public void testSetChromosomeLocationsAndLengths() throws Exception {
Chromosome chr1 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("1");
chr1.setId(new Integer(101));
Chromosome chr2 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("2");
chr1.setId(new Integer(102));
Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon1.setId(new Integer(107));
exon1.setLength(new Integer(1000));
Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon2.setId(new Integer(108));
Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon3.setId(new Integer(109));
// exon 2 has two chromosome locations, shouldn't get chromosome[Location] references
Location exon1OnChr = createLocation(chr1, exon1, "1", 51, 100, Location.class);
exon1OnChr.setId(new Integer(1010));
Location exon2OnChr = createLocation(chr2, exon2, "1", 201, 250, Location.class);
exon2OnChr.setId(new Integer(1011));
Location exon2OnChrDup = createLocation(chr1, exon2, "1", 501, 550, Location.class);
exon2OnChrDup.setId(new Integer(1012));
Location exon3OnChr = createLocation(chr2, exon3, "1", 601, 650, Location.class);
exon3OnChr.setId(new Integer(1013));
Set<InterMineObject> toStore =
new HashSet<InterMineObject>(
Arrays.asList(
new InterMineObject[] {
chr1, chr2, exon1, exon2, exon3, exon1OnChr, exon2OnChr, exon2OnChrDup, exon3OnChr
}));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
CalculateLocations cl = new CalculateLocations(osw);
cl.setChromosomeLocationsAndLengths();
ObjectStore os = osw.getObjectStore();
Exon resExon1 = (Exon) os.getObjectById(new Integer(107));
Exon resExon2 = (Exon) os.getObjectById(new Integer(108));
Exon resExon3 = (Exon) os.getObjectById(new Integer(109));
assertEquals(chr1.getId(), resExon1.getChromosome().getId());
assertEquals(exon1OnChr.getId(), resExon1.getChromosomeLocation().getId());
assertNull(resExon2.getChromosome());
assertNull(resExon2.getChromosomeLocation());
assertEquals(chr2.getId(), resExon3.getChromosome().getId());
assertEquals(exon3OnChr.getId(), resExon3.getChromosomeLocation().getId());
// exon1 has length set so should stay as 1000, exon3 should get length 50 set from location
assertEquals(new Integer(1000), resExon1.getLength());
assertEquals(new Integer(50), resExon3.getLength());
// nothing done to exon2
assertNull(resExon2.getLength());
}
