diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 698fa280c7..c5bccfa23c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -63,9 +63,12 @@
compile
- junit
- junit
- test
+ org.junit.jupiter
+ junit-jupiter-engine
+
+
+ org.junit.jupiter
+ junit-jupiter-params
org.biojava
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
index 6e1cae5d8b..8c50e19bc2 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
@@ -26,26 +26,26 @@
import org.biojava.nbio.genome.parsers.gff.Feature;
import org.biojava.nbio.genome.parsers.gff.FeatureList;
import org.biojava.nbio.genome.parsers.gff.Location;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
/**
* @author mckeee1
*
*/
-public class FeatureListTest {
+class FeatureListTest {
@Test
- public void testAddIndex() throws Exception
+ void testAddIndex() throws Exception
{
FeatureList fl = new FeatureList();
fl.add(new Feature("seqname", "source", "type", new Location(1, 2), (double)0, 0, "gene_id \"gene_id_1\"; transcript_id \"transcript_id_1\";"));
fl.addIndex("transcript_id");
- Assert.assertEquals(1, fl.selectByAttribute("transcript_id").size());
+ Assertions.assertEquals(1, fl.selectByAttribute("transcript_id").size());
FeatureList f2 = new FeatureList();
f2.addIndex("transcript_id");
f2.add(new Feature("seqname", "source", "type", new Location(1, 2), (double)0, 0, "gene_id \"gene_id_1\"; transcript_id \"transcript_id_1\";"));
- Assert.assertEquals(1, f2.selectByAttribute("transcript_id").size());
+ Assertions.assertEquals(1, f2.selectByAttribute("transcript_id").size());
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
index 3c81c50916..9c3a8877c6 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
@@ -28,9 +28,9 @@
import org.biojava.nbio.core.sequence.GeneSequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.io.FastaWriterHelper;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -45,20 +45,20 @@
*
* @author Scooter Willis
*/
-public class GeneFeatureHelperTest {
+class GeneFeatureHelperTest {
private static final Logger logger = LoggerFactory.getLogger(GeneFeatureHelperTest.class);
- @Before
+ @BeforeEach
public void setUp() throws Exception {
}
- @After
+ @AfterEach
public void tearDown() throws Exception {
}
@Test
- public void testZeroLocation() throws Exception {
+ void testZeroLocation() throws Exception {
@SuppressWarnings("unused")
FeatureList listGenes = GFF3Reader.read("src/test/resources/amphimedon.gff3");
@@ -71,7 +71,7 @@ public void testZeroLocation() throws Exception {
*/
@Test
- public void testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile() throws Exception {
+ void testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile() throws Exception {
// logger.info("loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile");
File fastaSequenceFile = new File("src/test/resources/volvox_all.fna");
File uppercaseFastaFile = new File("src/test/resources/volvox_all_genes_exon_uppercase.fna");
@@ -93,7 +93,7 @@ public void testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile() throws Exce
* Test of outputFastaSequenceLengthGFF3 method, of class GeneFeatureHelper.
*/
@Test
- public void testOutputFastaSequenceLengthGFF3() throws Exception {
+ void testOutputFastaSequenceLengthGFF3() throws Exception {
// logger.info("outputFastaSequenceLengthGFF3");
File fastaSequenceFile = new File("src/test/resources/volvox_all.fna");
@@ -112,7 +112,7 @@ public void testOutputFastaSequenceLengthGFF3() throws Exception {
*/
@Test
- public void testAddGFF3Note() throws Exception {
+ void testAddGFF3Note() throws Exception {
Map chromosomeSequenceList = GeneFeatureHelper
.loadFastaAddGeneFeaturesFromGmodGFF3(new File("src/test/resources/volvox_all.fna"), new File(
"src/test/resources/volvox.gff3"), false);
@@ -128,7 +128,7 @@ public void testAddGFF3Note() throws Exception {
* output.
*/
@Test
- public void testGetProteinSequences() throws Exception {
+ void testGetProteinSequences() throws Exception {
Map chromosomeSequenceList = GeneFeatureHelper
.loadFastaAddGeneFeaturesFromGmodGFF3(new File("src/test/resources/volvox_all.fna"), new File(
"src/test/resources/volvox.gff3"), false);
@@ -148,7 +148,7 @@ public void testGetProteinSequences() throws Exception {
* Test of getGeneSequences method, of class GeneFeatureHelper.
*/
@Test
- public void testGetGeneSequences() throws Exception {
+ void testGetGeneSequences() throws Exception {
// logger.info("getGeneSequences");
Map chromosomeSequenceList = GeneFeatureHelper
.loadFastaAddGeneFeaturesFromGmodGFF3(new File("src/test/resources/volvox_all.fna"), new File(
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
index 9ddd43357a..a86b8718c5 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
@@ -21,7 +21,8 @@
package org.biojava.nbio.genome;
import org.biojava.nbio.genome.util.ChromosomeMappingTools;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.Arrays;
@@ -32,10 +33,10 @@
/**
* Created by Yana Valasatava on 8/14/17.
*/
-public class TestChromosomeMappingTools {
+class TestChromosomeMappingTools {
@Test
- public void testGetCDSLengthForward() {
+ void testGetCDSLengthForward() {
List exonStarts = new ArrayList<>(Arrays.asList(10, 30, 50, 70));
List exonEnds = new ArrayList<>(Arrays.asList(20, 40, 60, 80));
@@ -46,11 +47,11 @@ public void testGetCDSLengthForward() {
ChromosomeMappingTools.setCoordinateSystem(0);
int cdsTest = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
- assertEquals(cdsDesired, cdsTest);
+ Assertions.assertEquals(cdsDesired, cdsTest);
}
@Test
- public void testGetCDSLengthReverseAsc() {
+ void testGetCDSLengthReverseAsc() {
List exonStarts = new ArrayList<>(Arrays.asList(10, 50, 70));
List exonEnds = new ArrayList<>(Arrays.asList(20, 60, 80));
@@ -61,11 +62,11 @@ public void testGetCDSLengthReverseAsc() {
ChromosomeMappingTools.setCoordinateSystem(0);
int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
- assertEquals(cdsDesired, cdsTest);
+ Assertions.assertEquals(cdsDesired, cdsTest);
}
@Test
- public void testGetCDSLengthReverseDesc() {
+ void testGetCDSLengthReverseDesc() {
List exonStarts = new ArrayList<>(Arrays.asList(70, 50, 10));
List exonEnds = new ArrayList<>(Arrays.asList(80, 60, 20));
@@ -76,6 +77,6 @@ public void testGetCDSLengthReverseDesc() {
ChromosomeMappingTools.setCoordinateSystem(0);
int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
- assertEquals(cdsDesired, cdsTest);
+ Assertions.assertEquals(cdsDesired, cdsTest);
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
index 4999cfa6fb..257b88e3e1 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -22,8 +22,8 @@
import com.google.common.collect.Range;
import org.biojava.nbio.genome.util.ChromosomeMappingTools;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.Arrays;
@@ -32,10 +32,10 @@
/**
* Created by andreas on 7/19/16.
*/
-public class TestGenomeMapping {
+class TestGenomeMapping {
@Test
- public void testGenomeMappingToolGetCDSRanges(){
+ void testGenomeMappingToolGetCDSRanges(){
List lst1 = new ArrayList<>(Arrays.asList( 86346823, 86352858, 86354529));
List lst2 = new ArrayList<>(Arrays.asList(86348878, 86352984, 86354692));
@@ -45,21 +45,21 @@ public void testGenomeMappingToolGetCDSRanges(){
List> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
// makes sure the first list does not get changed;
- Assert.assertEquals(86346823, (int) lst1.get(0));
+ Assertions.assertEquals(86346823, (int) lst1.get(0));
- Assert.assertEquals(86348749, (int) result.get(0).lowerEndpoint());
- Assert.assertEquals(86352858, (int) result.get(1).lowerEndpoint());
- Assert.assertEquals(86354529, (int) result.get(2).lowerEndpoint());
+ Assertions.assertEquals(86348749, (int) result.get(0).lowerEndpoint());
+ Assertions.assertEquals(86352858, (int) result.get(1).lowerEndpoint());
+ Assertions.assertEquals(86354529, (int) result.get(2).lowerEndpoint());
- Assert.assertEquals(86348878, (int) result.get(0).upperEndpoint());
- Assert.assertEquals(86352984, (int) result.get(1).upperEndpoint());
- Assert.assertEquals(86387027, (int) result.get(2).upperEndpoint());
+ Assertions.assertEquals(86348878, (int) result.get(0).upperEndpoint());
+ Assertions.assertEquals(86352984, (int) result.get(1).upperEndpoint());
+ Assertions.assertEquals(86387027, (int) result.get(2).upperEndpoint());
}
@Test
- public void testGenomeMappingToolGetCDSRangesSERINC2(){
+ void testGenomeMappingToolGetCDSRangesSERINC2(){
List lst1 = new ArrayList<>(Arrays.asList(31413812, 31415872, 31423692));
List lst2 = new ArrayList<>(Arrays.asList(31414777, 31415907, 31423854));
@@ -69,7 +69,7 @@ public void testGenomeMappingToolGetCDSRangesSERINC2(){
List> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
// makes sure the first list does not get changed;
- Assert.assertEquals(31423818, (int) result.get(0).lowerEndpoint());
+ Assertions.assertEquals(31423818, (int) result.get(0).lowerEndpoint());
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
index 5543682f17..4c98225b04 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
@@ -20,29 +20,28 @@
*/
package org.biojava.nbio.genome;
-import static org.junit.Assert.*;
-
import org.biojava.nbio.genome.parsers.gff.Location;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
-public class TestIssue355 {
+class TestIssue355 {
@Test
- public void testIssue1() {
+ void testIssue1() {
Location l1 = Location.fromBio(51227320, 51227381, '+');
Location l2 = Location.fromBio(51227323, 51227382, '+');
Location union = l1.union(l2);
- assertEquals(51227320,union.bioStart());
- assertEquals(51227382,union.bioEnd());
+ Assertions.assertEquals(51227320, union.bioStart());
+ Assertions.assertEquals(51227382, union.bioEnd());
}
@Test
- public void testIssue2() {
+ void testIssue2() {
Location l1 = Location.fromBio(100, 200, '+');
Location l2 = Location.fromBio(1, 99, '+');
Location intersection = l1.intersection(l2);
- assertNull(intersection);
+ Assertions.assertNull(intersection);
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
index 1289cb757e..42893cf22b 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
@@ -20,15 +20,14 @@
*/
package org.biojava.nbio.genome;
-import static org.junit.Assert.*;
-
import org.biojava.nbio.genome.parsers.gff.Location;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
-public class TestLocation {
+class TestLocation {
@Test
- public void testLocation() {
+ void testLocation() {
// tests taken from Location.main()
//Location p3_7= new Location( 3, 7 );
@@ -49,70 +48,70 @@ public void testLocation() {
Location r5_8= new Location( 5, 8 );
//distance
- assertEquals(7, L(14,14).distance( L(3,7) ));
- assertEquals(7, L(3,7).distance( L(14,14) ));
- assertEquals(3, L(1,4).distance( L(7, 10) ));
+ Assertions.assertEquals(7, L(14,14).distance( L(3,7) ));
+ Assertions.assertEquals(7, L(3,7).distance( L(14,14) ));
+ Assertions.assertEquals(3, L(1,4).distance( L(7, 10) ));
//union
- assertEquals(p10_17, p10_12.union( p14_17 ));
- assertEquals(p10_17, p14_17.union( p10_12 ));
- assertEquals(p15_19, p15_19.union( p15_16 ));
+ Assertions.assertEquals(p10_17, p10_12.union( p14_17 ));
+ Assertions.assertEquals(p10_17, p14_17.union( p10_12 ));
+ Assertions.assertEquals(p15_19, p15_19.union( p15_16 ));
//intersection
- assertEquals(new Location( 21, 25 ), r13_17.union( r21_25 ).intersection( r21_25 ));
+ Assertions.assertEquals(new Location( 21, 25 ), r13_17.union( r21_25 ).intersection( r21_25 ));
//isBefore
- assertTrue( r2_5.isBefore( r5_8 ));
- assertTrue( !r2_5.isBefore( r4_7 ));
+ Assertions.assertTrue(r2_5.isBefore( r5_8 ));
+ Assertions.assertTrue(!r2_5.isBefore( r4_7 ));
//isAfter
- assertTrue(r5_8.isAfter( r2_5 ));
- assertTrue(!r5_8.isAfter( r4_7 ));
+ Assertions.assertTrue(r5_8.isAfter( r2_5 ));
+ Assertions.assertTrue(!r5_8.isAfter( r4_7 ));
//contains
- assertTrue(p15_19.contains( p16_19 ));
+ Assertions.assertTrue(p15_19.contains( p16_19 ));
//overlaps
- assertTrue(r2_5.overlaps( r4_7 ));
- assertTrue(r2_5.overlaps( r0_3 ));
- assertTrue(!r5_8.overlaps( r2_5 ));
- assertTrue(!r2_5.overlaps( r5_8 ));
+ Assertions.assertTrue(r2_5.overlaps( r4_7 ));
+ Assertions.assertTrue(r2_5.overlaps( r0_3 ));
+ Assertions.assertTrue(!r5_8.overlaps( r2_5 ));
+ Assertions.assertTrue(!r2_5.overlaps( r5_8 ));
//prefix
- assertEquals(L(2,3), L(2,20).prefix(1));
- assertEquals(L(2,19), L(2,20).prefix(-1));
- assertEquals( L(2,10), L(2,20).prefix( L(10,12)));
+ Assertions.assertEquals(L(2,3), L(2,20).prefix(1));
+ Assertions.assertEquals(L(2,19), L(2,20).prefix(-1));
+ Assertions.assertEquals(L(2,10), L(2,20).prefix( L(10,12)));
//suffix
- assertEquals(L(3,20), L(2,20).suffix(1));
- assertEquals(L(19,20), L(2,20).suffix(-1));
- assertEquals(L(12,20), L(2,20).suffix( L(10,12)));
+ Assertions.assertEquals(L(3,20), L(2,20).suffix(1));
+ Assertions.assertEquals(L(19,20), L(2,20).suffix(-1));
+ Assertions.assertEquals(L(12,20), L(2,20).suffix( L(10,12)));
}
@Test
- public void testLocationIntersections() {
+ void testLocationIntersections() {
// One inside another
Location r21_25 = new Location( 21, 25 );
Location r1_100 = new Location(1, 100 );
- assertEquals(r21_25, r21_25.intersection( r1_100));
- assertEquals(r21_25, r1_100.intersection( r21_25));
+ Assertions.assertEquals(r21_25, r21_25.intersection( r1_100));
+ Assertions.assertEquals(r21_25, r1_100.intersection( r21_25));
// Non overlapping
Location r10_100 = new Location(10, 100 );
Location r1_9 = new Location( 1, 9 );
- assertNull(r10_100.intersection( r1_9));
- assertNull(r1_9.intersection( new Location( 9, 10 )));
+ Assertions.assertNull(r10_100.intersection( r1_9));
+ Assertions.assertNull(r1_9.intersection( new Location( 9, 10 )));
// Partially overlappping
Location r1_25 = new Location( 1, 25 );
Location r21_100 = new Location(21, 100 );
- assertEquals(r21_25, r1_25.intersection( r21_100));
- assertEquals(r21_25, r21_100.intersection( r1_25));
+ Assertions.assertEquals(r21_25, r1_25.intersection( r21_100));
+ Assertions.assertEquals(r21_25, r21_100.intersection( r1_25));
}
//shorthand for testing
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
index 7cde3d3ec9..3e1385f3a2 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
@@ -20,8 +20,8 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.File;
import java.io.IOException;
@@ -34,7 +34,7 @@
/**
* Abstract unit test for implementations of FastqReader.
*/
-public abstract class AbstractFastqReaderTest {
+abstract class AbstractFastqReaderTest {
/** Array of example files that should throw IOExceptions. */
static final String[] ERROR_EXAMPLES = new String[]
{
@@ -87,21 +87,21 @@ public abstract class AbstractFastqReaderTest {
public void testCreateFastq()
{
Fastq fastq = createFastq();
- Assert.assertNotNull(fastq);
+ Assertions.assertNotNull(fastq);
}
@Test
public void testCreateFastqReader()
{
FastqReader reader = createFastqReader();
- Assert.assertNotNull(reader);
+ Assertions.assertNotNull(reader);
}
@Test
public void testCreateFastqWriter()
{
FastqWriter writer = createFastqWriter();
- Assert.assertNotNull(writer);
+ Assertions.assertNotNull(writer);
}
@Test
@@ -111,7 +111,7 @@ public void testReadFile() throws Exception
try
{
reader.read((File) null);
- Assert.fail("read((File) null) expected IllegalArgumentException");
+ Assertions.fail("read((File) null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -121,7 +121,7 @@ public void testReadFile() throws Exception
{
File noSuchFile = new File("no such file");
reader.read(noSuchFile);
- Assert.fail("read(no such file) expected IOException");
+ Assertions.fail("read(no such file) expected IOException");
}
catch (IOException e)
{
@@ -135,14 +135,14 @@ public void testReadEmptyFile() throws Exception
FastqReader reader = createFastqReader();
File empty = Files.createTempFile("abstractFastqReaderTest",null).toFile();
Iterable iterable = reader.read(empty);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- Assert.assertEquals(0, count);
+ Assertions.assertEquals(0, count);
}
@Test
@@ -154,14 +154,14 @@ public void testReadRoundTripSingleFile() throws Exception
FastqWriter writer = createFastqWriter();
writer.write(single, fastq);
Iterable iterable = reader.read(single);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- Assert.assertEquals(1, count);
+ Assertions.assertEquals(1, count);
}
@Test
@@ -175,14 +175,14 @@ public void testReadRoundTripMultipleFile() throws Exception
FastqWriter writer = createFastqWriter();
writer.write(multiple, fastq0, fastq1, fastq2);
Iterable iterable = reader.read(multiple);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- Assert.assertEquals(3, count);
+ Assertions.assertEquals(3, count);
}
@Test
@@ -192,7 +192,7 @@ public void testReadURL() throws Exception
try
{
reader.read((URL) null);
- Assert.fail("read((URL) null) expected IllegalArgumentException");
+ Assertions.fail("read((URL) null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -202,7 +202,7 @@ public void testReadURL() throws Exception
{
URL noSuchURL = new URL("file:///no such url");
reader.read(noSuchURL);
- Assert.fail("read(no such URL) expected IOException");
+ Assertions.fail("read(no such URL) expected IOException");
}
catch (IOException e)
{
@@ -216,14 +216,14 @@ public void testReadEmptyURL() throws Exception
FastqReader reader = createFastqReader();
URL empty = getClass().getResource("empty.fastq");
Iterable iterable = reader.read(empty);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- Assert.assertEquals(0, count);
+ Assertions.assertEquals(0, count);
}
@Test
@@ -233,7 +233,7 @@ public void testReadInputStream() throws Exception
try
{
reader.read((InputStream) null);
- Assert.fail("read((InputStream) null) expected IllegalArgumentException");
+ Assertions.fail("read((InputStream) null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -247,14 +247,14 @@ public void testReadEmptyInputStream() throws Exception
FastqReader reader = createFastqReader();
InputStream empty = getClass().getResourceAsStream("empty.fastq");
Iterable iterable = reader.read(empty);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- Assert.assertEquals(0, count);
+ Assertions.assertEquals(0, count);
empty.close();
}
@@ -264,15 +264,15 @@ public void testWrappedSequence() throws Exception
FastqReader reader = createFastqReader();
InputStream wrappedSequence = getClass().getResourceAsStream("wrapped-sequence.fastq");
Iterable iterable = reader.read(wrappedSequence);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
- Assert.assertEquals("ACTG", f.getSequence());
+ Assertions.assertNotNull(f);
+ Assertions.assertEquals("ACTG", f.getSequence());
count++;
}
- Assert.assertEquals(1, count);
+ Assertions.assertEquals(1, count);
wrappedSequence.close();
}
@@ -282,15 +282,15 @@ public void testWrappedQuality() throws Exception
FastqReader reader = createFastqReader();
InputStream wrappedQuality = getClass().getResourceAsStream("wrapped-quality.fastq");
Iterable iterable = reader.read(wrappedQuality);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
- Assert.assertEquals("ZZZZ", f.getQuality());
+ Assertions.assertNotNull(f);
+ Assertions.assertEquals("ZZZZ", f.getQuality());
count++;
}
- Assert.assertEquals(1, count);
+ Assertions.assertEquals(1, count);
wrappedQuality.close();
}
@@ -300,15 +300,15 @@ public void testMultipleWrappedQuality() throws Exception
FastqReader reader = createFastqReader();
InputStream wrappedQuality = getClass().getResourceAsStream("multiple-wrapped-quality.fastq");
Iterable iterable = reader.read(wrappedQuality);
- Assert.assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- Assert.assertNotNull(f);
- Assert.assertEquals("ZZZZ", f.getQuality());
+ Assertions.assertNotNull(f);
+ Assertions.assertEquals("ZZZZ", f.getQuality());
count++;
}
- Assert.assertEquals(4, count);
+ Assertions.assertEquals(4, count);
wrappedQuality.close();
}
@@ -322,7 +322,7 @@ public void testErrorExamples() throws Exception
try
{
reader.read(inputStream);
- Assert.fail("error example " + errorExample + " expected IOException");
+ Assertions.fail("error example " + errorExample + " expected IOException");
}
catch (IOException e)
{
@@ -430,7 +430,7 @@ public void complete() throws IOException {
// empty
}
});
- Assert.fail("parse(null, ) expected IllegalArgumentException");
+ Assertions.fail("parse(null, ) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -446,7 +446,7 @@ public void testParseNullParseListener() throws Exception
try
{
reader.parse(new StringReader(input), null);
- Assert.fail("parse(, null) expected IllegalArgumentException");
+ Assertions.fail("parse(, null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
index cf2b695968..f2000b5096 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
@@ -20,8 +20,8 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.ByteArrayOutputStream;
import java.io.File;
@@ -34,7 +34,7 @@
/**
* Abstract unit test for implementations of FastqWriter.
*/
-public abstract class AbstractFastqWriterTest {
+abstract class AbstractFastqWriterTest {
/**
* Create and return a new FASTQ formatted sequence suitable for testing.
@@ -54,14 +54,14 @@ public abstract class AbstractFastqWriterTest {
public void testCreateFastq()
{
Fastq fastq = createFastq();
- Assert.assertNotNull(fastq);
+ Assertions.assertNotNull(fastq);
}
@Test
public void testCreateFastqWriter()
{
FastqWriter writer = createFastqWriter();
- Assert.assertNotNull(writer);
+ Assertions.assertNotNull(writer);
}
@Test
@@ -72,16 +72,16 @@ public void testAppendVararg() throws Exception
Fastq fastq0 = createFastq();
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
- Assert.assertSame(appendable, writer.append(appendable, fastq0));
- Assert.assertSame(appendable, writer.append(appendable, fastq0, fastq1));
- Assert.assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2));
- Assert.assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2, null));
- Assert.assertSame(appendable, writer.append(appendable, (Fastq) null));
+ Assertions.assertSame(appendable, writer.append(appendable, fastq0));
+ Assertions.assertSame(appendable, writer.append(appendable, fastq0, fastq1));
+ Assertions.assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2));
+ Assertions.assertSame(appendable, writer.append(appendable, fastq0, fastq1, fastq2, null));
+ Assertions.assertSame(appendable, writer.append(appendable, (Fastq) null));
try
{
writer.append((Appendable) null, fastq0);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -98,20 +98,20 @@ public void testAppendIterable() throws Exception
Fastq fastq1 = createFastq();
Fastq fastq2 = createFastq();
List list = new ArrayList();
- Assert.assertSame(appendable, writer.append(appendable, list));
+ Assertions.assertSame(appendable, writer.append(appendable, list));
list.add(fastq0);
- Assert.assertSame(appendable, writer.append(appendable, list));
+ Assertions.assertSame(appendable, writer.append(appendable, list));
list.add(fastq1);
- Assert.assertSame(appendable, writer.append(appendable, list));
+ Assertions.assertSame(appendable, writer.append(appendable, list));
list.add(fastq2);
- Assert.assertSame(appendable, writer.append(appendable, list));
+ Assertions.assertSame(appendable, writer.append(appendable, list));
list.add(null);
- Assert.assertSame(appendable, writer.append(appendable, list));
+ Assertions.assertSame(appendable, writer.append(appendable, list));
try
{
writer.append((Appendable) null, list);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -120,7 +120,7 @@ public void testAppendIterable() throws Exception
try
{
writer.append(appendable, (Iterable) null);
- Assert.fail("append(,null) expected IllegalArgumentException");
+ Assertions.fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -149,7 +149,7 @@ public void testWriteFileVararg() throws Exception
try
{
writer.write((File) null, fastq0);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -189,7 +189,7 @@ public void testWriteFileIterable() throws Exception
try
{
writer.write((File) null, fastq0);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -198,7 +198,7 @@ public void testWriteFileIterable() throws Exception
try
{
writer.write(file5, (Iterable) null);
- Assert.fail("append(,null) expected IllegalArgumentException");
+ Assertions.fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -223,7 +223,7 @@ public void testWriteOutputStreamVararg() throws Exception
try
{
writer.write((OutputStream) null, fastq0);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -253,7 +253,7 @@ public void testWriteOutputStreamIterable() throws Exception
try
{
writer.write((OutputStream) null, fastq0);
- Assert.fail("append(null,) expected IllegalArgumentException");
+ Assertions.fail("append(null,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -262,7 +262,7 @@ public void testWriteOutputStreamIterable() throws Exception
try
{
writer.write(outputStream, (Iterable) null);
- Assert.fail("append(,null) expected IllegalArgumentException");
+ Assertions.fail("append(,null) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
index b07e237ef2..c6789e622f 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
@@ -26,19 +26,18 @@
import java.util.List;
import java.util.Map;
-import org.junit.Test;
-import static org.junit.Assert.*;
-
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
/**
* Round trip conversion functional tests.
*/
-public final class ConvertTest {
+final class ConvertTest {
@Test
- public void testConvert() throws Exception
+ void testConvert() throws Exception
{
Map readers = Maps.newHashMap();
readers.put(FastqVariant.FASTQ_SANGER, new SangerFastqReader());
@@ -88,13 +87,13 @@ public void testConvert() throws Exception
List observed = Lists.newArrayList(resultReader.read(tmp));
List expected = Lists.newArrayList(resultReader.read(getClass().getResource(expectedFileName)));
- assertEquals(expected.size(), observed.size());
+ Assertions.assertEquals(expected.size(), observed.size());
for (int i = 0; i < expected.size(); i++)
{
- assertEquals(expected.get(i).getDescription(), observed.get(i).getDescription());
- assertEquals(expected.get(i).getSequence(), observed.get(i).getSequence());
- assertEquals(expected.get(i).getQuality(), observed.get(i).getQuality());
- assertEquals(expected.get(i).getVariant(), observed.get(i).getVariant());
+ Assertions.assertEquals(expected.get(i).getDescription(), observed.get(i).getDescription());
+ Assertions.assertEquals(expected.get(i).getSequence(), observed.get(i).getSequence());
+ Assertions.assertEquals(expected.get(i).getQuality(), observed.get(i).getQuality());
+ Assertions.assertEquals(expected.get(i).getVariant(), observed.get(i).getVariant());
}
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
index 5803068276..3307256126 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
@@ -21,24 +21,25 @@
package org.biojava.nbio.genome.io.fastq;
import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import org.junit.function.ThrowingRunnable;
/**
* Unit test for FastqBuilder.
*/
-public final class FastqBuilderTest {
+final class FastqBuilderTest {
@Test
- public void testConstructor()
+ void testConstructor()
{
FastqBuilder fastqBuilder = new FastqBuilder();
- Assert.assertNotNull(fastqBuilder);
+ Assertions.assertNotNull(fastqBuilder);
}
@Test
- public void testConstructorFastq()
+ void testConstructorFastq()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -49,17 +50,17 @@ public void testConstructorFastq()
Fastq fastq = fastqBuilder.build();
FastqBuilder fastqBuilder2 = new FastqBuilder(fastq);
- Assert.assertNotNull(fastqBuilder2);
+ Assertions.assertNotNull(fastqBuilder2);
Fastq fastq2 = fastqBuilder2.build();
- Assert.assertEquals("description", fastq2.getDescription());
- Assert.assertEquals("sequence", fastq2.getSequence());
- Assert.assertEquals("quality_", fastq2.getQuality());
- Assert.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq2.getVariant());
+ Assertions.assertEquals("description", fastq2.getDescription());
+ Assertions.assertEquals("sequence", fastq2.getSequence());
+ Assertions.assertEquals("quality_", fastq2.getQuality());
+ Assertions.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq2.getVariant());
}
@Test
- public void testConstructorNullFastq()
+ void testConstructorNullFastq()
{
Assert.assertThrows(IllegalArgumentException.class, new ThrowingRunnable() {
@Override
@@ -70,13 +71,13 @@ public void run() {
}
@Test
- public void testBuildDefault()
+ void testBuildDefault()
{
try
{
FastqBuilder fastqBuilder = new FastqBuilder();
fastqBuilder.build();
- Assert.fail("build default expected IllegalStateException");
+ Assertions.fail("build default expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -85,7 +86,7 @@ public void testBuildDefault()
}
@Test
- public void testBuildNullDescription()
+ void testBuildNullDescription()
{
try
{
@@ -96,7 +97,7 @@ public void testBuildNullDescription()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build null description expected IllegalArgumentException");
+ Assertions.fail("build null description expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -105,7 +106,7 @@ public void testBuildNullDescription()
}
@Test
- public void testBuildNullSequence()
+ void testBuildNullSequence()
{
try
{
@@ -116,7 +117,7 @@ public void testBuildNullSequence()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build null sequence expected IllegalArgumentException");
+ Assertions.fail("build null sequence expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -125,7 +126,7 @@ public void testBuildNullSequence()
}
@Test
- public void testBuildNullAppendSequence()
+ void testBuildNullAppendSequence()
{
try
{
@@ -136,7 +137,7 @@ public void testBuildNullAppendSequence()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build null append sequence expected IllegalArgumentException");
+ Assertions.fail("build null append sequence expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -145,7 +146,7 @@ public void testBuildNullAppendSequence()
}
@Test
- public void testBuildNullQuality()
+ void testBuildNullQuality()
{
try
{
@@ -156,7 +157,7 @@ public void testBuildNullQuality()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build null quality expected IllegalArgumentException");
+ Assertions.fail("build null quality expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -165,7 +166,7 @@ public void testBuildNullQuality()
}
@Test
- public void testBuildNullAppendQuality()
+ void testBuildNullAppendQuality()
{
try
{
@@ -176,7 +177,7 @@ public void testBuildNullAppendQuality()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build null append quality expected IllegalArgumentException");
+ Assertions.fail("build null append quality expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -185,7 +186,7 @@ public void testBuildNullAppendQuality()
}
@Test
- public void testBuildNullVariant()
+ void testBuildNullVariant()
{
try
{
@@ -196,7 +197,7 @@ public void testBuildNullVariant()
.withVariant(null);
fastqBuilder.build();
- Assert.fail("build null variant expected IllegalArgumentException");
+ Assertions.fail("build null variant expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -205,7 +206,7 @@ public void testBuildNullVariant()
}
@Test
- public void testBuildMissingDescription()
+ void testBuildMissingDescription()
{
try
{
@@ -215,7 +216,7 @@ public void testBuildMissingDescription()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build missing description expected IllegalStateException");
+ Assertions.fail("build missing description expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -224,7 +225,7 @@ public void testBuildMissingDescription()
}
@Test
- public void testBuildMissingSequence()
+ void testBuildMissingSequence()
{
try
{
@@ -234,7 +235,7 @@ public void testBuildMissingSequence()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build missing sequence expected IllegalStateException");
+ Assertions.fail("build missing sequence expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -243,7 +244,7 @@ public void testBuildMissingSequence()
}
@Test
- public void testBuildMissingQuality()
+ void testBuildMissingQuality()
{
try
{
@@ -253,7 +254,7 @@ public void testBuildMissingQuality()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build missing quality expected IllegalStateException");
+ Assertions.fail("build missing quality expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -262,7 +263,7 @@ public void testBuildMissingQuality()
}
@Test
- public void testBuildDefaultVariant()
+ void testBuildDefaultVariant()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -270,16 +271,16 @@ public void testBuildDefaultVariant()
.withQuality("quality_");
Fastq fastq = fastqBuilder.build();
- Assert.assertEquals("description", fastqBuilder.getDescription());
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
- Assert.assertEquals("description", fastq.getDescription());
- Assert.assertEquals("sequence", fastq.getSequence());
- Assert.assertEquals("quality_", fastq.getQuality());
- Assert.assertEquals(FastqBuilder.DEFAULT_VARIANT, fastq.getVariant());
+ Assertions.assertEquals("description", fastqBuilder.getDescription());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals("description", fastq.getDescription());
+ Assertions.assertEquals("sequence", fastq.getSequence());
+ Assertions.assertEquals("quality_", fastq.getQuality());
+ Assertions.assertEquals(FastqBuilder.DEFAULT_VARIANT, fastq.getVariant());
}
@Test
- public void testBuild()
+ void testBuild()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -287,16 +288,16 @@ public void testBuild()
.withQuality("quality_")
.withVariant(FastqVariant.FASTQ_SOLEXA);
Fastq fastq = fastqBuilder.build();
- Assert.assertEquals("description", fastqBuilder.getDescription());
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
- Assert.assertEquals("description", fastq.getDescription());
- Assert.assertEquals("sequence", fastq.getSequence());
- Assert.assertEquals("quality_", fastq.getQuality());
- Assert.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
+ Assertions.assertEquals("description", fastqBuilder.getDescription());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals("description", fastq.getDescription());
+ Assertions.assertEquals("sequence", fastq.getSequence());
+ Assertions.assertEquals("quality_", fastq.getQuality());
+ Assertions.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
}
@Test
- public void testBuildAppendSequence()
+ void testBuildAppendSequence()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -305,16 +306,16 @@ public void testBuildAppendSequence()
.withQuality("quality_")
.withVariant(FastqVariant.FASTQ_SOLEXA);
Fastq fastq = fastqBuilder.build();
- Assert.assertEquals("description", fastqBuilder.getDescription());
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
- Assert.assertEquals("description", fastq.getDescription());
- Assert.assertEquals("sequence", fastq.getSequence());
- Assert.assertEquals("quality_", fastq.getQuality());
- Assert.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
+ Assertions.assertEquals("description", fastqBuilder.getDescription());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals("description", fastq.getDescription());
+ Assertions.assertEquals("sequence", fastq.getSequence());
+ Assertions.assertEquals("quality_", fastq.getQuality());
+ Assertions.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
}
@Test
- public void testBuildAppendQuality()
+ void testBuildAppendQuality()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -323,48 +324,48 @@ public void testBuildAppendQuality()
.appendQuality("ity_")
.withVariant(FastqVariant.FASTQ_SOLEXA);
Fastq fastq = fastqBuilder.build();
- Assert.assertEquals("description", fastqBuilder.getDescription());
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
- Assert.assertEquals("description", fastq.getDescription());
- Assert.assertEquals("sequence", fastq.getSequence());
- Assert.assertEquals("quality_", fastq.getQuality());
- Assert.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
+ Assertions.assertEquals("description", fastqBuilder.getDescription());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals("description", fastq.getDescription());
+ Assertions.assertEquals("sequence", fastq.getSequence());
+ Assertions.assertEquals("quality_", fastq.getQuality());
+ Assertions.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
}
@Test
- public void testBuildNonMatchingSequenceQualityScoreLengthsBothNull()
+ void testBuildNonMatchingSequenceQualityScoreLengthsBothNull()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
.withVariant(FastqVariant.FASTQ_SOLEXA);
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
}
@Test
- public void testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull()
+ void testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
.withQuality("0123")
.withVariant(FastqVariant.FASTQ_SOLEXA);
- Assert.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
}
@Test
- public void testBuildNonMatchingSequenceQualityScoreLengthsQualityNull()
+ void testBuildNonMatchingSequenceQualityScoreLengthsQualityNull()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
.withSequence("ACTG")
.withVariant(FastqVariant.FASTQ_SOLEXA);
- Assert.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
}
@Test
- public void testBuildNonMatchingSequenceQualityScoreLengths0()
+ void testBuildNonMatchingSequenceQualityScoreLengths0()
{
try
{
@@ -375,7 +376,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengths0()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build sequence length > quality length expected IllegalStateException");
+ Assertions.fail("build sequence length > quality length expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -384,7 +385,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengths0()
}
@Test
- public void testBuildNonMatchingSequenceQualityScoreLengths1()
+ void testBuildNonMatchingSequenceQualityScoreLengths1()
{
try
{
@@ -395,7 +396,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengths1()
.withVariant(FastqVariant.FASTQ_SOLEXA);
fastqBuilder.build();
- Assert.fail("build sequence length < quality length expected IllegalStateException");
+ Assertions.fail("build sequence length < quality length expected IllegalStateException");
}
catch (IllegalStateException e)
{
@@ -404,7 +405,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengths1()
}
@Test
- public void testBuildMultiple()
+ void testBuildMultiple()
{
FastqBuilder fastqBuilder = new FastqBuilder()
.withDescription("description")
@@ -414,12 +415,12 @@ public void testBuildMultiple()
for (int i = 0; i < 10; i++)
{
Fastq fastq = fastqBuilder.withSequence("sequence" + i).build();
- Assert.assertEquals("description", fastqBuilder.getDescription());
- Assert.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
- Assert.assertEquals("description", fastq.getDescription());
- Assert.assertEquals("sequence" + i, fastq.getSequence());
- Assert.assertEquals("quality__", fastq.getQuality());
- Assert.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
+ Assertions.assertEquals("description", fastqBuilder.getDescription());
+ Assertions.assertTrue(fastqBuilder.sequenceAndQualityLengthsMatch());
+ Assertions.assertEquals("description", fastq.getDescription());
+ Assertions.assertEquals("sequence" + i, fastq.getSequence());
+ Assertions.assertEquals("quality__", fastq.getQuality());
+ Assertions.assertEquals(FastqVariant.FASTQ_SOLEXA, fastq.getVariant());
}
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
index 62d7ee9368..31102b251d 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
@@ -21,25 +21,26 @@
package org.biojava.nbio.genome.io.fastq;
import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import org.junit.function.ThrowingRunnable;
/**
* Unit test for Fastq.
*/
-public final class FastqTest {
+final class FastqTest {
@Test
- public void testConstructor()
+ void testConstructor()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertNotNull(fastq);
+ Assertions.assertNotNull(fastq);
try
{
new Fastq(null, "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.fail("ctr(null description) expected IllegalArgumentException");
+ Assertions.fail("ctr(null description) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -48,7 +49,7 @@ public void testConstructor()
try
{
new Fastq("description", null, "quality_", FastqVariant.FASTQ_SANGER);
- Assert.fail("ctr(null sequence) expected IllegalArgumentException");
+ Assertions.fail("ctr(null sequence) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -57,7 +58,7 @@ public void testConstructor()
try
{
new Fastq("description", "sequence", null, FastqVariant.FASTQ_SANGER);
- Assert.fail("ctr(null quality) expected IllegalArgumentException");
+ Assertions.fail("ctr(null quality) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -66,7 +67,7 @@ public void testConstructor()
try
{
new Fastq("description", "sequence", "quality_", null);
- Assert.fail("ctr(null variant) expected IllegalArgumentException");
+ Assertions.fail("ctr(null variant) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -75,45 +76,45 @@ public void testConstructor()
}
@Test
- public void testDescription()
+ void testDescription()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertTrue(fastq.getDescription() != null);
- Assert.assertEquals("description", fastq.getDescription());
+ Assertions.assertTrue(fastq.getDescription() != null);
+ Assertions.assertEquals("description", fastq.getDescription());
}
@Test
- public void testSequence()
+ void testSequence()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertTrue(fastq.getSequence() != null);
- Assert.assertEquals("sequence", fastq.getSequence());
+ Assertions.assertTrue(fastq.getSequence() != null);
+ Assertions.assertEquals("sequence", fastq.getSequence());
}
@Test
- public void testQuality()
+ void testQuality()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertTrue(fastq.getQuality() != null);
- Assert.assertEquals("quality_", fastq.getQuality());
+ Assertions.assertTrue(fastq.getQuality() != null);
+ Assertions.assertEquals("quality_", fastq.getQuality());
}
@Test
- public void testVariant()
+ void testVariant()
{
Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertTrue(fastq.getVariant() != null);
- Assert.assertEquals(FastqVariant.FASTQ_SANGER, fastq.getVariant());
+ Assertions.assertTrue(fastq.getVariant() != null);
+ Assertions.assertEquals(FastqVariant.FASTQ_SANGER, fastq.getVariant());
}
@Test
- public void testBuilder()
+ void testBuilder()
{
- Assert.assertNotNull(Fastq.builder());
+ Assertions.assertNotNull(Fastq.builder());
}
@Test
- public void testBuilderNullFastq()
+ void testBuilderNullFastq()
{
Assert.assertThrows(IllegalArgumentException.class, new ThrowingRunnable() {
@Override
@@ -124,39 +125,39 @@ public void run() {
}
@Test
- public void testEquals()
+ void testEquals()
{
Fastq fastq0 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
Fastq fastq1 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertFalse(fastq0.equals(null));
- Assert.assertFalse(fastq1.equals(null));
- Assert.assertFalse(fastq0.equals(new Object()));
- Assert.assertFalse(fastq1.equals(new Object()));
- Assert.assertTrue(fastq0.equals(fastq0));
- Assert.assertTrue(fastq1.equals(fastq1));
- Assert.assertFalse(fastq0 == fastq1);
- Assert.assertFalse(fastq0.equals(fastq1));
- Assert.assertFalse(fastq1.equals(fastq0));
+ Assertions.assertFalse(fastq0.equals(null));
+ Assertions.assertFalse(fastq1.equals(null));
+ Assertions.assertFalse(fastq0.equals(new Object()));
+ Assertions.assertFalse(fastq1.equals(new Object()));
+ Assertions.assertTrue(fastq0.equals(fastq0));
+ Assertions.assertTrue(fastq1.equals(fastq1));
+ Assertions.assertFalse(fastq0 == fastq1);
+ Assertions.assertFalse(fastq0.equals(fastq1));
+ Assertions.assertFalse(fastq1.equals(fastq0));
}
@Test
- public void testHashCode()
+ void testHashCode()
{
Fastq fastq0 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
Fastq fastq1 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
- Assert.assertEquals(fastq0.hashCode(), fastq0.hashCode());
- Assert.assertEquals(fastq1.hashCode(), fastq1.hashCode());
+ Assertions.assertEquals(fastq0.hashCode(), fastq0.hashCode());
+ Assertions.assertEquals(fastq1.hashCode(), fastq1.hashCode());
if (fastq0.equals(fastq1))
{
- Assert.assertEquals(fastq0.hashCode(), fastq1.hashCode());
- Assert.assertEquals(fastq1.hashCode(), fastq0.hashCode());
+ Assertions.assertEquals(fastq0.hashCode(), fastq1.hashCode());
+ Assertions.assertEquals(fastq1.hashCode(), fastq0.hashCode());
}
if (fastq1.equals(fastq0))
{
- Assert.assertEquals(fastq0.hashCode(), fastq1.hashCode());
- Assert.assertEquals(fastq1.hashCode(), fastq0.hashCode());
+ Assertions.assertEquals(fastq0.hashCode(), fastq1.hashCode());
+ Assertions.assertEquals(fastq1.hashCode(), fastq0.hashCode());
}
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
index 469601e624..43672b517b 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
@@ -27,493 +27,340 @@
import org.biojava.nbio.core.sequence.features.QualityFeature;
import org.biojava.nbio.core.sequence.features.QuantityFeature;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+import java.util.stream.StreamSupport;
/**
* Unit test for FastqTools.
*/
-public final class FastqToolsTest {
+final class FastqToolsTest {
private final FastqBuilder builder = new FastqBuilder().withDescription("foo").withSequence("ACTG").withQuality("ZZZZ");
@Test
- public void testCreateDNASequence() throws CompoundNotFoundException
+ void testCreateDNASequence() throws CompoundNotFoundException
{
DNASequence sequence = FastqTools.createDNASequence(builder.build());
- Assert.assertNotNull(sequence);
+ Assertions.assertNotNull(sequence);
}
@Test
- public void testCreateDNASequenceNullFastq() throws CompoundNotFoundException
+ void testCreateDNASequenceNullFastq()
{
- try
- {
- FastqTools.createDNASequence(null);
- Assert.fail("createDNASequence(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createDNASequence(null));
}
@Test
- public void testCreateDNASequenceWithQualityScores() throws CompoundNotFoundException
+ void testCreateDNASequenceWithQualityScores() throws CompoundNotFoundException
{
DNASequence sequence = FastqTools.createDNASequenceWithQualityScores(builder.build());
- Assert.assertNotNull(sequence);
+ Assertions.assertNotNull(sequence);
List, NucleotideCompound>> features = sequence.getFeaturesByType("qualityScores");
- Assert.assertNotNull(features);
- Assert.assertEquals(1, features.size());
+ Assertions.assertNotNull(features);
+ Assertions.assertEquals(1, features.size());
QualityFeature, NucleotideCompound> qualityScores = (QualityFeature, NucleotideCompound>) features.get(0);
- Assert.assertEquals(sequence.getLength(), qualityScores.getQualities().size());
- Assert.assertEquals(sequence.getLength(), qualityScores.getLocations().getLength());
+ Assertions.assertEquals(sequence.getLength(), qualityScores.getQualities().size());
+ Assertions.assertEquals(sequence.getLength(), qualityScores.getLocations().getLength());
}
@Test
- public void testCreateDNASequenceWithQualityScoresNullFastq() throws CompoundNotFoundException
+ void testCreateDNASequenceWithQualityScoresNullFastq()
{
- try
- {
- FastqTools.createDNASequenceWithQualityScores(null);
- Assert.fail("createDNASequenceWithQualityScores(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createDNASequenceWithQualityScores(null));
}
@Test
- public void testCreateDNASequenceWithErrorProbabilies() throws CompoundNotFoundException
+ void testCreateDNASequenceWithErrorProbabilies() throws CompoundNotFoundException
{
DNASequence sequence = FastqTools.createDNASequenceWithErrorProbabilities(builder.build());
- Assert.assertNotNull(sequence);
+ Assertions.assertNotNull(sequence);
List, NucleotideCompound>> features = sequence.getFeaturesByType("errorProbabilities");
- Assert.assertNotNull(features);
- Assert.assertEquals(1, features.size());
+ Assertions.assertNotNull(features);
+ Assertions.assertEquals(1, features.size());
QuantityFeature, NucleotideCompound> errorProbabilities = (QuantityFeature, NucleotideCompound>) features.get(0);
- Assert.assertEquals(sequence.getLength(), errorProbabilities.getQuantities().size());
- Assert.assertEquals(sequence.getLength(), errorProbabilities.getLocations().getLength());
+ Assertions.assertEquals(sequence.getLength(), errorProbabilities.getQuantities().size());
+ Assertions.assertEquals(sequence.getLength(), errorProbabilities.getLocations().getLength());
}
@Test
- public void testCreateDNASequenceWithErrorProbabilitiesNullFastq() throws CompoundNotFoundException
+ void testCreateDNASequenceWithErrorProbabilitiesNullFastq()
{
- try
- {
- FastqTools.createDNASequenceWithErrorProbabilities(null);
- Assert.fail("createDNASequenceWithErrorProbabilities(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createDNASequenceWithErrorProbabilities(null));
}
@Test
- public void testCreateDNASequenceWithQualityScoresAndErrorProbabilities() throws CompoundNotFoundException
+ void testCreateDNASequenceWithQualityScoresAndErrorProbabilities() throws CompoundNotFoundException
{
DNASequence sequence = FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(builder.build());
- Assert.assertNotNull(sequence);
+ Assertions.assertNotNull(sequence);
List, NucleotideCompound>> qualityScoresFeatures = sequence.getFeaturesByType("qualityScores");
- Assert.assertNotNull(qualityScoresFeatures);
- Assert.assertEquals(1, qualityScoresFeatures.size());
+ Assertions.assertNotNull(qualityScoresFeatures);
+ Assertions.assertEquals(1, qualityScoresFeatures.size());
QualityFeature, NucleotideCompound> qualityScores = (QualityFeature, NucleotideCompound>) qualityScoresFeatures.get(0);
- Assert.assertEquals(sequence.getLength(), qualityScores.getQualities().size());
- Assert.assertEquals(sequence.getLength(), qualityScores.getLocations().getLength());
+ Assertions.assertEquals(sequence.getLength(), qualityScores.getQualities().size());
+ Assertions.assertEquals(sequence.getLength(), qualityScores.getLocations().getLength());
List, NucleotideCompound>> errorProbabilitiesFeatures = sequence.getFeaturesByType("errorProbabilities");
- Assert.assertNotNull(errorProbabilitiesFeatures);
- Assert.assertEquals(1, errorProbabilitiesFeatures.size());
+ Assertions.assertNotNull(errorProbabilitiesFeatures);
+ Assertions.assertEquals(1, errorProbabilitiesFeatures.size());
QuantityFeature, NucleotideCompound> errorProbabilities = (QuantityFeature, NucleotideCompound>) errorProbabilitiesFeatures.get(0);
- Assert.assertEquals(sequence.getLength(), errorProbabilities.getQuantities().size());
- Assert.assertEquals(sequence.getLength(), errorProbabilities.getLocations().getLength());
+ Assertions.assertEquals(sequence.getLength(), errorProbabilities.getQuantities().size());
+ Assertions.assertEquals(sequence.getLength(), errorProbabilities.getLocations().getLength());
}
@Test
- public void testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq() throws CompoundNotFoundException
+ void testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq()
{
- try
- {
- FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(null);
- Assert.fail("createDNASequenceWithQualityScoresAndErrorProbabilities(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(null));
}
@Test
- public void testCreateQualityScores()
+ void testCreateQualityScores()
{
Fastq fastq = builder.build();
QualityFeature, NucleotideCompound> qualityScores = FastqTools.createQualityScores(fastq);
- Assert.assertNotNull(qualityScores);
- Assert.assertEquals(fastq.getSequence().length(), qualityScores.getQualities().size());
+ Assertions.assertNotNull(qualityScores);
+ Assertions.assertEquals(fastq.getSequence().length(), qualityScores.getQualities().size());
}
@Test
- public void testCreateQualityScoresNullFastq()
+ void testCreateQualityScoresNullFastq()
{
- try
- {
- FastqTools.createQualityScores(null);
- Assert.fail("createQualityScores(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createQualityScores(null));
}
@Test
- public void testCreateErrorProbabilities()
+ void testCreateErrorProbabilities()
{
Fastq fastq = builder.build();
QuantityFeature, NucleotideCompound> errorProbabilities = FastqTools.createErrorProbabilities(fastq);
- Assert.assertNotNull(errorProbabilities);
- Assert.assertEquals(fastq.getSequence().length(), errorProbabilities.getQuantities().size());
+ Assertions.assertNotNull(errorProbabilities);
+ Assertions.assertEquals(fastq.getSequence().length(), errorProbabilities.getQuantities().size());
}
@Test
- public void testCreateErrorProbabilitiesNullFastq()
+ void testCreateErrorProbabilitiesNullFastq()
{
- try
- {
- FastqTools.createErrorProbabilities(null);
- Assert.fail("createErrorProbabilities(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.createErrorProbabilities(null));
}
@Test
- public void testQualityScores()
+ void testQualityScores()
{
Iterable qualityScores = FastqTools.qualityScores(builder.build());
- Assert.assertNotNull(qualityScores);
- int count = 0;
- for (Number qualityScore : qualityScores)
- {
- Assert.assertNotNull(qualityScore);
- count++;
- }
- Assert.assertEquals(4, count);
+ List scoresList = StreamSupport.stream(qualityScores.spliterator(), false)
+ .collect(Collectors.toList());
+ Assertions.assertAll(
+ () -> Assertions.assertEquals(4, scoresList.size()),
+ () -> Assertions.assertFalse(scoresList.contains(null))
+ );
}
@Test
- public void testQualityScoresNullFastq()
+ void testQualityScoresNullFastq()
{
- try
- {
- FastqTools.qualityScores(null);
- Assert.fail("qualityScores(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.qualityScores(null));
}
@Test
- public void testQualityScoresIntArray()
+ void testQualityScoresIntArray()
{
int[] qualityScores = new int[4];
FastqTools.qualityScores(builder.build(), qualityScores);
- for (int i = 0; i < 4; i++)
- {
- Assert.assertTrue(qualityScores[i] != 0);
- }
+
+ Assertions.assertTrue(Arrays.stream(qualityScores).allMatch(score -> score != 0), () ->
+ "Array contains zero at some position: " + Arrays.toString(qualityScores));
}
@Test
- public void testQualityScoresIntArrayNullFastq()
+ void testQualityScoresIntArrayNullFastq()
{
- try
- {
- FastqTools.qualityScores(null, new int[0]);
- Assert.fail("qualityScores(null, int[]) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.qualityScores(null, new int[0]));
}
@Test
- public void testQualityScoresNullIntArray()
+ void testQualityScoresNullIntArray()
{
- try
- {
- FastqTools.qualityScores(builder.build(), null);
- Assert.fail("qualityScores(fastq, null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.qualityScores(fastq, null));
}
@Test
- public void testQualityScoresQualityScoresTooSmall()
+ void testQualityScoresQualityScoresTooSmall()
{
- try
- {
- FastqTools.qualityScores(builder.build(), new int[3]);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.qualityScores(fastq, new int[3]));
}
@Test
- public void testQualityScoresQualityScoresTooLarge()
+ void testQualityScoresQualityScoresTooLarge()
{
- try
- {
- FastqTools.qualityScores(builder.build(), new int[5]);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.qualityScores(fastq, new int[5]));
}
@Test
- public void testErrorProbabilities()
+ void testErrorProbabilities()
{
Iterable errorProbabilities = FastqTools.errorProbabilities(builder.build());
- Assert.assertNotNull(errorProbabilities);
- int count = 0;
- for (Number errorProbability : errorProbabilities)
- {
- Assert.assertNotNull(errorProbability);
- count++;
- }
- Assert.assertEquals(4, count);
+ List scores = StreamSupport.stream(errorProbabilities.spliterator(), false)
+ .collect(Collectors.toList());
+
+ Assertions.assertNotNull(scores);
+ Assertions.assertEquals(4, scores.size());
+ Assertions.assertTrue(scores.stream().allMatch(Objects::nonNull));
}
@Test
- public void testErrorProbabilitiesNullFastq()
+ void testErrorProbabilitiesNullFastq()
{
- try
- {
- FastqTools.errorProbabilities(null);
- Assert.fail("errorProbabilities(null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.errorProbabilities(null));
}
@Test
- public void testErrorProbabilitiesDoubleArray()
+ void testErrorProbabilitiesDoubleArray()
{
double[] errorProbabilities = new double[4];
FastqTools.errorProbabilities(builder.build(), errorProbabilities);
- for (int i = 0; i < 0; i++)
- {
- Assert.assertTrue(errorProbabilities[i] > 0.0d);
- }
+ Assertions.assertTrue(
+ Arrays.stream(errorProbabilities).allMatch(p -> p > 0.0),
+ () -> "Expected all probabilities to be > 0.0, but got: " + Arrays.toString(errorProbabilities)
+ );
}
@Test
- public void testErrorProbabilitiesDoubleArrayNullFastq()
+ void testErrorProbabilitiesDoubleArrayNullFastq()
{
- try
- {
- FastqTools.errorProbabilities(null, new double[0]);
- Assert.fail("errorProbabilities(null, double[]) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.errorProbabilities(null, new double[0]));
}
@Test
- public void testErrorProbabilitiesNullErrorProbabilities()
+ void testErrorProbabilitiesNullErrorProbabilities()
{
- try
- {
- FastqTools.errorProbabilities(builder.build(), null);
- Assert.fail("errorProbabilities(fastq, null) expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.errorProbabilities(fastq, null));
}
@Test
- public void testErrorProbabilitiesErrorProbabilitiesTooSmall()
+ void testErrorProbabilitiesErrorProbabilitiesTooSmall()
{
- try
- {
- FastqTools.errorProbabilities(builder.build(), new double[3]);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.errorProbabilities(fastq, new double[3]));
}
@Test
- public void testErrorProbabilitiesErrorProbabilitiesTooLarge()
+ void testErrorProbabilitiesErrorProbabilitiesTooLarge()
{
- try
- {
- FastqTools.errorProbabilities(builder.build(), new double[5]);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.errorProbabilities(fastq, new double[5]));
}
@Test
- public void testConvertNullFastq()
+ void testConvertNullFastq()
{
- try
- {
- FastqTools.convert(null, FastqVariant.FASTQ_SANGER);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.convert(null, FastqVariant.FASTQ_SANGER));
}
@Test
- public void testConvertNullVariant()
+ void testConvertNullVariant()
{
- try
- {
- FastqTools.convert(builder.build(), null);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.convert(fastq, null));
}
@Test
- public void testConvertSameVariant()
+ void testConvertSameVariant()
{
Fastq fastq = builder.build();
- Assert.assertEquals(fastq, FastqTools.convert(fastq, fastq.getVariant()));
+ Assertions.assertEquals(fastq, FastqTools.convert(fastq, fastq.getVariant()));
}
@Test
- public void testConvertQualitiesNullFastq()
+ void testConvertQualitiesNullFastq()
{
- try
- {
- FastqTools.convertQualities(null, FastqVariant.FASTQ_SANGER);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.convertQualities(null, FastqVariant.FASTQ_SANGER));
}
@Test
- public void testConvertQualitiesNullVariant()
+ void testConvertQualitiesNullVariant()
{
- try
- {
- FastqTools.convertQualities(builder.build(), null);
- Assert.fail("expected IllegalArgumentException");
- }
- catch (IllegalArgumentException e)
- {
- // expected
- }
+ Fastq fastq = builder.build();
+ Assertions.assertThrows(IllegalArgumentException.class, () -> FastqTools.convertQualities(fastq, null));
}
@Test
- public void testConvertQualitiesSameVariant()
+ void testConvertQualitiesSameVariant()
{
Fastq fastq = builder.build();
- Assert.assertEquals(fastq.getQuality(), FastqTools.convertQualities(fastq, fastq.getVariant()));
+ Assertions.assertEquals(fastq.getQuality(), FastqTools.convertQualities(fastq, fastq.getVariant()));
}
@Test
- public void testConvertQualitiesSangerToSolexa()
+ void testConvertQualitiesSangerToSolexa()
{
Fastq fastq = builder.build();
- Assert.assertEquals("yyyy", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SOLEXA));
+ Assertions.assertEquals("yyyy", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SOLEXA));
}
@Test
- public void testConvertQualitiesSangerToIllumina()
+ void testConvertQualitiesSangerToIllumina()
{
Fastq fastq = builder.build();
- Assert.assertEquals("yyyy", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_ILLUMINA));
+ Assertions.assertEquals("yyyy", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_ILLUMINA));
}
@Test
- public void testConvertQualitiesSolexaToSanger()
+ void testConvertQualitiesSolexaToSanger()
{
Fastq fastq = builder.withVariant(FastqVariant.FASTQ_SOLEXA).build();
- Assert.assertEquals(";;;;", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SANGER));
+ Assertions.assertEquals(";;;;", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SANGER));
}
@Test
- public void testConvertQualitiesIlluminaToSanger()
+ void testConvertQualitiesIlluminaToSanger()
{
Fastq fastq = builder.withVariant(FastqVariant.FASTQ_ILLUMINA).build();
- Assert.assertEquals(";;;;", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SANGER));
+ Assertions.assertEquals(";;;;", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SANGER));
}
@Test
- public void testConvertQualitiesSolexaToIllumina()
+ void testConvertQualitiesSolexaToIllumina()
{
Fastq fastq = builder.withVariant(FastqVariant.FASTQ_SOLEXA).build();
- Assert.assertEquals("ZZZZ", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_ILLUMINA));
+ Assertions.assertEquals("ZZZZ", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_ILLUMINA));
}
@Test
- public void testConvertQualitiesIlluminaToSolexa()
+ void testConvertQualitiesIlluminaToSolexa()
{
Fastq fastq = builder.withVariant(FastqVariant.FASTQ_ILLUMINA).build();
- Assert.assertEquals("ZZZZ", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SOLEXA));
+ Assertions.assertEquals("ZZZZ", FastqTools.convertQualities(fastq, FastqVariant.FASTQ_SOLEXA));
}
@Test
- public void testToList()
+ void testToList()
{
- List list = new ArrayList();
- Assert.assertSame(list, FastqTools.toList(list));
+ List list = new ArrayList<>();
+ Assertions.assertSame(list, FastqTools.toList(list));
}
@Test
- public void testToListNotAList()
+ void testToListNotAList()
{
- Collection collection = new HashSet();
- Assert.assertTrue(FastqTools.toList(collection) instanceof List);
- Assert.assertNotSame(collection, FastqTools.toList(collection));
+ Collection collection = new HashSet<>();
+ Assertions.assertTrue(FastqTools.toList(collection) instanceof List);
+ Assertions.assertNotSame(collection, FastqTools.toList(collection));
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
index f8b0855a8e..a47896b714 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
@@ -22,66 +22,66 @@
import static org.biojava.nbio.genome.io.fastq.FastqVariant.*;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
/**
* Unit test for FastqVariant.
*/
-public final class FastqVariantTest {
+final class FastqVariantTest {
@Test
- public void testDescription()
+ void testDescription()
{
for (FastqVariant variant : values())
{
- Assert.assertNotNull(variant.getDescription());
+ Assertions.assertNotNull(variant.getDescription());
}
}
@Test
- public void testIsSanger()
+ void testIsSanger()
{
- Assert.assertTrue(FASTQ_SANGER.isSanger());
- Assert.assertFalse(FASTQ_SOLEXA.isSanger());
- Assert.assertFalse(FASTQ_ILLUMINA.isSanger());
+ Assertions.assertTrue(FASTQ_SANGER.isSanger());
+ Assertions.assertFalse(FASTQ_SOLEXA.isSanger());
+ Assertions.assertFalse(FASTQ_ILLUMINA.isSanger());
}
@Test
- public void testIsSolexa()
+ void testIsSolexa()
{
- Assert.assertFalse(FASTQ_SANGER.isSolexa());
- Assert.assertTrue(FASTQ_SOLEXA.isSolexa());
- Assert.assertFalse(FASTQ_ILLUMINA.isSolexa());
+ Assertions.assertFalse(FASTQ_SANGER.isSolexa());
+ Assertions.assertTrue(FASTQ_SOLEXA.isSolexa());
+ Assertions.assertFalse(FASTQ_ILLUMINA.isSolexa());
}
@Test
- public void testIsIllumina()
+ void testIsIllumina()
{
- Assert.assertFalse(FASTQ_SANGER.isIllumina());
- Assert.assertFalse(FASTQ_SOLEXA.isIllumina());
- Assert.assertTrue(FASTQ_ILLUMINA.isIllumina());
+ Assertions.assertFalse(FASTQ_SANGER.isIllumina());
+ Assertions.assertFalse(FASTQ_SOLEXA.isIllumina());
+ Assertions.assertTrue(FASTQ_ILLUMINA.isIllumina());
}
@Test
- public void testParseFastqVariant()
+ void testParseFastqVariant()
{
- Assert.assertEquals(null, parseFastqVariant(null));
- Assert.assertEquals(null, parseFastqVariant(""));
- Assert.assertEquals(null, parseFastqVariant("not a valid FASTQ variant"));
- Assert.assertEquals(FASTQ_SANGER, parseFastqVariant("FASTQ_SANGER"));
- Assert.assertEquals(FASTQ_SANGER, parseFastqVariant("fastq-sanger"));
+ Assertions.assertEquals(null, parseFastqVariant(null));
+ Assertions.assertEquals(null, parseFastqVariant(""));
+ Assertions.assertEquals(null, parseFastqVariant("not a valid FASTQ variant"));
+ Assertions.assertEquals(FASTQ_SANGER, parseFastqVariant("FASTQ_SANGER"));
+ Assertions.assertEquals(FASTQ_SANGER, parseFastqVariant("fastq-sanger"));
}
@Test
- public void testQualityLessThanMinimumQualityScore()
+ void testQualityLessThanMinimumQualityScore()
{
for (FastqVariant variant : values())
{
try
{
variant.quality(variant.minimumQualityScore() - 1);
- Assert.fail("expected IllegalArgumentException");
+ Assertions.fail("expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -91,14 +91,14 @@ public void testQualityLessThanMinimumQualityScore()
}
@Test
- public void testQualityMoreThanMaximumQualityScore()
+ void testQualityMoreThanMaximumQualityScore()
{
for (FastqVariant variant : values())
{
try
{
variant.quality(variant.maximumQualityScore() + 1);
- Assert.fail("expected IllegalArgumentException");
+ Assertions.fail("expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -108,13 +108,13 @@ public void testQualityMoreThanMaximumQualityScore()
}
@Test
- public void testQualityQualityScoreRoundTrip()
+ void testQualityQualityScoreRoundTrip()
{
for (FastqVariant variant : values())
{
for (int i = variant.minimumQualityScore(); i < (variant.maximumQualityScore() + 1); i++)
{
- Assert.assertEquals(i, variant.qualityScore(variant.quality(i)));
+ Assertions.assertEquals(i, variant.qualityScore(variant.quality(i)));
}
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
index d7b0a8b9d2..1d2adf76b6 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
@@ -20,8 +20,8 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
-import static org.junit.Assert.*;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.InputStream;
@@ -31,7 +31,7 @@
/**
* Unit test for IlluminaFastqReader.
*/
-public final class IlluminaFastqReaderTest
+final class IlluminaFastqReaderTest
extends AbstractFastqReaderTest
{
@@ -59,119 +59,119 @@ public FastqWriter createFastqWriter()
}
@Test
- public void testValidateDescription() throws Exception
+ void testValidateDescription() throws Exception
{
IlluminaFastqReader reader = new IlluminaFastqReader();
URL invalidDescription = getClass().getResource("illumina-invalid-description.fastq");
try
{
reader.read(invalidDescription);
- fail("read(invalidDescription) expected IOException");
+ Assertions.fail("read(invalidDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ Assertions.assertTrue(e.getMessage().contains("description must begin with a '@' character"));
}
}
@Test
- public void testValidateRepeatDescription() throws Exception
+ void testValidateRepeatDescription() throws Exception
{
IlluminaFastqReader reader = new IlluminaFastqReader();
URL invalidRepeatDescription = getClass().getResource("illumina-invalid-repeat-description.fastq");
try
{
reader.read(invalidRepeatDescription);
- fail("read(invalidRepeatDescription) expected IOException");
+ Assertions.fail("read(invalidRepeatDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ Assertions.assertTrue(e.getMessage().contains("repeat description must match description"));
}
}
@Test
- public void testWrappingAsIllumina() throws Exception
+ void testWrappingAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_as_illumina.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(3, count);
+ Assertions.assertEquals(3, count);
inputStream.close();
}
@Test
- public void testFullRangeAsIllumina() throws Exception
+ void testFullRangeAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("illumina_full_range_as_illumina.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(2, count);
+ Assertions.assertEquals(2, count);
inputStream.close();
}
@Test
- public void testMiscDnaAsIllumina() throws Exception
+ void testMiscDnaAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_as_illumina.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testMiscRnaAsIllumina() throws Exception
+ void testMiscRnaAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_as_illumina.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testLongReadsAsIllumina() throws Exception
+ void testLongReadsAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_as_illumina.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(10, count);
+ Assertions.assertEquals(10, count);
inputStream.close();
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriterTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriterTest.java
index c9701595fa..384e204ff0 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriterTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriterTest.java
@@ -21,12 +21,12 @@
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
/**
* Unit test for IlluminaFastqWriter.
*/
-public final class IlluminaFastqWriterTest
+final class IlluminaFastqWriterTest
extends AbstractFastqWriterTest
{
@@ -48,7 +48,7 @@ public Fastq createFastq()
}
@Test
- public void testConvertNotIlluminaVariant() throws Exception
+ void testConvertNotIlluminaVariant() throws Exception
{
IlluminaFastqWriter writer = new IlluminaFastqWriter();
Appendable appendable = new StringBuilder();
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
index af6f67319f..3e99a4cdc8 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
@@ -20,18 +20,17 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
-import static org.junit.Assert.*;
-
/**
* Unit test for SangerFastqReader.
*/
-public final class SangerFastqReaderTest
+final class SangerFastqReaderTest
extends AbstractFastqReaderTest
{
@@ -65,197 +64,197 @@ public void testValidateDescription() throws Exception
try
{
reader.read(invalidDescription);
- fail("read(invalidDescription) expected IOException");
+ Assertions.fail("read(invalidDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ Assertions.assertTrue(e.getMessage().contains("description must begin with a '@' character"));
}
}
@Test
- public void testValidateRepeatDescription() throws Exception
+ void testValidateRepeatDescription() throws Exception
{
SangerFastqReader reader = new SangerFastqReader();
URL invalidRepeatDescription = getClass().getResource("sanger-invalid-repeat-description.fastq");
try
{
reader.read(invalidRepeatDescription);
- fail("read(invalidRepeatDescription) expected IOException");
+ Assertions.fail("read(invalidRepeatDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ Assertions.assertTrue(e.getMessage().contains("repeat description must match description"));
}
}
@Test
- public void testWrappingOriginal() throws Exception
+ void testWrappingOriginal() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_original_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(3, count);
+ Assertions.assertEquals(3, count);
inputStream.close();
}
@Test
- public void testWrappingAsSanger() throws Exception
+ void testWrappingAsSanger() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_as_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(3, count);
+ Assertions.assertEquals(3, count);
inputStream.close();
}
@Test
- public void testFullRangeOriginal() throws Exception
+ void testFullRangeOriginal() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("sanger_full_range_original_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(2, count);
+ Assertions.assertEquals(2, count);
inputStream.close();
}
@Test
- public void testFullRangeAsSanger() throws Exception
+ void testFullRangeAsSanger() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("sanger_full_range_as_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(2, count);
+ Assertions.assertEquals(2, count);
inputStream.close();
}
@Test
- public void testMiscDnaOriginal() throws Exception
+ void testMiscDnaOriginal() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_original_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testMiscDnaAsSanger() throws Exception
+ void testMiscDnaAsSanger() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_as_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testMiscRnaOriginal() throws Exception
+ void testMiscRnaOriginal() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_original_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testMiscRnaAsSanger() throws Exception
+ void testMiscRnaAsSanger() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_as_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testLongReadsOriginal() throws Exception
+ void testLongReadsOriginal() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_original_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(10, count);
+ Assertions.assertEquals(10, count);
inputStream.close();
}
@Test
- public void testLongReadsAsSanger() throws Exception
+ void testLongReadsAsSanger() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_as_sanger.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(10, count);
+ Assertions.assertEquals(10, count);
inputStream.close();
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqWriterTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqWriterTest.java
index f94db84e0a..fcb1638c71 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqWriterTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqWriterTest.java
@@ -21,12 +21,12 @@
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
/**
* Unit test for SangerFastqWriter.
*/
-public final class SangerFastqWriterTest
+final class SangerFastqWriterTest
extends AbstractFastqWriterTest
{
@@ -48,7 +48,7 @@ public Fastq createFastq()
}
@Test
- public void testConvertNotSangerVariant() throws Exception
+ void testConvertNotSangerVariant() throws Exception
{
SangerFastqWriter writer = new SangerFastqWriter();
Appendable appendable = new StringBuilder();
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
index 5f6f041c84..cd87c53dc6 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
@@ -20,19 +20,18 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
-import static org.junit.Assert.*;
-
/**
* Unit test for SolexaFastqReader.
*/
-public final class SolexaFastqReaderTest
+final class SolexaFastqReaderTest
extends AbstractFastqReaderTest
{
@@ -60,119 +59,119 @@ public FastqWriter createFastqWriter()
}
@Test
- public void testValidateDescription() throws Exception
+ void testValidateDescription() throws Exception
{
SolexaFastqReader reader = new SolexaFastqReader();
URL invalidDescription = getClass().getResource("solexa-invalid-description.fastq");
try
{
reader.read(invalidDescription);
- fail("read(invalidDescription) expected IOException");
+ Assertions.fail("read(invalidDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ Assertions.assertTrue(e.getMessage().contains("description must begin with a '@' character"));
}
}
@Test
- public void testValidateRepeatDescription() throws Exception
+ void testValidateRepeatDescription() throws Exception
{
SolexaFastqReader reader = new SolexaFastqReader();
URL invalidRepeatDescription = getClass().getResource("solexa-invalid-repeat-description.fastq");
try
{
reader.read(invalidRepeatDescription);
- fail("read(invalidRepeatDescription) expected IOException");
+ Assertions.fail("read(invalidRepeatDescription) expected IOException");
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ Assertions.assertTrue(e.getMessage().contains("repeat description must match description"));
}
}
@Test
- public void testWrappingAsSolexa() throws Exception
+ void testWrappingAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_as_solexa.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(3, count);
+ Assertions.assertEquals(3, count);
inputStream.close();
}
@Test
- public void testFullRangeAsSolexa() throws Exception
+ void testFullRangeAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("solexa_full_range_as_solexa.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(2, count);
+ Assertions.assertEquals(2, count);
inputStream.close();
}
@Test
- public void testMiscDnaAsSolexa() throws Exception
+ void testMiscDnaAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_as_solexa.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testMiscRnaAsSolexa() throws Exception
+ void testMiscRnaAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_as_solexa.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(4, count);
+ Assertions.assertEquals(4, count);
inputStream.close();
}
@Test
- public void testLongReadsAsSolexa() throws Exception
+ void testLongReadsAsSolexa() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_as_solexa.fastq");
Iterable iterable = reader.read(inputStream);
- assertNotNull(iterable);
+ Assertions.assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
- assertNotNull(f);
+ Assertions.assertNotNull(f);
count++;
}
- assertEquals(10, count);
+ Assertions.assertEquals(10, count);
inputStream.close();
}
}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqWriterTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqWriterTest.java
index 2f2011e849..0927bf0cff 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqWriterTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqWriterTest.java
@@ -21,12 +21,12 @@
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
/**
* Unit test for SolexaFastqWriter.
*/
-public final class SolexaFastqWriterTest
+final class SolexaFastqWriterTest
extends AbstractFastqWriterTest
{
@@ -48,7 +48,7 @@ public Fastq createFastq()
}
@Test
- public void testConvertNotSolexaVariant() throws Exception
+ void testConvertNotSolexaVariant() throws Exception
{
SolexaFastqWriter writer = new SolexaFastqWriter();
Appendable appendable = new StringBuilder();
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
index a80f44a43d..02d49d3177 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
@@ -20,8 +20,8 @@
*/
package org.biojava.nbio.genome.io.fastq;
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
import java.io.StringReader;
@@ -29,10 +29,10 @@
/**
* Unit test for StreamingFastqParser.
*/
-public class StreamingFastqParserTest {
+class StreamingFastqParserTest {
@Test
- public void testStreamNullReadable() throws Exception
+ void testStreamNullReadable() throws Exception
{
try
{
@@ -42,7 +42,7 @@ public void fastq(final Fastq fastq) {
// empty
}
});
- Assert.fail("stream(null,,) expected IllegalArgumentException");
+ Assertions.fail("stream(null,,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -51,7 +51,7 @@ public void fastq(final Fastq fastq) {
}
@Test
- public void testStreamNullVariant() throws Exception
+ void testStreamNullVariant() throws Exception
{
try
{
@@ -62,7 +62,7 @@ public void fastq(final Fastq fastq) {
// empty
}
});
- Assert.fail("stream(null,,) expected IllegalArgumentException");
+ Assertions.fail("stream(null,,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{
@@ -71,13 +71,13 @@ public void fastq(final Fastq fastq) {
}
@Test
- public void testStreamNullListener() throws Exception
+ void testStreamNullListener() throws Exception
{
try
{
final String input = "";
StreamingFastqParser.stream(new StringReader(input), FastqVariant.FASTQ_SANGER, null);
- Assert.fail("stream(null,,) expected IllegalArgumentException");
+ Assertions.fail("stream(null,,) expected IllegalArgumentException");
}
catch (IllegalArgumentException e)
{