/**
* Copyright Copyright 2014 Simon Andrews
*
* This file is part of BamQC.
*
* BamQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* BamQC is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with BamQC; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
/*
* Changelog:
* - Piero Dalle Pezze: Added printout, testBooleans, class standardization.
* - Bart Ailey: Class creation.
*/
package test.java.uk.ac.babraham.BamQC.Modules;
import static org.junit.Assert.*;
import java.util.List;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import uk.ac.babraham.BamQC.Modules.SequenceQualityDistribution;
/**
*
* @author Bart Ailey
* @author Piero Dalle Pezze
*
*/
public class SequenceQualityDistributionTest {
private static Logger log = Logger.getLogger(SequenceQualityDistributionTest.class);
private SequenceQualityDistribution sequenceQualityDistribution = null;
private TestObjectFactory testObjectFactory = null;
private List<SAMRecord> samRecords = null;
@Before
public void setUp() throws Exception {
testObjectFactory = new TestObjectFactory();
samRecords = testObjectFactory.getSamRecords();
sequenceQualityDistribution = new SequenceQualityDistribution();
}
@After
public void tearDown() throws Exception {
testObjectFactory = null;
samRecords = null;
sequenceQualityDistribution = null;
}
@Test
public void testProcessSequence() {
System.out.println("Running test SequenceQualityDistributionTest.testProcessSequence");
log.info("Running test SequenceQualityDistributionTest.testProcessSequence");
for (SAMRecord samRecord : samRecords) {
sequenceQualityDistribution.processSequence(samRecord);
}
List<Integer> distribution = sequenceQualityDistribution.getDistribution();
assertEquals(0, (int) distribution.get(0));
assertEquals(0, (int) distribution.get(1));
assertEquals(0, (int) distribution.get(2));
assertEquals(2, (int) distribution.get(3));
assertEquals(0, (int) distribution.get(4));
assertEquals(0, (int) distribution.get(5));
assertEquals(1, (int) distribution.get(6));
}
@Test(expected= IndexOutOfBoundsException.class)
public void testProcessSequenceException() {
System.out.println("Running test SequenceQualityDistributionTest.testProcessSequenceException");
log.info("Running test SequenceQualityDistributionTest.testProcessSequenceException");
for (SAMRecord samRecord : samRecords) {
sequenceQualityDistribution.processSequence(samRecord);
}
List<Integer> distribution = sequenceQualityDistribution.getDistribution();
assertEquals(0, (int) distribution.get(7));
}
@Test
public void testBooleans() {
System.out.println("Running test SequenceQualityDistributionTest.testBooleans");
log.info("Running test SequenceQualityDistributionTest.testBooleans");
assertTrue(sequenceQualityDistribution.ignoreInReport());
assertFalse(sequenceQualityDistribution.needsToSeeAnnotation());
assertFalse(sequenceQualityDistribution.raisesError());
assertFalse(sequenceQualityDistribution.raisesWarning());
assertTrue(sequenceQualityDistribution.needsToSeeSequences());
}
}