new unit test for stockholm file parsing

andreasprlic · andreasprlic · commit 3f87f0671969 · 2012-11-09T01:21:45.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9836 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/test/java/org/biojava3/alignment/io/TestStockholmParser.java b/biojava3-alignment/src/test/java/org/biojava3/alignment/io/TestStockholmParser.java
@@ -0,0 +1,75 @@
+package org.biojava3.alignment.io;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.zip.GZIPInputStream;
+
+import org.biojava3.core.sequence.template.AbstractSequence;
+
+
+import junit.framework.TestCase;
+
+public class TestStockholmParser extends TestCase {
+
+//	public void testStockholmParser(){
+//
+//		InputStream inStream = this.getClass().getResourceAsStream("/test.sth");
+//
+//		StockholmFileParser fileParser = new StockholmFileParser();
+//
+//		BufferedReader buf;
+//		if (inStream == null) {
+//			fail("input stream is null!");
+//		}
+//
+//		buf = new BufferedReader(new InputStreamReader(inStream));
+//
+//		try {
+//			StockholmStructure data = fileParser.parseFile(buf);					
+//			System.out.println(data);
+//
+//			assertTrue(data.getBioSequences().size()==5);
+//
+//			AbstractSequence<?> seq = data.getBioSequences().get(0);
+//			assertTrue(seq != null );
+//
+//			assertEquals(seq.getSequenceAsString(),"MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS");
+//
+//		} catch (Exception e) {
+//
+//			e.printStackTrace();
+//			fail(e.getMessage());
+//		}
+//
+//
+//	}
+
+	public void testPiwi(){
+		try {
+			InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/piwi.sth.gz"));
+
+			assertNotNull(inStream);
+
+			StockholmFileParser fileParser = new StockholmFileParser();
+
+			StockholmStructure data = fileParser.parse(inStream);					
+			
+			assertTrue("Did not get enough sequences!", data.getBioSequences().size()==20);
+
+			AbstractSequence<?> seq = data.getBioSequences().get(0);
+			assertTrue(seq != null );
+			
+			assertTrue(seq.getSequenceAsString().length() > 20);
+
+		} catch (Exception e) {
+
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
+
+
+	}
+
+}
