Skip to content

Commit 9e1c80c

Browse files
dmyersturnbulldmyersturnbull
committed
Fixed use of assertEquals() on doubles.
1 parent 3773af1 commit 9e1c80c

9 files changed

Lines changed: 67 additions & 48 deletions

‎biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalIdentityScorerTest.java‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -35,6 +35,8 @@
3535

3636
public class FractionalIdentityScorerTest {
3737

38+
private static final double PRECISION = 0.00000001;
39+
3840
private ProteinSequence query, target;
3941
private GapPenalty gaps;
4042
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -77,20 +79,20 @@ public void testGetTarget() {
7779

7880
@Test
7981
public void testGetMaxScore() {
80-
assertEquals(scorer1.getMaxScore(), 4);
81-
assertEquals(scorer2.getMaxScore(), 4);
82+
assertEquals(scorer1.getMaxScore(), 4, PRECISION);
83+
assertEquals(scorer2.getMaxScore(), 4, PRECISION);
8284
}
8385

8486
@Test
8587
public void testGetMinScore() {
86-
assertEquals(scorer1.getMinScore(), 0);
87-
assertEquals(scorer2.getMinScore(), 0);
88+
assertEquals(scorer1.getMinScore(), 0, PRECISION);
89+
assertEquals(scorer2.getMinScore(), 0, PRECISION);
8890
}
8991

9092
@Test
9193
public void testGetScore() {
92-
assertEquals(scorer1.getScore(), 1);
93-
assertEquals(scorer2.getScore(), 4);
94+
assertEquals(scorer1.getScore(), 1, PRECISION);
95+
assertEquals(scorer2.getScore(), 4, PRECISION);
9496
}
9597

9698
}

‎biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalSimilarityScorerTest.java‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,8 @@
3636

3737
public class FractionalSimilarityScorerTest {
3838

39+
private static final double PRECISION = 0.00000001;
40+
3941
private ProteinSequence query, target;
4042
private GapPenalty gaps;
4143
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -78,20 +80,20 @@ public void testGetTarget() {
7880

7981
@Test
8082
public void testGetMaxScore() {
81-
assertEquals(scorer1.getMaxScore(), 5);
82-
assertEquals(scorer2.getMaxScore(), 4);
83+
assertEquals(scorer1.getMaxScore(), 5, PRECISION);
84+
assertEquals(scorer2.getMaxScore(), 4, PRECISION);
8385
}
8486

8587
@Test
8688
public void testGetMinScore() {
87-
assertEquals(scorer1.getMinScore(), 0);
88-
assertEquals(scorer2.getMinScore(), 0);
89+
assertEquals(scorer1.getMinScore(), 0, PRECISION);
90+
assertEquals(scorer2.getMinScore(), 0, PRECISION);
8991
}
9092

9193
@Test
9294
public void testGetScore() {
93-
assertEquals(scorer1.getScore(), 2);
94-
assertEquals(scorer2.getScore(), 3);
95+
assertEquals(scorer1.getScore(), 2, PRECISION);
96+
assertEquals(scorer2.getScore(), 3, PRECISION);
9597
}
9698

9799
}

‎biojava3-alignment/src/test/java/org/biojava3/alignment/GuideTreeTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -87,7 +87,7 @@ public void testGetRoot() {
8787

8888
@Test
8989
public void testGetScoreMatrix() {
90-
assertArrayEquals(tree.getScoreMatrix(), new int[][] {
90+
assertArrayEquals(tree.getScoreMatrix(), new double[][] {
9191
{4, 4, 0, 3},
9292
{4, 6, 0, 3},
9393
{0, 0, 5, 0},

‎biojava3-alignment/src/test/java/org/biojava3/alignment/LocalAlignmentTest.java‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,14 +37,17 @@
3737
*
3838
*/
3939
public class LocalAlignmentTest {
40+
41+
private static final double PRECISION = 0.00000001;
42+
4043
@Test
4144
public void shouldAllowZeroLengthMatches() {
4245
DNASequence query = new DNASequence("C", DNACompoundSet.getDNACompoundSet());
4346
DNASequence target = new DNASequence("A", DNACompoundSet.getDNACompoundSet());
4447
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
4548
SimpleGapPenalty gapP = new SimpleGapPenalty((short)5, (short)2);
4649
PairwiseSequenceAligner<DNASequence, NucleotideCompound> result = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);
47-
assertEquals(0, result.getScore());
50+
assertEquals(0, result.getScore(), PRECISION);
4851
assertEquals(0, result.getProfile().getLength());
4952
}
5053
}

‎biojava3-alignment/src/test/java/org/biojava3/alignment/NeedlemanWunschTest.java‎

Lines changed: 13 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -23,9 +23,10 @@
2323

2424
package org.biojava3.alignment;
2525

26-
import static org.junit.Assert.*;
26+
import static org.junit.Assert.assertEquals;
27+
import static org.junit.Assert.assertFalse;
28+
import static org.junit.Assert.assertTrue;
2729

28-
import org.biojava3.alignment.routines.GuanUberbacher;
2930
import org.biojava3.alignment.template.GapPenalty;
3031
import org.biojava3.alignment.template.SubstitutionMatrix;
3132
import org.biojava3.core.sequence.DNASequence;
@@ -39,6 +40,8 @@
3940

4041
public class NeedlemanWunschTest {
4142

43+
private static final double PRECISION = 0.00000001;
44+
4245
private ProteinSequence query, target;
4346
private GapPenalty gaps;
4447
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -62,7 +65,7 @@ public void testNeedlemanWunsch() {
6265
nw.setTarget(target);
6366
nw.setGapPenalty(gaps);
6467
nw.setSubstitutionMatrix(blosum62);
65-
assertEquals(nw.getScore(), alignment.getScore());
68+
assertEquals(nw.getScore(), alignment.getScore(), PRECISION);
6669
}
6770

6871
@Test
@@ -165,20 +168,20 @@ public void testGetProfile() {
165168

166169
@Test
167170
public void testGetMaxScore() {
168-
assertEquals(alignment.getMaxScore(), 21);
169-
assertEquals(self.getMaxScore(), 21);
171+
assertEquals(alignment.getMaxScore(), 21, PRECISION);
172+
assertEquals(self.getMaxScore(), 21, PRECISION);
170173
}
171174

172175
@Test
173176
public void testGetMinScore() {
174-
assertEquals(alignment.getMinScore(), -27);
175-
assertEquals(self.getMinScore(), -28);
177+
assertEquals(alignment.getMinScore(), -27, PRECISION);
178+
assertEquals(self.getMinScore(), -28, PRECISION);
176179
}
177180

178181
@Test
179182
public void testGetScore() {
180-
assertEquals(alignment.getScore(), -6);
181-
assertEquals(self.getScore(), 21);
183+
assertEquals(alignment.getScore(), -6, PRECISION);
184+
assertEquals(self.getScore(), 21, PRECISION);
182185
}
183186

184187
@Test
@@ -257,7 +260,7 @@ public void anchors_should_not_change_score() {
257260
anchored.addAnchor(1, 1);
258261
anchored.addAnchor(2, 2);
259262
anchored.addAnchor(3, 3);
260-
assertEquals(aligner.getScore(), anchored.getScore());
263+
assertEquals(aligner.getScore(), anchored.getScore(), PRECISION);
261264
}
262265
/**
263266
* @author Daniel Cameron

‎biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleProfileProfileAlignerTest.java‎

Lines changed: 12 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,8 @@
3737

3838
public class SimpleProfileProfileAlignerTest {
3939

40+
private static final double PRECISION = 0.00000001;
41+
4042
private ProteinSequence protein1, protein2, protein3, protein4;
4143
private GapPenalty gaps;
4244
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -72,7 +74,7 @@ public void testSimpleProfileProfileAligner() {
7274
alig.setTarget(prof2);
7375
alig.setGapPenalty(gaps);
7476
alig.setSubstitutionMatrix(blosum62);
75-
assertEquals(alig.getScore(), sppa1.getScore());
77+
assertEquals(alig.getScore(), sppa1.getScore(), PRECISION);
7678
}
7779

7880
@Test
@@ -213,23 +215,23 @@ public void testGetProfile() {
213215

214216
@Test
215217
public void testGetMaxScore() {
216-
assertEquals(sppa1.getMaxScore(), 21);
217-
assertEquals(sppa2.getMaxScore(), 21);
218-
assertEquals(sppa3.getMaxScore(), 21);
218+
assertEquals(sppa1.getMaxScore(), 21, PRECISION);
219+
assertEquals(sppa2.getMaxScore(), 21, PRECISION);
220+
assertEquals(sppa3.getMaxScore(), 21, PRECISION);
219221
}
220222

221223
@Test
222224
public void testGetMinScore() {
223-
assertEquals(sppa1.getMinScore(), -12);
224-
assertEquals(sppa2.getMinScore(), -12);
225-
assertEquals(sppa3.getMinScore(), -13);
225+
assertEquals(sppa1.getMinScore(), -12, PRECISION);
226+
assertEquals(sppa2.getMinScore(), -12, PRECISION);
227+
assertEquals(sppa3.getMinScore(), -13, PRECISION);
226228
}
227229

228230
@Test
229231
public void testGetScore() {
230-
assertEquals(sppa1.getScore(), 21);
231-
assertEquals(sppa2.getScore(), -6);
232-
assertEquals(sppa3.getScore(), 3);
232+
assertEquals(sppa1.getScore(), 21, PRECISION);
233+
assertEquals(sppa2.getScore(), -6, PRECISION);
234+
assertEquals(sppa3.getScore(), 3, PRECISION);
233235
}
234236

235237
@Test

‎biojava3-alignment/src/test/java/org/biojava3/alignment/SmithWatermanTest.java‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -34,6 +34,8 @@
3434

3535
public class SmithWatermanTest {
3636

37+
private static final double PRECISION = 0.00000001;
38+
3739
private ProteinSequence query, target;
3840
private GapPenalty gaps;
3941
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -187,20 +189,20 @@ public void testGetProfile() {
187189

188190
@Test
189191
public void testGetMaxScore() {
190-
assertEquals(alignment.getMaxScore(), 50);
191-
assertEquals(self.getMaxScore(), 36);
192+
assertEquals(alignment.getMaxScore(), 50, PRECISION);
193+
assertEquals(self.getMaxScore(), 36, PRECISION);
192194
}
193195

194196
@Test
195197
public void testGetMinScore() {
196-
assertEquals(alignment.getMinScore(), 0);
197-
assertEquals(self.getMinScore(), 0);
198+
assertEquals(alignment.getMinScore(), 0, PRECISION);
199+
assertEquals(self.getMinScore(), 0, PRECISION);
198200
}
199201

200202
@Test
201203
public void testGetScore() {
202-
assertEquals(alignment.getScore(), 18);
203-
assertEquals(self.getScore(), 36);
204+
assertEquals(alignment.getScore(), 18, PRECISION);
205+
assertEquals(self.getScore(), 36, PRECISION);
204206
}
205207

206208
@Test

‎biojava3-alignment/src/test/java/org/biojava3/alignment/TestDNAAlignment.java‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -44,6 +44,9 @@
4444

4545
public class TestDNAAlignment extends TestCase {
4646

47+
private static final double PRECISION = 0.00000001;
48+
49+
4750
public void testDNAAlignment() {
4851

4952
try {
@@ -130,7 +133,7 @@ public void testMixedCaseInputStringsMatchUnderlyingBases() {
130133
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
131134
SimpleGapPenalty gapP = new SimpleGapPenalty((short)5, (short)2);
132135
// should be a full match with +5 per match
133-
assertEquals(5 * query.getLength(), Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix).getScore());
136+
assertEquals(5.0 * query.getLength(), Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix).getScore(), PRECISION);
134137
}
135138
/**
136139
* @author Daniel Cameron

‎biojava3-alignment/src/test/java/org/biojava3/alignment/routines/GuanUberbacherTest.java‎

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -41,6 +41,8 @@
4141

4242
public class GuanUberbacherTest {
4343

44+
private static final double PRECISION = 0.00000001;
45+
4446
private ProteinSequence query, target;
4547
private GapPenalty gaps;
4648
private SubstitutionMatrix<AminoAcidCompound> blosum62;
@@ -64,7 +66,7 @@ public void testGuanUberbacher() {
6466
gu.setTarget(target);
6567
gu.setGapPenalty(gaps);
6668
gu.setSubstitutionMatrix(blosum62);
67-
assertEquals(gu.getScore(), alignment.getScore());
69+
assertEquals(gu.getScore(), alignment.getScore(), PRECISION);
6870
}
6971

7072
@Test
@@ -81,20 +83,20 @@ public void testGetProfile() {
8183

8284
@Test
8385
public void testGetMaxScore() {
84-
assertEquals(alignment.getMaxScore(), 21);
85-
assertEquals(self.getMaxScore(), 21);
86+
assertEquals(alignment.getMaxScore(), 21, PRECISION);
87+
assertEquals(self.getMaxScore(), 21, PRECISION);
8688
}
8789

8890
@Test
8991
public void testGetMinScore() {
90-
assertEquals(alignment.getMinScore(), -27);
91-
assertEquals(self.getMinScore(), -28);
92+
assertEquals(alignment.getMinScore(), -27, PRECISION);
93+
assertEquals(self.getMinScore(), -28, PRECISION);
9294
}
9395

9496
@Test
9597
public void testGetScore() {
96-
assertEquals(alignment.getScore(), -6);
97-
assertEquals(self.getScore(), 21);
98+
assertEquals(alignment.getScore(), -6, PRECISION);
99+
assertEquals(self.getScore(), 21, PRECISION);
98100
}
99101

100102
@Test

0 commit comments

Comments
 (0)