/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.bio.readsfilters;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import org.junit.Test;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;
import fr.ens.biologie.genomique.eoulsan.bio.readsfilters.ReadFilter;
import fr.ens.biologie.genomique.eoulsan.bio.readsfilters.TrimPolyNEndReadFilter;
public class TrimPolyNEndReadFilterTest {
@Test
public void testAcceptReadSequence() throws EoulsanException {
ReadFilter filter = new TrimPolyNEndReadFilter();
filter.init();
assertFalse(filter.accept(null));
ReadSequence read = new ReadSequence();
assertFalse(filter.accept(read));
read.setName("read1");
assertFalse(filter.accept(read));
read.setQuality("xxxxxxxx");
assertFalse(filter.accept(read));
read = new ReadSequence(0, "toto", "ATGCATGC", "xxxxxxxx");
assertTrue(filter.accept(read));
assertEquals("ATGCATGC", read.getSequence());
assertEquals("xxxxxxxx", read.getQuality());
read = new ReadSequence(0, "toto", "ATGCATGN", "xxxxxxxx");
assertTrue(filter.accept(read));
assertEquals("ATGCATGN", read.getSequence());
assertEquals("xxxxxxxx", read.getQuality());
read = new ReadSequence(0, "toto", "ATGCATNN", "xxxxxxxx");
assertTrue(filter.accept(read));
assertEquals("ATGCAT", read.getSequence());
assertEquals("xxxxxx", read.getQuality());
read = new ReadSequence(0, "toto", "ATGCANNN", "xxxxxxxx");
assertTrue(filter.accept(read));
assertEquals("ATGCA", read.getSequence());
assertEquals("xxxxx", read.getQuality());
read = new ReadSequence(0, "toto", "ATGCNNNN", "xxxxxxxx");
assertTrue(filter.accept(read));
assertEquals("ATGC", read.getSequence());
assertEquals("xxxx", read.getQuality());
}
}