@AfterClass
public void close() throws IOException {
bimfd.close();
famfd.close();
pedfd.close();
mapfd.close();
tpedfd.close();
}
@Test
public void PED_writer() throws Exception {
File newPed = new File(testPed.getAbsolutePath().replace(testPed.getName(), "new.ped"));
PedFileWriter w = new PedFileWriter(newPed);
try {
w.writeAll(pedfd.getAllEntries());
boolean filesAreEqual = DirectoryCompare.compareFileContent(testPed, newPed);
assertTrue(filesAreEqual);
} finally {
w.close();
}
}
@Test
public void PED_construct() throws Exception {
assertEquals(6, pedfd.getNrOfElements());
}
// TODO
@Test
public void PED_getEntries() throws Exception {
// 1 1 0 0 1 1 A A G T
assertEquals('A', pedfd.getAllEntries().get(0).getBialleles().get(0).getAllele1());
assertEquals('A', pedfd.getAllEntries().get(0).getBialleles().get(0).getAllele2());
assertEquals('G', pedfd.getAllEntries().get(0).getBialleles().get(1).getAllele1());
assertEquals('T', pedfd.getAllEntries().get(0).getBialleles().get(1).getAllele2());
assertEquals('A', pedfd.getAllEntries().get(1).getBialleles().get(0).getAllele1());
assertEquals('C', pedfd.getAllEntries().get(1).getBialleles().get(0).getAllele2());
assertEquals('T', pedfd.getAllEntries().get(1).getBialleles().get(1).getAllele1());
assertEquals('G', pedfd.getAllEntries().get(1).getBialleles().get(1).getAllele2());
assertEquals('C', pedfd.getAllEntries().get(5).getBialleles().get(0).getAllele1());
assertEquals('C', pedfd.getAllEntries().get(5).getBialleles().get(0).getAllele2());
assertEquals('T', pedfd.getAllEntries().get(5).getBialleles().get(1).getAllele1());
assertEquals('T', pedfd.getAllEntries().get(5).getBialleles().get(1).getAllele2());
assertEquals("3", pedfd.getAllEntries().get(2).getFamily());
assertEquals("0", pedfd.getAllEntries().get(2).getFather());
assertEquals("0", pedfd.getAllEntries().get(2).getMother());
assertEquals(1.0, pedfd.getAllEntries().get(2).getPhenotype());
assertEquals("1", pedfd.getAllEntries().get(2).getIndividual());
assertEquals(1, pedfd.getAllEntries().get(2).getSex());
assertEquals("3", pedfd.getEntries(2, 3).get(0).getFamily());
assertEquals('G', pedfd.getEntries(2, 3).get(0).getBialleles().get(1).getAllele2());
assertEquals("3", pedfd.getEntries(0, 3).get(2).getFamily());
assertEquals('G', pedfd.getEntries(0, 3).get(2).getBialleles().get(1).getAllele1());
assertEquals("4", pedfd.getEntries(2, 4).get(1).getFamily());
assertEquals(2.0, pedfd.getEntries(2, 4).get(1).getPhenotype());
assertEquals('C', pedfd.getEntries(0, 6).get(4).getBialleles().get(0).getAllele1());
assertEquals('C', pedfd.getEntries(1, 6).get(3).getBialleles().get(0).getAllele2());
assertEquals('G', pedfd.getEntries(2, 6).get(2).getBialleles().get(1).getAllele1());
assertEquals('T', pedfd.getEntries(3, 6).get(1).getBialleles().get(1).getAllele2());
}