コード例 #1
0
  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());
  }
コード例 #2
0
  public void testCreateSpanningLocations() throws Exception {
    Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon1.setId(new Integer(107));
    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));

    Location exon1OnChr = createLocation(getChromosome(), exon1, "1", 51, 100, Location.class);
    exon1OnChr.setId(new Integer(1010));
    Location exon2OnChr = createLocation(getChromosome(), exon2, "1", 201, 250, Location.class);
    exon2OnChr.setId(new Integer(1011));
    Location exon3OnChr = createLocation(getChromosome(), exon3, "1", 201, 400, Location.class);
    exon3OnChr.setId(new Integer(1012));

    Transcript trans1 =
        (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
    trans1.setId(new Integer(201));

    Transcript trans2 =
        (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
    trans2.setId(new Integer(202));

    Location trans2OnChr = createLocation(getChromosome(), trans2, "1", 61, 300, Location.class);

    Gene gene = (Gene) DynamicUtil.createObject(Collections.singleton(Gene.class));
    gene.setId(new Integer(301));

    exon1.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
    exon2.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));

    // the location of exon3 should be ignored by createSpanningLocations() because trans2
    // already has a location
    exon3.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans2})));

    trans1.setGene(gene);
    trans2.setGene(gene);

    Set<InterMineObject> toStore =
        new HashSet<InterMineObject>(
            Arrays.asList(
                new InterMineObject[] {
                  getChromosome(),
                  gene,
                  trans1,
                  trans2,
                  exon1,
                  exon2,
                  exon3,
                  exon1OnChr,
                  exon2OnChr,
                  trans2OnChr
                }));

    for (InterMineObject imo : toStore) {
      osw.store(imo);
    }

    CalculateLocations cl = new CalculateLocations(osw);
    cl.createSpanningLocations("Transcript", "Exon", "exons");
    cl.createSpanningLocations("Gene", "Transcript", "transcripts");

    ObjectStore os = osw.getObjectStore();
    Transcript resTrans1 = (Transcript) os.getObjectById(new Integer(201));

    Assert.assertEquals(1, resTrans1.getLocations().size());
    Location resTrans1Location = (Location) resTrans1.getLocations().iterator().next();
    Assert.assertEquals(51, resTrans1Location.getStart().intValue());
    Assert.assertEquals(250, resTrans1Location.getEnd().intValue());

    Transcript resTrans2 = (Transcript) os.getObjectById(new Integer(202));

    Assert.assertEquals(1, resTrans2.getLocations().size());
    Location resTrans2Location = (Location) resTrans2.getLocations().iterator().next();
    Assert.assertEquals(61, resTrans2Location.getStart().intValue());
    Assert.assertEquals(300, resTrans2Location.getEnd().intValue());

    Gene resGene = (Gene) os.getObjectById(new Integer(301));
    Assert.assertEquals(1, resGene.getLocations().size());
    Location resGeneLocation = (Location) resGene.getLocations().iterator().next();
    Assert.assertEquals(51, resGeneLocation.getStart().intValue());
    Assert.assertEquals(300, resGeneLocation.getEnd().intValue());
  }