package protein;
import org.apache.hadoop.io.Text;
import protein.LocalAlignment;
import serial.SerialLocalAlignment;
import junit.framework.TestCase;
/** Tests for {@link LocalAlignment}. */
public class LocalAlignmentTest extends TestCase {
/** Test for {@link LocalAlignment#getLocalAlignment(Text, Text, int, int, int, int)}. */
public void testGetLocalAlignment() {
String a = ">1 asdfasdfasdf";
String b = ">2 asdfzzzzasdfqiwjkre";
Text aText = new Text(a);
Text bText = new Text(b);
LocalAlignment localHadoop = LocalAlignment.getLocalAlignment(aText, bText, 10, -5, -5, -2);
SerialLocalAlignment localSerial = SerialLocalAlignment.align(a, b, 10, -5, -5, -2);
assertEquals(localSerial.getScore(), localHadoop.getScore());
assertEquals(localSerial.getDistance(), localHadoop.getDistance());
assertNotSame(0, localHadoop.getScore());
localHadoop = LocalAlignment.getLocalAlignment(bText, aText, 10, -5, -5, -2);
assertEquals(localSerial.getScore(), localHadoop.getScore());
assertEquals(localSerial.getDistance(), localHadoop.getDistance());
assertNotSame(0, localHadoop.getScore());
System.out.println(localHadoop.getScore() + " " + localHadoop.getDistance());
}
}