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()); }