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package org.biojava.bio.dist;
import junit.framework.AssertionFailedError;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.IllegalSymbolException;
/**
* Tests that check whether translated distributions behave properly.
*
* @author Thomas Down
* @since 1.4
*/
public class TranslatedDistributionTest extends TestCase {
private double a = 0.1;
private double g = 0.3;
private double c = 0.25;
private double t = 0.35;
private double delta = 0.000001;
public TranslatedDistributionTest(String name) {
super(name);
}
public void testWeights()
throws Exception
{
try {
Distribution d1 = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
d1.setWeight(DNATools.a(), a);
d1.setWeight(DNATools.c(), c);
d1.setWeight(DNATools.g(), g);
d1.setWeight(DNATools.t(), t);
Distribution d2 = new TranslatedDistribution(
DNATools.complementTable(),
d1,
DistributionFactory.DEFAULT
);
assertEquals(a, d2.getWeight(DNATools.t()), delta);
assertEquals(c, d2.getWeight(DNATools.g()), delta);
assertEquals(g, d2.getWeight(DNATools.c()), delta);
assertEquals(t, d2.getWeight(DNATools.a()), delta);
d1.setWeight(DNATools.a(), t);
d1.setWeight(DNATools.c(), g);
d1.setWeight(DNATools.g(), c);
d1.setWeight(DNATools.t(), a);
assertEquals(a, d2.getWeight(DNATools.a()), delta);
assertEquals(c, d2.getWeight(DNATools.c()), delta);
assertEquals(g, d2.getWeight(DNATools.g()), delta);
assertEquals(t, d2.getWeight(DNATools.t()), delta);
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Can't retrieve weight: "
+ ise.getMessage());
}
}
}
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