biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java

andreasprlic · andreasprlic · commit 0ddff0058e4c · 2013-10-13T11:47:24.000-07:00
diff --git a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java
@@ -0,0 +1,58 @@
+/**
+ * 
+ */
+package org.biojava3.core.sequence.io;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+
+import org.biojava3.core.sequence.DNASequence;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * @author mckeee1
+ * 
+ */
+public class GenbankWriterTest {
+
+	public GenbankWriterTest() {}
+	
+	@BeforeClass
+	public static void setUpClass() throws Exception {}
+
+	@AfterClass
+	public static void tearDownClass() throws Exception {}
+
+	@Before
+	public void setUp() {}
+
+	@After
+	public void tearDown() {}
+	
+	@Test
+	public void testProcess() throws Exception {
+		File dnaFile = new File("src/test/resources/NM_000266.gb");
+		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( dnaFile );
+		ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
+		ArrayList<DNASequence> seqs = new ArrayList<DNASequence>();
+		for(DNASequence seq : dnaSequences.values()) {
+			seqs.add(seq);
+		}
+		GenbankWriterHelper.writeNucleotideSequence(fragwriter, seqs,
+				GenbankWriterHelper.LINEAR_DNA);
+		//System.out.println(fragwriter.toString());
+		ByteArrayInputStream fragreader = new ByteArrayInputStream(fragwriter.toByteArray());
+		dnaSequences = GenbankReaderHelper.readGenbankDNASequence( fragreader );
+		fragwriter.close();
+		assertEquals(seqs.get(0).getSequenceAsString(),dnaSequences.values().iterator().next().getSequenceAsString());
+	}
+}
