@AfterClass
public void close() throws IOException {
bimfd.close();
famfd.close();
pedfd.close();
mapfd.close();
tpedfd.close();
}
@Test
public void BIM_writer() throws Exception {
File newBim = new File(testBim.getAbsolutePath().replace(testBim.getName(), "new.bim"));
BimFileWriter w = new BimFileWriter(newBim);
try {
w.writeAll(bimfd.getAllEntries());
boolean filesAreEqual = DirectoryCompare.compareFileContent(testBim, newBim);
assertTrue(filesAreEqual);
} finally {
w.close();
}
}
@Test
public void BIM_getEntries() throws Exception {
assertEquals(1, bimfd.getEntries(0, 1).size());
assertEquals(1, bimfd.getEntries(1, 2).size());
assertEquals(2, bimfd.getEntries(0, 2).size());
assertEquals(2, bimfd.getAllEntries().size());
assertEquals("snp1", bimfd.getEntries(0, 1).get(0).getSNP());
assertEquals('A', bimfd.getEntries(0, 1).get(0).getBiallele().getAllele1());
assertEquals(0.0, bimfd.getEntries(1, 2).get(0).getcM());
assertEquals("1", bimfd.getEntries(1, 2).get(0).getChromosome());
assertEquals('C', bimfd.getAllEntries().get(0).getBiallele().getAllele2());
assertEquals('T', bimfd.getAllEntries().get(1).getBiallele().getAllele2());
assertEquals(1, bimfd.getAllEntries().get(0).getBpPos());
assertEquals(2, bimfd.getAllEntries().get(1).getBpPos());
assertEquals("snp2", bimfd.getAllEntries().get(1).getSNP());
}
@Test
public void BIM_construct() throws Exception {
assertEquals(2, bimfd.getNrOfElements());
}