private Chromosome getChromosome() {
if (chromosome == null) {
chromosome = (Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chromosome.setPrimaryIdentifier("X");
chromosome.setLength(new Integer(10000));
chromosome.setId(new Integer(101));
}
return chromosome;
}
private void createOverlapTestData() throws Exception {
Chromosome chr = (Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr.setPrimaryIdentifier("X");
chr.setLength(new Integer(1000));
chr.setId(new Integer(101));
Set<InterMineObject> toStore = new HashSet<InterMineObject>();
toStore.add(chr);
int[][] exonInfo = {
{1000, 1, 1},
{1001, 2, 10},
{1002, 10, 15},
{1003, 16, 19},
{1004, 16, 19},
{1005, 20, 29},
{1006, 30, 100},
{1007, 30, 34},
{1008, 32, 95},
{1009, 38, 53},
{1010, 40, 50},
{1011, 44, 44},
{1012, 54, 54},
{1013, 54, 54},
{1014, 60, 70},
{1015, 120, 140},
{1016, 141, 145},
{1017, 146, 180},
{1018, 220, 240},
{1019, 240, 245},
{1020, 245, 280},
};
Exon[] exons = new Exon[exonInfo.length];
Location[] exonLocs = new Location[exonInfo.length];
for (int i = 0; i < exons.length; i++) {
exons[i] = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
int exonId = exonInfo[i][0];
int start = exonInfo[i][1];
int end = exonInfo[i][2];
exons[i].setId(new Integer(exonId));
exons[i].setLength(new Integer(end - start + 1));
exons[i].setChromosome(chr);
exonLocs[i] = createLocation(chr, exons[i], "1", start, end, Location.class);
exonLocs[i].setId(new Integer(1000 + exonId));
}
ReversePrimer rp =
(ReversePrimer) DynamicUtil.createObject(Collections.singleton(ReversePrimer.class));
rp.setId(new Integer(3000));
rp.setLength(new Integer(100));
rp.setChromosome(chr);
Location rpLoc = createLocation(chr, rp, "1", 1, 100, Location.class);
rpLoc.setId(new Integer(3001));
toStore.add(rp);
toStore.add(rpLoc);
toStore.addAll(Arrays.asList(exons));
toStore.addAll(Arrays.asList(exonLocs));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
}
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());
}