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package org.biojava.utils.walker;
import junit.framework.TestCase;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.ComponentFeature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.bio.symbol.RangeLocation;
/**
* Test some walkers for some viewers, ensuring that they get the events we
* would expect.
*
* @author Matthew Pocock
*/
public class WalkerTest
extends TestCase {
private FeatureFilter booring1;
private FeatureFilter booring2;
private FeatureFilter booring4;
private FeatureFilter and;
private FeatureFilter andOr;
protected void setUp() {
booring1 = new FeatureFilter.OverlapsLocation(new RangeLocation(20, 50));
booring2 = new FeatureFilter.ByClass(StrandedFeature.class);
booring4 = new FeatureFilter.ByClass(ComponentFeature.class);
and = new FeatureFilter.And(booring1, booring2);
andOr = new FeatureFilter.And(booring1,
new FeatureFilter.Or(booring2, booring4));
}
public void testCountAll() {
try {
CountAll ca = new CountAll();
Walker walker = WalkerFactory.getInstance().getWalker(ca);
walker.walk(booring1, ca);
assertEquals("One filter: " + booring1, 1, ca.count);
ca.count = 0;
walker.walk(and, ca);
assertEquals("Three filters: " + and, 3, ca.count);
ca.count = 0;
walker.walk(andOr, ca);
assertEquals("Five filters: " + andOr, 5, ca.count);
} catch (BioException be) {
throw (AssertionError) new AssertionError(
"Could not instantiate visitor").initCause(be);
}
}
public void testCountSome() {
try {
CountByClass cbc = new CountByClass();
Walker walker = WalkerFactory.getInstance().getWalker(cbc);
walker.walk(booring1, cbc);
assertEquals("One filter, none interesting", 0, cbc.count);
cbc.count = 0;
walker.walk(booring2, cbc);
assertEquals("One filter, one interesting", 1, cbc.count);
cbc.count = 0;
walker.walk(andOr, cbc);
assertEquals("Five filter, two interesting", 2, cbc.count);
} catch (BioException be) {
throw (AssertionError) new AssertionError(
"Could not instantiate visitor").initCause(be);
}
}
public void testCountWithFallback() {
try {
CountWithFallback cwf = new CountWithFallback();
Walker walker = WalkerFactory.getInstance().getWalker(cwf);
walker.walk(booring1, cwf);
assertEquals("One filter, one booring", 0, cwf.others);
assertEquals("One filter, zero interesting", 1, cwf.byLoc);
cwf.others = cwf.byLoc = 0;
walker.walk(booring2, cwf);
assertEquals("One filter, one booring", 1, cwf.others);
assertEquals("One filter, zero interesting", 0, cwf.byLoc);
cwf.others = cwf.byLoc = 0;
walker.walk(andOr, cwf);
assertEquals("One filter, four booring", 4, cwf.others);
assertEquals("One filter, one interesting", 1, cwf.byLoc);
} catch (BioException be) {
throw (AssertionError) new AssertionError(
"Could not instantiate visitor").initCause(be);
}
}
public void testReturnAll() {
try {
ReturnOne ra = new ReturnOne();
Walker walker = WalkerFactory.getInstance().getWalker(ra);
walker.walk(booring1, ra);
assertEquals("One filter", new Integer(1), walker.getValue());
walker.walk(andOr, ra);
assertEquals("Five filters", new Integer(1), walker.getValue());
} catch (BioException be) {
throw (AssertionError) new AssertionError(
"Could not instantiate visitor").initCause(be);
}
}
public class CountAll implements Visitor {
int count = 0;
public void featureFilter(FeatureFilter filter) {
System.err.println("Increasing counter: " + filter);
count++;
}
}
public class CountByClass
implements Visitor {
int count = 0;
public void byClass(FeatureFilter.ByClass byClass) {
count++;
}
}
public class CountWithFallback
implements Visitor {
int byLoc = 0;
int others = 0;
public void featureFilter(FeatureFilter filter) {
System.err.println("Feature: " + filter);
others++;
}
public void overlapsLocation(FeatureFilter.OverlapsLocation overlaps) {
System.err.println("OverlapsLocation: " + overlaps);
byLoc++;
}
}
public class ReturnOne
implements Visitor {
public Integer featureFilter(FeatureFilter filter) {
return new Integer(1);
}
}
}
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