*/
abstract class AbstractFastqWriterTest
extends TestCase
{
/**
* Create and return a new FASTQ formatted sequence suitable for testing.
*
* @return a new FASTQ formatted sequence suitable for testing.
*/
protected abstract Fastq createFastq();
/**
* Create and return a new instance of an implementation of FastqWriter to test.
*
* @return a new instance of an implementation of FastqWriter to test
*/
protected abstract FastqWriter createFastqWriter();
public void testCreateFastq()
{
Fastq fastq = createFastq();
assertNotNull(fastq);
}
public void testCreateFastqWriter()
{
FastqWriter writer = createFastqWriter();
assertNotNull(writer);
}
public void testAppendVararg() throws Exception
{
FastqWriter writer = createFastqWriter();
Appendable appendable = new StringBuilder();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
assertSame(appendable, writer.append(appendable, fastq0));
assertSame(appendable, writer.append(appendable, fastq0, fastq1));
assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2));
assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2, null));
assertSame(appendable, writer.append(appendable, (Fastq) null));
try
{
writer.append((Appendable) null, fastq0);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testAppendIterable() throws Exception
{
FastqWriter writer = createFastqWriter();
Appendable appendable = new StringBuilder();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
List<Fastq> list = new ArrayList<Fastq>();
assertSame(appendable, writer.append(appendable, list));
list.add(fastq0);
assertSame(appendable, writer.append(appendable, list));
list.add(fastq1);
assertSame(appendable, writer.append(appendable, list));
list.add(fastq2);
assertSame(appendable, writer.append(appendable, list));
list.add(null);
assertSame(appendable, writer.append(appendable, list));
try
{
writer.append((Appendable) null, list);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
writer.append(appendable, (Iterable<Fastq>) null);
fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testWriteFileVararg() throws Exception
{
FastqWriter writer = createFastqWriter();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
File file0 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file0, fastq0);
File file1 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file1, fastq0, fastq1);
File file2 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file2, fastq0, fastq1, fastq2);
File file3 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file3, fastq0, fastq1, fastq2, null);
File file4 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file4, (Fastq) null);
try
{
writer.write((File) null, fastq0);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testWriteFileIterable() throws Exception
{
FastqWriter writer = createFastqWriter();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
List<Fastq> list = new ArrayList<Fastq>();
File file0 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file0, list);
list.add(fastq0);
File file1 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file1, list);
list.add(fastq1);
File file2 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file2, list);
list.add(fastq2);
File file3 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file3, list);
list.add(null);
File file4 = File.createTempFile("abstractFastqWriterTest", null);
writer.write(file4, list);
File file5 = File.createTempFile("abstractFastqWriterTest", null);
try
{
writer.write((File) null, fastq0);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
writer.write(file5, (Iterable<Fastq>) null);
fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testWriteOutputStreamVararg() throws Exception
{
FastqWriter writer = createFastqWriter();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
OutputStream outputStream = new ByteArrayOutputStream();
writer.write(outputStream, fastq0);
writer.write(outputStream, fastq0, fastq1);
writer.write(outputStream, fastq0, fastq1, fastq2);
writer.write(outputStream, fastq0, fastq1, fastq2, null);
writer.write(outputStream, (Fastq) null);
try
{
writer.write((OutputStream) null, fastq0);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
public void testWriteOutputStreamIterable() throws Exception
{
FastqWriter writer = createFastqWriter();
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
OutputStream outputStream = new ByteArrayOutputStream();
List<Fastq> list = new ArrayList<Fastq>();
writer.write(outputStream, list);
list.add(fastq0);
writer.write(outputStream, list);
list.add(fastq1);
writer.write(outputStream, list);
list.add(fastq2);
writer.write(outputStream, list);
list.add(null);
writer.write(outputStream, list);
try
{
writer.write((OutputStream) null, fastq0);
fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
try
{
writer.write(outputStream, (Iterable<Fastq>) null);
fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
// expected
}
}
}
|
