package genepi.haplogrep;
import phylotree.Phylotree;
import phylotree.PhylotreeManager;
import org.junit.Assert;
import java.io.IOException;
import java.util.List;
import org.jdom.JDOMException;
import org.junit.BeforeClass;
import org.junit.Test;
import search.ranking.HammingRanking;
import search.ranking.KulczynskiRanking;
import search.ranking.results.RankedResult;
import core.TestSample;
import exceptions.parse.HsdFileException;
import exceptions.parse.sample.InvalidPolymorphismException;
import exceptions.parse.samplefile.InvalidColumnCountException;
import junit.framework.TestCase;
public class HaplogroupTest {
private static Phylotree phylotree = null;
@BeforeClass
public static void init() throws NumberFormatException, IOException, JDOMException, InvalidPolymorphismException
{
phylotree = PhylotreeManager.getInstance().getPhylotree("phylotree17.xml","weights17.txt");
}
@Test
public void testH2a2() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("K1a+150 1-16569 150T 497T 16093C 1189C 10398G 10550G 11299C 14798C 16224C 16311C 9055A 14167T 3480G 9698C 1811G 11467G 12308G 12372A 73G 11719A 14766T 2706G 7028T 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("K1a+150", result.get(0).getHaplogroup().toString());
}
@Test
public void testK1a24() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("K1a24 1-16569 15625A 150T 497T 16093C 1189C 10398G 10550G 11299C 14798C 16224C 16311C 9055A 14167T 3480G 9698C 1811G 11467G 12308G 12372A 73G 11719A 14766T 2706G 7028T 1438G 4769G 750G 8860G 15326G 263G "),new HammingRanking());
Assert.assertEquals("K1a24", result.get(0).getHaplogroup().toString());
}
@Test
public void testK1a30() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("K1a30 1-16569 15650A 150T 497T 16093C 1189C 10398G 10550G 11299C 14798C 16224C 16311C 9055A 14167T 3480G 9698C 1811G 11467G 12308G 12372A 73G 11719A 14766T 2706G 7028T 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("K1a30", result.get(0).getHaplogroup().toString());
}
@Test
public void testH2a() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 H2a2 263G 8860G 15326G 750G"),new HammingRanking());
Assert.assertEquals("H2a", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_16291() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+16291 1-16569 16291T 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+16291", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_13708() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+13708 1-16569 13708A 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+13708", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_152() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+152 1-16569 152C 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+152", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_195() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+195 1-16569 195C 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+195", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_195_146() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+195+146 1-16569 146C 195C 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+195+146", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_16129() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+16129 1-16569 16129A 1438G 4769G 750G 8860G 15326G 263G"),new HammingRanking());
Assert.assertEquals("H+16129", result.get(0).getHaplogroup().toString());
}
@Test
public void testHG_H2_16129_kulcz() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("HG_H2+16129 1-16569 16129A 1438G 4769G 750G 8860G 15326G 263G"),new KulczynskiRanking());
Assert.assertEquals("H+16129", result.get(0).getHaplogroup().toString());
}
@Test
public void testH_152() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 H_152 263G 8860G 15326G 750G"),new HammingRanking());
Assert.assertEquals("H2a", result.get(0).getHaplogroup().toString());
}
@Test
public void testH() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 263G 8860G 15326G 750G 4769G 1438G"),new HammingRanking());
Assert.assertEquals("H", result.get(0).getHaplogroup().toString());
}
@Test
public void testHV() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 263G 8860G 15326G 750G 4769G 1438G 2706G 7028T"),new HammingRanking());
Assert.assertEquals("HV", result.get(0).getHaplogroup().toString());
}
@Test
public void testR0() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 263G 8860G 15326G 750G 4769G 1438G 2706G 7028T 14766T"),new HammingRanking());
Assert.assertEquals("R0", result.get(0).getHaplogroup().toString());
}
@Test
public void testL5a1a() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 73G 152C 182T 189G 195C 247A 263G 315.1C 455.1T 455.2T 455.3C 522del 523del 709A 750G 769A 825A 851G 930A 1018A 1438G 1822C 2706G 3423C 3594T 4104G 4496T 4769G 5004C 5111T 5147A 5656G 6182A 6297C 7028T 256T 7424G 7521A 7873T 7972G 8155A 8188G 8582T 8655T 8701G 8754T 8860G 9305A 9329A 9540C 9899C 10398G 10688A 10810C 10873C 11015G 11025C 11719A 11881T 12236A 12432T 12705T 12950G 13105G 13506T 13650T 13722G 14212C 14239T 14581C 14766T 14905A 14971C 15217A 15326G 15884A 16129A 16148T 16166G 16187T 16189C 16223T 16278T 16311C 16355T 16362C"),new HammingRanking());
Assert.assertEquals("L5a1a", result.get(0).getHaplogroup().toString());
}
@Test
public void testH13a2a() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("1 1-16569 H13a2a 263G 309.1C 315.1C 709A 750G 1008G 1438G 1768A 2259T 4769G 8860G 14872T 15326G 16519C"),new HammingRanking());
Assert.assertEquals("H13a2a", result.get(0).getHaplogroup().toString());
}
@Test
public void testL3e1c() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("549 1-16569 L3e1c 73G 150T 189G 200G 263G 309.1C 315.1C 750G 1438G 2352C 2706G 3106N 3675G 4769G 5460A 6221C 6587T 7028T 8289.1C 8289.2C 8289.3C 8289.4C 8289.5C 8289.6T 8289.7C 8289.8T 8289.9A 8289.10C 8289.11C 8289.12C 8289.13C 8289.14C 8289.15T 8289.16C 8289.17T 8289.18A 8860G 9540C 10398G 10819G 10873C 11719A 12705T 14152G 14212C 14323A 14766T 15301A 15326G 15670C 15942C 16327T "),new HammingRanking());
Assert.assertEquals("L3e1c", result.get(0).getHaplogroup().toString());
}
@Test
public void testH13a2b1() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("549 1-16569 H13a2b1 263G 315.1C 709A 750G 1438G 2259T 4639C 4769G 5899.1C 7322G 8860G 13762G 14872T 15001C 15326G 16311C 16519C "),new HammingRanking());
Assert.assertEquals("H13a2b1", result.get(0).getHaplogroup().toString());
}
@Test
public void testH2a2b() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("549 1-16569 H2a2b 263G 309.1C 309.2T 4080C 8860G 15326G 16291T"),new HammingRanking());
Assert.assertEquals("H2a2b3", result.get(0).getHaplogroup().toString());
}
@Test //GH #11
public void testW1_119() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
List<RankedResult> result = phylotree.search(TestSample.parse("ID 1-16569 W1+119 73G 94A 103A 118C 119C 189G 195C 198T 204C 207A 263G 709A 750G 1243C 1438G 2706G 3505G 4769G 5046A 5460A 7028T 7864T 8251A 8860G 8994A 11674T 11719A 11947G 12414C 12705T 14766T 15326G 15884C 16223T 16278T 16292T 16295T 16519C"),new HammingRanking());
Assert.assertEquals("W1+119", result.get(0).getHaplogroup().toString());
}
}
