Ejemplo n.º 1
0
  @Test
  public void testLoadDataSourceTrack() throws Exception {
    String path = TestUtils.DATA_DIR + "sessions/tdf_session.xml";
    rewriteRestoreSession(path);

    DataSourceTrack track = (DataSourceTrack) IGV.getInstance().getAllTracks().get(0);
    assertEquals(true, TestUtils.runMethod(track, "getNormalize"));
    assertEquals("NA12878.SLX.egfr.sam.tdf", track.getName());
  }
Ejemplo n.º 2
0
  @Test
  public void testLoadCombinedDataSourceSession() throws Exception {
    String sessionpath = TestUtils.DATA_DIR + "sessions/subtypes_wdiff.xml";
    rewriteRestoreSession(sessionpath);

    String combPart0 = "TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_E11_155884";
    String combPart1 = "TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_D05_223156";

    DataTrack track0 =
        Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart0));
    DataTrack track1 =
        Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart1));

    DataSourceTrack combTrack =
        (DataSourceTrack)
            Iterables.find(
                IGV.getInstance().getDataTracks(),
                new ContIdPredicate(new String[] {combPart0, combPart1}));

    assertTrue(combTrack.getRenderer() instanceof BarChartRenderer);
    assertEquals("Difference", combTrack.getName());

    String chr = "chr1";
    int start = 0;
    int end = 1000;

    LocusScore sumScore0 = track0.getSummaryScores(chr, start, end, 0).get(0);
    LocusScore sumScore1 = track1.getSummaryScores(chr, start, end, 0).get(0);
    LocusScore sumScoreComb = combTrack.getSummaryScores(chr, start, end, 0).get(0);

    assertEquals(sumScore0.getStart(), sumScore1.getStart());
    assertEquals(sumScore0.getStart(), sumScoreComb.getStart());
    assertEquals(sumScore1.getEnd(), sumScoreComb.getEnd());

    assertEquals(sumScore0.getScore() - sumScore1.getScore(), sumScoreComb.getScore(), 1e-10);
  }