import java.io.IOException;
import java.net.MalformedURLException;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.Test;
public class ScoreMatrixFileTest
{
+ @AfterMethod(alwaysRun=true)
+ public void tearDownAfterTest()
+ {
+ ScoreModels.getInstance().reset();
+ }
+
/**
* Test a successful parse of a (small) score matrix file
*
assertNull(sm.getDescription());
assertTrue(sm.isDNA());
assertFalse(sm.isProtein());
+ assertEquals(sm.getMinimumScore(), 1.1f);
assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
assertEquals(sm.getPairwiseScore('a', 't'), 1.4f);
assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f);
assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f);
- assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
- assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
+ // X (upper) and '.' unmapped - get minimum score
+ assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f);
+ assertEquals(sm.getPairwiseScore('A', '.'), 1.1f);
assertEquals(sm.getPairwiseScore('-', '-'), 7.6f);
assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
}
assertFalse(sm.isDNA());
assertTrue(sm.isProtein());
assertEquals(20, sm.getSize());
- assertEquals(sm.getGapIndex(), -1);
assertEquals(sm.getPairwiseScore('A', 'A'), 7f);
assertEquals(sm.getPairwiseScore('A', 'R'), -3f);
assertNotNull(sm);
assertEquals(sm.getSize(), 3);
- assertEquals(sm.getGapIndex(), -1);
assertEquals(sm.getName(), "MyTest");
assertEquals(sm.getDescription(), "My description");
assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
public void testParse_ncbiFormat() throws MalformedURLException,
IOException
{
- assertNull(ScoreModels.getInstance().forName("MyNewTest"));
+ assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null));
String data = "ScoreMatrix MyNewTest\n" + "\tA\tB\tC\n"
+ "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
parser.parse();
- ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().forName(
- "MyNewTest");
+ ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().getScoreModel(
+ "MyNewTest", null);
assertNotNull(sm);
assertEquals(sm.getName(), "MyNewTest");
assertEquals(parser.getMatrixName(), "MyNewTest");