Package org.broad.igv.sam

Examples of org.broad.igv.sam.CoverageTrack

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    public void testLoadCoverageTrackSession() throws Exception{
        String path = TestUtils.DATA_DIR + "sessions/coverage_snpThreshold_NA06984.xml";
        rewriteRestoreSession(path);

        //We should have 1 coverage track
        CoverageTrack track = (CoverageTrack) IGV.getInstance().getAllTracks().get(0);

        assertTrue(track.isShowReference());
        assertEquals(0.5, track.getSnpThreshold(), 1e-5);
        assertTrue(track.getAutoScale());
    }
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    @Test
    public void testLoadAlignmentTrackSession() throws Exception{
        String path = TestUtils.DATA_DIR + "sessions/HG00171_wlocus_v5.xml";
        AlignmentTrack alTrack = getAlignmentTrack(path);

        CoverageTrack covTrack = alTrack.getCoverageTrack();
        assertTrue(alTrack.isShowSpliceJunctions());

        assertEquals(CoverageTrack.DEFAULT_SHOW_REFERENCE, covTrack.isShowReference());
        assertEquals(CoverageTrack.DEFAULT_AUTOSCALE, covTrack.getAutoScale());
        assertEquals(0.1337f, covTrack.getSnpThreshold(), 1e-5);
    }
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        this.color = color;
        if(this.coverageTrack != null) this.coverageTrack.setColor(color);
    }

    public void setCoverageTrack(CoverageTrack covTrack) {
        this.coverageTrack = new CoverageTrack(covTrack);
        this.coverageTrack.setColor(color);
        //Don't want to color SNPs, so we just set an impossibly high threshold
        coverageTrack.setSnpThreshold(2.0f);

        coverageTrack.setAutoScale(true);
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Related Classes of org.broad.igv.sam.CoverageTrack

  • org.broad.igv.data.CoverageDataSource
  • org.broad.igv.feature.LocusScore
  • org.broad.igv.goby.GobyCountArchiveDataSource
  • org.broad.igv.PreferenceManager
  • org.broad.igv.renderer.BarChartRenderer
  • org.broad.igv.renderer.DataRange
  • org.broad.igv.renderer.SashimiJunctionRenderer
  • org.broad.igv.session.IGVSessionReaderTestHeaded
  • org.broad.igv.tdf.TDFDataSource
  • org.broad.igv.tdf.TDFReader
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