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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.nbio.genome;
import com.google.common.collect.Range;
import org.biojava.nbio.genome.util.ChromosomeMappingTools;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* Created by andreas on 7/19/16.
*/
public class TestGenomeMapping {
@Ignore("The test requires the network")
@Test
public void testGenomeMappingToolGetCDSRanges(){
List<Integer> lst1 = new ArrayList<>(Arrays.asList( 86346823, 86352858, 86354529));
List<Integer> lst2 = new ArrayList<>(Arrays.asList(86348878, 86352984, 86354692));
int cdsStart=86348749, cdsEnd=86387027;
List<Range<Integer>> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
// makes sure the first list does not get changed;
Assert.assertEquals(86346823, (int) lst1.get(0));
Assert.assertEquals(86348749, (int) result.get(0).lowerEndpoint());
Assert.assertEquals(86352858, (int) result.get(1).lowerEndpoint());
Assert.assertEquals(86354529, (int) result.get(2).lowerEndpoint());
Assert.assertEquals(86348878, (int) result.get(0).upperEndpoint());
Assert.assertEquals(86352984, (int) result.get(1).upperEndpoint());
Assert.assertEquals(86387027, (int) result.get(2).upperEndpoint());
}
@Ignore("The test requires the network")
@Test
public void testGenomeMappingToolGetCDSRangesSERINC2(){
List<Integer> lst1 = new ArrayList<>(Arrays.asList(31413812, 31415872, 31423692));
List<Integer> lst2 = new ArrayList<>(Arrays.asList(31414777, 31415907, 31423854));
int cdsStart=31423818, cdsEnd=31434199;
List<Range<Integer>> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
// makes sure the first list does not get changed;
Assert.assertEquals(31423818, (int) result.get(0).lowerEndpoint());
}
}
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