@AfterClass
public void close() throws IOException {
bimfd.close();
famfd.close();
pedfd.close();
mapfd.close();
tpedfd.close();
}
@Test
public void MAP_writer() throws Exception {
File newMap = new File(testMap.getAbsolutePath().replace(testMap.getName(), "new.map"));
MapFileWriter w = new MapFileWriter(newMap);
try {
w.writeAll(mapfd.getAllEntries());
boolean filesAreEqual = DirectoryCompare.compareFileContent(testMap, newMap);
assertTrue(filesAreEqual);
} finally {
w.close();
}
}
@Test
public void MAP_getEntries() throws Exception {
assertEquals(1, mapfd.getEntries(0, 1).size());
assertEquals(1, mapfd.getEntries(1, 2).size());
assertEquals(2, mapfd.getEntries(0, 2).size());
assertEquals(2, mapfd.getAllEntries().size());
assertEquals("snp1", mapfd.getEntries(0, 1).get(0).getSNP());
assertEquals(0.0, mapfd.getEntries(1, 2).get(0).getcM());
assertEquals("1", mapfd.getEntries(1, 2).get(0).getChromosome());
assertEquals(1, mapfd.getAllEntries().get(0).getBpPos());
assertEquals(2, mapfd.getAllEntries().get(1).getBpPos());
assertEquals("snp2", mapfd.getAllEntries().get(1).getSNP());
}
@Test
public void MAP_construct() throws Exception {
assertEquals(2, mapfd.getNrOfElements());
}