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package org.biojava.bio.dist;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import junit.framework.AssertionFailedError;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.Alphabet;
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 serilization works as advertised.
*
* @author Mark Schreiber
* @since 1.21
*/
public class DistSerTest extends TestCase {
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 dist2;
private Distribution gap;
private Distribution pair;
private OrderNDistribution orderN;
private Alphabet comp;
public DistSerTest(String name){
super(name);
}
protected void setUp() {
// create distributions
try {
dist = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
gap = new GapDistribution(DNATools.getDNA());
pair = new PairDistribution(dist,gap);
List l = Collections.nCopies(3,DNATools.getDNA());
comp = AlphabetManager.getCrossProductAlphabet(l);
orderN = (OrderNDistribution)OrderNDistributionFactory.DEFAULT.createDistribution(comp);
} 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);
DistributionTrainerContext dtc = new SimpleDistributionTrainerContext();
dtc.registerDistribution(orderN);
for(Iterator i = ((FiniteAlphabet)comp).iterator(); i.hasNext();){
dtc.addCount(orderN,(Symbol)i.next(),1.0);
}
dtc.train();
} catch (IllegalSymbolException ise) {
throw new AssertionFailedError("Unable to set weights: "
+ ise.getMessage());
} catch (ChangeVetoException cve) {
throw new AssertionFailedError("Unable to set weights: "
+ cve.getMessage());
}
}
public void testSimpleSerialization()throws Exception{
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(os);
oos.writeObject(dist);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(os.toByteArray()));
dist2 = (Distribution)ois.readObject();
ois.close();
assertTrue(DistributionTools.areEmissionSpectraEqual(dist, dist2));
assertEquals(dist.getAlphabet(), dist2.getAlphabet());
}
public void testGapSerialization()throws Exception{
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(os);
oos.writeObject(gap);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(os.toByteArray()));
dist2 = (Distribution)ois.readObject();
ois.close();
assertTrue(DistributionTools.areEmissionSpectraEqual(gap, dist2));
}
public void testPairSerialization()throws Exception{
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(os);
oos.writeObject(pair);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(os.toByteArray()));
dist2 = (Distribution)ois.readObject();
ois.close();
assertTrue(DistributionTools.areEmissionSpectraEqual(pair, dist2));
}
public void testOrderNSerialization()throws Exception{
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(os);
oos.writeObject(orderN);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(os.toByteArray()));
dist2 = (Distribution)ois.readObject();
ois.close();
assertTrue(orderN.getAlphabet()== dist2.getAlphabet());
assertTrue(orderN.getConditionedAlphabet() == ((OrderNDistribution)dist2).getConditionedAlphabet());
assertTrue(orderN.getConditioningAlphabet() == ((OrderNDistribution)dist2).getConditioningAlphabet());
for(Iterator i = ((FiniteAlphabet)orderN.getConditioningAlphabet()).iterator(); i.hasNext();){
Symbol s = (Symbol)i.next();
assertTrue(DistributionTools.areEmissionSpectraEqual(orderN.getDistribution(s), orderN.getDistribution(s)));
}
assertTrue(orderN.conditionedDistributions().size() == ((OrderNDistribution)dist2).conditionedDistributions().size());
for(Iterator i = ((FiniteAlphabet)orderN.getConditioningAlphabet()).iterator(); i.hasNext();){
Symbol s = (Symbol)i.next();
assertTrue(DistributionTools.areEmissionSpectraEqual(((OrderNDistribution)dist2).getDistribution(s),
((OrderNDistribution)dist2).getDistribution(s)));
}
for(Iterator i = ((FiniteAlphabet)orderN.getConditioningAlphabet()).iterator(); i.hasNext();){
Symbol s = (Symbol)i.next();
assertTrue(DistributionTools.areEmissionSpectraEqual(orderN.getDistribution(s), ((OrderNDistribution)dist2).getDistribution(s)));
}
}
public void testBug2360() throws Exception{
Distribution d = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
ByteArrayOutputStream boas = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(boas);
try{
oos.writeObject(d);
}catch(NullPointerException npe){
fail("Failed to write Distribution");
}
}
}
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