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package org.biojava.bio.dist;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import junit.framework.AssertionFailedError;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.IllegalAlphabetException;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.Symbol;
import org.biojava.utils.ChangeVetoException;
/**
* Tests that simple distributions work as advertised.
*
* @author Matthew Pocock
* @since 1.2
*/
public class DistributionTest extends TestCase {
private double delta = 0.00001;
private double a = 0.1;
private double g = 0.3;
private double c = 0.25;
private double t = 0.35;
private Distribution dist;
private Distribution gap;
private Distribution gapDist;
public DistributionTest(String name) {
super(name);
}
protected void setUp() {
// create distributions
try {
dist = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
gap = new GapDistribution(DNATools.getDNA());
gapDist = new PairDistribution(gap, dist);
} catch (IllegalAlphabetException iae) {
throw new AssertionFailedError("Can't initialize test distributions " + iae.getMessage());
}
// set the weights in dist
try {
dist.setWeight(DNATools.a(), a);
dist.setWeight(DNATools.g(), g);
dist.setWeight(DNATools.c(), c);
dist.setWeight(DNATools.t(), t);
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Unable to set weights: "
+ ise.getMessage());
} catch (ChangeVetoException cve) {
throw new AssertionFailedError("Unable to set weights: "
+ cve.getMessage());
}
}
// make sure that we get out the weights out that we put in
public void testSimpleDistribution() {
try {
assertEquals("gap", 0.0, dist.getWeight(dist.getAlphabet().getGapSymbol()), delta);
assertEquals(DNATools.a().toString(), a, dist.getWeight(DNATools.a()), delta);
assertEquals(DNATools.g().toString(), g, dist.getWeight(DNATools.g()), delta);
assertEquals(DNATools.c().toString(), c, dist.getWeight(DNATools.c()), delta);
assertEquals(DNATools.t().toString(), t, dist.getWeight(DNATools.t()), delta);
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Can't retrieve weight: "
+ ise.getMessage());
}
}
// check that the ambiguity stuff works
public void testAmbiguities() {
try {
// implicit from sets
Set syms = new HashSet();
double tot = 0.0;
assertEquals(syms.toString(), tot, dist.getWeight(dist.getAlphabet().getAmbiguity(syms)), delta);
syms.add(DNATools.a());
tot += a;
assertEquals(syms.toString(), tot, dist.getWeight(dist.getAlphabet().getAmbiguity(syms)), delta);
syms.add(DNATools.g());
tot += g;
assertEquals(syms.toString(), tot, dist.getWeight(dist.getAlphabet().getAmbiguity(syms)), delta);
syms.add(DNATools.c());
tot += c;
assertEquals(syms.toString(), tot, dist.getWeight(dist.getAlphabet().getAmbiguity(syms)), delta);
syms.add(DNATools.t());
tot += t;
assertEquals(syms.toString(), tot, dist.getWeight(dist.getAlphabet().getAmbiguity(syms)), delta);
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Can't retrieve weight: "
+ ise.getMessage());
}
}
// check gap distribution
public void testGapDistribution() {
try {
assertEquals("real-gap", 1.0
, gap.getWeight(AlphabetManager.getGapSymbol()), delta);
assertEquals("gap", 1.0, gap.getWeight(gap.getAlphabet().getGapSymbol()), delta);
assertEquals(DNATools.a().toString(), 1.0, gap.getWeight(DNATools.a()), delta);
assertEquals(DNATools.g().toString(), 1.0, gap.getWeight(DNATools.g()), delta);
assertEquals(DNATools.c().toString(), 1.0, gap.getWeight(DNATools.c()), delta);
assertEquals(DNATools.t().toString(), 1.0, gap.getWeight(DNATools.t()), delta);
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Can't retrieve weight: "
+ ise.getMessage());
}
}
public void testGapDist() {
try {
Symbol[] syms = new Symbol[2];
syms[0] = gap.getAlphabet().getGapSymbol();
List symL = Arrays.asList(syms);
for(Iterator si = ((FiniteAlphabet) dist.getAlphabet()).iterator(); si.hasNext(); ) {
Symbol s = (Symbol) si.next();
syms[1] = s;
Symbol sym = gapDist.getAlphabet().getSymbol(symL);
assertEquals(sym.toString(), gapDist.getWeight(sym), dist.getWeight(s), delta);
}
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Can't retrieve weight: "
+ ise.getMessage());
}
}
}
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