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brandstaetterbrandstaetter
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undid some unnecessary reformatting that made the code harder to read in FastqBuilderTest.java
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9568 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 45149a6 commit 9e64084

1 file changed

Lines changed: 77 additions & 19 deletions

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‎biojava3-genome/src/test/java/org/biojava3/genome/parsers/fastq/FastqBuilderTest.java‎

Lines changed: 77 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -20,9 +20,6 @@
2020
*/
2121
package org.biojava3.genome.parsers.fastq;
2222

23-
import org.biojava3.genome.parsers.fastq.FastqVariant;
24-
import org.biojava3.genome.parsers.fastq.FastqBuilder;
25-
import org.biojava3.genome.parsers.fastq.Fastq;
2623
import junit.framework.TestCase;
2724

2825
/**
@@ -47,7 +44,11 @@ public void testBuildDefault() {
4744

4845
public void testBuildNullDescription() {
4946
try {
50-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription(null).withSequence("sequence").withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
47+
FastqBuilder fastqBuilder = new FastqBuilder()
48+
.withDescription(null)
49+
.withSequence("sequence")
50+
.withQuality("quality_")
51+
.withVariant(FastqVariant.FASTQ_SOLEXA);
5152

5253
fastqBuilder.build();
5354
fail("build null description expected IllegalArgumentException");
@@ -58,7 +59,11 @@ public void testBuildNullDescription() {
5859

5960
public void testBuildNullSequence() {
6061
try {
61-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence(null).withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
62+
FastqBuilder fastqBuilder = new FastqBuilder()
63+
.withDescription("description")
64+
.withSequence(null)
65+
.withQuality("quality_")
66+
.withVariant(FastqVariant.FASTQ_SOLEXA);
6267

6368
fastqBuilder.build();
6469
fail("build null sequence expected IllegalArgumentException");
@@ -69,7 +74,11 @@ public void testBuildNullSequence() {
6974

7075
public void testBuildNullAppendSequence() {
7176
try {
72-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").appendSequence(null).withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
77+
FastqBuilder fastqBuilder = new FastqBuilder()
78+
.withDescription("description")
79+
.appendSequence(null)
80+
.withQuality("quality_")
81+
.withVariant(FastqVariant.FASTQ_SOLEXA);
7382

7483
fastqBuilder.build();
7584
fail("build null append sequence expected IllegalArgumentException");
@@ -80,7 +89,11 @@ public void testBuildNullAppendSequence() {
8089

8190
public void testBuildNullQuality() {
8291
try {
83-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").withQuality(null).withVariant(FastqVariant.FASTQ_SOLEXA);
92+
FastqBuilder fastqBuilder = new FastqBuilder()
93+
.withDescription("description")
94+
.withSequence("sequence")
95+
.withQuality(null)
96+
.withVariant(FastqVariant.FASTQ_SOLEXA);
8497

8598
fastqBuilder.build();
8699
fail("build null quality expected IllegalArgumentException");
@@ -91,7 +104,11 @@ public void testBuildNullQuality() {
91104

92105
public void testBuildNullAppendQuality() {
93106
try {
94-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").appendQuality(null).withVariant(FastqVariant.FASTQ_SOLEXA);
107+
FastqBuilder fastqBuilder = new FastqBuilder()
108+
.withDescription("description")
109+
.withSequence("sequence")
110+
.appendQuality(null)
111+
.withVariant(FastqVariant.FASTQ_SOLEXA);
95112

96113
fastqBuilder.build();
97114
fail("build null append quality expected IllegalArgumentException");
@@ -102,7 +119,11 @@ public void testBuildNullAppendQuality() {
102119

103120
public void testBuildNullVariant() {
104121
try {
105-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").withQuality("quality_").withVariant(null);
122+
FastqBuilder fastqBuilder = new FastqBuilder()
123+
.withDescription("description")
124+
.withSequence("sequence")
125+
.withQuality("quality_")
126+
.withVariant(null);
106127

107128
fastqBuilder.build();
108129
fail("build null variant expected IllegalArgumentException");
@@ -113,7 +134,10 @@ public void testBuildNullVariant() {
113134

114135
public void testBuildMissingDescription() {
115136
try {
116-
FastqBuilder fastqBuilder = new FastqBuilder().withSequence("sequence").withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
137+
FastqBuilder fastqBuilder = new FastqBuilder()
138+
.withSequence("sequence")
139+
.withQuality("quality_")
140+
.withVariant(FastqVariant.FASTQ_SOLEXA);
117141

118142
fastqBuilder.build();
119143
fail("build missing description expected IllegalStateException");
@@ -124,7 +148,10 @@ public void testBuildMissingDescription() {
124148

125149
public void testBuildMissingSequence() {
126150
try {
127-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
151+
FastqBuilder fastqBuilder = new FastqBuilder()
152+
.withDescription("description")
153+
.withQuality("quality_")
154+
.withVariant(FastqVariant.FASTQ_SOLEXA);
128155

129156
fastqBuilder.build();
130157
fail("build missing sequence expected IllegalStateException");
@@ -135,7 +162,10 @@ public void testBuildMissingSequence() {
135162

136163
public void testBuildMissingQuality() {
137164
try {
138-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").withVariant(FastqVariant.FASTQ_SOLEXA);
165+
FastqBuilder fastqBuilder = new FastqBuilder()
166+
.withDescription("description")
167+
.withSequence("sequence")
168+
.withVariant(FastqVariant.FASTQ_SOLEXA);
139169

140170
fastqBuilder.build();
141171
fail("build missing quality expected IllegalStateException");
@@ -145,7 +175,10 @@ public void testBuildMissingQuality() {
145175
}
146176

147177
public void testBuildDefaultVariant() {
148-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").withQuality("quality_");
178+
FastqBuilder fastqBuilder = new FastqBuilder()
179+
.withDescription("description")
180+
.withSequence("sequence")
181+
.withQuality("quality_");
149182

150183
Fastq fastq = fastqBuilder.build();
151184
assertEquals("description", fastqBuilder.getDescription());
@@ -157,7 +190,11 @@ public void testBuildDefaultVariant() {
157190
}
158191

159192
public void testBuild() {
160-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
193+
FastqBuilder fastqBuilder = new FastqBuilder()
194+
.withDescription("description")
195+
.withSequence("sequence")
196+
.withQuality("quality_")
197+
.withVariant(FastqVariant.FASTQ_SOLEXA);
161198
Fastq fastq = fastqBuilder.build();
162199
assertEquals("description", fastqBuilder.getDescription());
163200
assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
@@ -168,7 +205,12 @@ public void testBuild() {
168205
}
169206

170207
public void testBuildAppendSequence() {
171-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").appendSequence("seq").appendSequence("uence").withQuality("quality_").withVariant(FastqVariant.FASTQ_SOLEXA);
208+
FastqBuilder fastqBuilder = new FastqBuilder()
209+
.withDescription("description")
210+
.appendSequence("seq")
211+
.appendSequence("uence")
212+
.withQuality("quality_")
213+
.withVariant(FastqVariant.FASTQ_SOLEXA);
172214
Fastq fastq = fastqBuilder.build();
173215
assertEquals("description", fastqBuilder.getDescription());
174216
assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
@@ -179,7 +221,12 @@ public void testBuildAppendSequence() {
179221
}
180222

181223
public void testBuildAppendQuality() {
182-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("sequence").appendQuality("qual").appendQuality("ity_").withVariant(FastqVariant.FASTQ_SOLEXA);
224+
FastqBuilder fastqBuilder = new FastqBuilder()
225+
.withDescription("description")
226+
.withSequence("sequence")
227+
.appendQuality("qual")
228+
.appendQuality("ity_")
229+
.withVariant(FastqVariant.FASTQ_SOLEXA);
183230
Fastq fastq = fastqBuilder.build();
184231
assertEquals("description", fastqBuilder.getDescription());
185232
assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
@@ -191,7 +238,11 @@ public void testBuildAppendQuality() {
191238

192239
public void testBuildNonMatchingSequenceQualityScoreLengths0() {
193240
try {
194-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("01234").withQuality("0123").withVariant(FastqVariant.FASTQ_SOLEXA);
241+
FastqBuilder fastqBuilder = new FastqBuilder()
242+
.withDescription("description")
243+
.withSequence("01234")
244+
.withQuality("0123")
245+
.withVariant(FastqVariant.FASTQ_SOLEXA);
195246

196247
fastqBuilder.build();
197248
fail("build sequence length > quality length expected IllegalStateException");
@@ -202,7 +253,11 @@ public void testBuildNonMatchingSequenceQualityScoreLengths0() {
202253

203254
public void testBuildNonMatchingSequenceQualityScoreLengths1() {
204255
try {
205-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withSequence("0123").withQuality("01234").withVariant(FastqVariant.FASTQ_SOLEXA);
256+
FastqBuilder fastqBuilder = new FastqBuilder()
257+
.withDescription("description")
258+
.withSequence("0123")
259+
.withQuality("01234")
260+
.withVariant(FastqVariant.FASTQ_SOLEXA);
206261

207262
fastqBuilder.build();
208263
fail("build sequence length < quality length expected IllegalStateException");
@@ -212,7 +267,10 @@ public void testBuildNonMatchingSequenceQualityScoreLengths1() {
212267
}
213268

214269
public void testBuildMultiple() {
215-
FastqBuilder fastqBuilder = new FastqBuilder().withDescription("description").withQuality("quality__").withVariant(FastqVariant.FASTQ_SOLEXA);
270+
FastqBuilder fastqBuilder = new FastqBuilder()
271+
.withDescription("description")
272+
.withQuality("quality__")
273+
.withVariant(FastqVariant.FASTQ_SOLEXA);
216274

217275
for (int i = 0; i < 10; i++) {
218276
Fastq fastq = fastqBuilder.withSequence("sequence" + i).build();

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