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package org.biojava.bio.dp;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.dist.Distribution;
import org.biojava.bio.dist.DistributionFactory;
import org.biojava.bio.dist.UniformDistribution;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.IllegalAlphabetException;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.utils.ChangeType;
import org.biojava.utils.ChangeVetoException;
/**
* Test the event forwarding mess in MarkovModel & impls.
*
* @author Matthew Pocock
*/
public class MarkovModelEventTest
extends TestCase {
public void testAddRemoveState() {
try {
// set up a model
SimpleMarkovModel smm = new SimpleMarkovModel(1, DNATools.getDNA(), "add/remove test");
EventCounter archC = new EventCounter("Architecture counter");
EventCounter paraC = new EventCounter("Parameter counter");
smm.addChangeListener(archC, MarkovModel.ARCHITECTURE);
smm.addChangeListener(paraC, MarkovModel.PARAMETER);
// make some silly states
DotState ds = new SimpleDotState("d1");
EmissionState es = new SimpleEmissionState(
"e1",
Annotation.EMPTY_ANNOTATION,
new int[]{1},
DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA()));
// add ds & check events
smm.addState(ds);
assertEquals("All architecture events allowed: " + archC, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("One architecture event: " + archC, 1, archC.getPostCounts());
assertEquals("No parameter events: " + paraC, 0, paraC.getPostCounts());
archC.zeroCounts();
paraC.zeroCounts();
// add es & check events
smm.addState(es);
assertEquals("All architecture events allowed: " + archC, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("One architecture event: " + archC, 1, archC.getPostCounts());
assertEquals("No parameter events: " + paraC, 0, paraC.getPostCounts());
archC.zeroCounts();
paraC.zeroCounts();
// create transition
smm.createTransition(ds, es);
assertEquals("All architecture events allowed: " + archC, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("One architecture event: " + archC, 1, archC.getPostCounts());
assertEquals("No parameter events: " + paraC, 0, paraC.getPostCounts());
archC.zeroCounts();
paraC.zeroCounts();
// delete transition
smm.destroyTransition(ds, es);
assertEquals("All architecture events allowed: " + archC, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("One architecture event: " + archC, 1, archC.getPostCounts());
assertEquals("No parameter events: " + paraC, 0, paraC.getPostCounts());
archC.zeroCounts();
paraC.zeroCounts();
// remove ds
smm.removeState(ds);
smm.removeState(es);
} catch (IllegalAlphabetException iae) {
throw (AssertionError) new AssertionError("Could not create distributions.").initCause(iae);
} catch (ChangeVetoException cve) {
throw (AssertionError) new AssertionError("Could not modify model.").initCause(cve);
} catch (IllegalSymbolException ise) {
throw (AssertionError) new AssertionError("Could not modify model.").initCause(ise);
} catch (IllegalTransitionException ite) {
throw (AssertionError) new AssertionError("Could not modify model.").initCause(ite);
}
}
public void testSetWeights() {
try {
// set up a model
SimpleMarkovModel smm = new SimpleMarkovModel(1, DNATools.getDNA(), "add/remove test");
EventCounter everything = new EventCounter("Everything");
EventCounter archC = new EventCounter("Architecture counter");
EventCounter paraC = new EventCounter("Parameter counter");
smm.addChangeListener(everything, ChangeType.UNKNOWN);
smm.addChangeListener(archC, MarkovModel.ARCHITECTURE);
smm.addChangeListener(paraC, MarkovModel.PARAMETER);
// make some silly states
DotState ds = new SimpleDotState("d1");
EmissionState es = new SimpleEmissionState(
"e1",
Annotation.EMPTY_ANNOTATION,
new int[]{1},
DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA()));
smm.addState(ds);
smm.addState(es);
smm.createTransition(ds, es);
everything.zeroCounts();
archC.zeroCounts();
paraC.zeroCounts();
// set the transition weight distribution
smm.setWeights(ds, new UniformDistribution((FiniteAlphabet) smm.getWeights(ds).getAlphabet()));
assertEquals("All architecture events allowed: " + archC + "\n\t" + everything, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC + "\n\t" + everything, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("No architecture event: " + archC + "\n\t" + everything, 0, archC.getPostCounts());
assertEquals("One parameter events: " + paraC + "\n\t" + everything, 1, paraC.getPostCounts());
everything.zeroCounts();
archC.zeroCounts();
paraC.zeroCounts();
// set the distribution associated with es
Distribution dist = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
es.setDistribution(dist);
assertEquals("All architecture events allowed: " + archC + "\n\t" + everything, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC + "\n\t" + everything, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("No architecture event: " + archC + "\n\t" + everything, 0, archC.getPostCounts());
assertEquals("One parameter events: " + paraC + "\n\t" + everything, 1, paraC.getPostCounts());
everything.zeroCounts();
archC.zeroCounts();
paraC.zeroCounts();
// set two individual weights in dist
dist.setWeight(DNATools.a(), 0.9);
dist.setWeight(DNATools.t(), 0.1);
assertEquals("All architecture events allowed: " + archC + "\n\t" + everything, archC.getPreCounts(), archC.getPostCounts());
assertEquals("All parameter events allowed: " + paraC + "\n\t" + everything, paraC.getPreCounts(), paraC.getPostCounts());
assertEquals("No architecture event: " + archC + "\n\t" + everything, 0, archC.getPostCounts());
assertEquals("Two parameter events: " + paraC + "\n\t" + everything, 2, paraC.getPostCounts());
} catch (IllegalAlphabetException iae) {
throw (AssertionError) new AssertionError("Could not create distributions.").initCause(iae);
} catch (ChangeVetoException cve) {
throw (AssertionError) new AssertionError("Could not modify model.").initCause(cve);
} catch (IllegalSymbolException ise) {
throw (AssertionError) new AssertionError("Could not modify model.").initCause(ise);
}
}
}
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