Add copy constructor to FastqBuilder.

heuermh · heuermh · commit 02b0ece17db3 · 2021-02-22T09:48:37.000-06:00
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java
@@ -145,4 +145,19 @@ public static final FastqBuilder builder()
 	{
 		return new FastqBuilder();
 	}
+
+	/**
+	 * Create and return a new FastqBuilder configured from the
+	 * specified FASTQ formatted sequence.
+	 * The FastqBuilder will not be null.
+	 *
+	 * @since 6.0.0
+	 * @param fastq FASTQ formatted sequence, must not be null
+	 * @return a new FastqBuilder configured from the specified FASTQ
+	 *    formatted sequence
+	 */
+	public static final FastqBuilder builder(final Fastq fastq)
+	{
+		return new FastqBuilder(fastq);
+	}
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java
@@ -51,6 +51,25 @@ public FastqBuilder()
 		// empty
 	}
 
+	/**
+	 * Create a new FASTQ formatted sequence builder configured
+	 * from the specified FASTQ formatted sequence.
+	 *
+	 * @since 6.0.0
+	 * @param fastq FASTQ formatted sequence, must not be null
+	 */
+	public FastqBuilder(final Fastq fastq)
+	{
+		if (fastq == null)
+		{
+			throw new IllegalArgumentException("fastq must not be null");
+		}
+		withDescription(fastq.getDescription());
+		withSequence(fastq.getSequence());
+		withQuality(fastq.getQuality());
+		withVariant(fastq.getVariant());
+	}
+
 
 	/**
 	 * Return the description for this FASTQ formatted sequence builder.
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
@@ -36,6 +36,41 @@ public void testConstructor()
 		Assert.assertNotNull(fastqBuilder);
 	}
 
+	@Test
+	public void testConstructorFastq()
+	{
+		FastqBuilder fastqBuilder = new FastqBuilder()
+			.withDescription("description")
+			.withSequence("sequence")
+			.withQuality("quality_")
+			.withVariant(FastqVariant.FASTQ_SOLEXA);
+
+		Fastq fastq = fastqBuilder.build();
+
+		FastqBuilder fastqBuilder2 = new FastqBuilder(fastq);
+		Assert.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());
+	}
+
+	@Test
+	public void testConstructorNullFastq()
+	{
+		try
+		{
+			new FastqBuilder(null);
+			Assert.fail("builder(null) expected IllegalArgumentException");
+		}
+		catch (IllegalArgumentException e)
+		{
+			// expected
+		}
+	}
+
 	@Test
 	public void testBuildDefault()
 	{
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
@@ -111,6 +111,20 @@ public void testBuilder()
 		Assert.assertNotNull(Fastq.builder());
 	}
 
+	@Test
+	public void testBuilderNullFastq()
+	{
+		try
+		{
+			Fastq.builder(null);
+			Assert.fail("builder(null) expected IllegalArgumentException");
+		}
+		catch (IllegalArgumentException e)
+		{
+			// expected
+		}
+	}
+
 	@Test
 	public void testEquals()
 	{
