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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.BioException;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.utils.ChangeVetoException;
/**
* JUnit test for FeatureHolderUtils
*
* @author Markus Brosch
*/
public class FeatureHolderUtilsTest extends TestCase {
protected Feature f1;
protected Feature f2;
protected Feature f3;
protected SimpleFeatureHolder fh1; //has f1, f2
protected SimpleFeatureHolder fh2; //has f2, f3
protected void setUp() throws Exception {
Sequence seq = DNATools.createDNASequence("attagagg", "seq");
f1 = generateFeatures(seq, "f1");
f2 = generateFeatures(seq, "f2");
f3 = generateFeatures(seq, "f3");
fh1 = new SimpleFeatureHolder();
fh1.addFeature(f1);
fh1.addFeature(f2); //also in fh2
fh2 = new SimpleFeatureHolder();
fh2.addFeature(f2); //also in fh1
fh2.addFeature(f3);
}
public void testUnion() throws ChangeVetoException {
FeatureHolder fh = FeatureHolderUtils.union(fh1, fh2);
assertTrue(fh.containsFeature(f1));
assertTrue(fh.containsFeature(f2));
assertTrue(fh.containsFeature(f3));
assertEquals(3, fh.countFeatures());
}
public void testIntersect() throws ChangeVetoException {
FeatureHolder fh = FeatureHolderUtils.intersect(fh1, fh2);
assertTrue(fh.containsFeature(f2));
assertFalse(fh.containsFeature(f1));
assertFalse(fh.containsFeature(f3));
assertEquals(1, fh.countFeatures());
}
public void testNot() throws ChangeVetoException {
FeatureHolder fh = FeatureHolderUtils.not(fh1, fh2);
assertTrue(fh.containsFeature(f1));
assertFalse(fh.containsFeature(f2));
assertFalse(fh.containsFeature(f3));
assertEquals(1, fh.countFeatures());
}
public void testFeatureHolderAsSet() {
Set set = FeatureHolderUtils.featureHolderAsSet(fh1);
assertTrue(set.contains(f1));
assertTrue(set.contains(f2));
assertFalse(set.contains(f3));
set.add(f3);
assertTrue(set.contains(f3));
set.remove(f3);
assertFalse(set.contains(f3));
}
private Feature generateFeatures(FeatureHolder fh, String type) throws BioException,
ChangeVetoException {
StrandedFeature.Template templ = new StrandedFeature.Template();
templ.type = type;
templ.location = new RangeLocation(1, 5);
templ.strand = StrandedFeature.POSITIVE;
templ.source = "foo";
templ.annotation = Annotation.EMPTY_ANNOTATION;
return fh.createFeature(templ);
}
}
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