Package org.broad.igv.data

Examples of org.broad.igv.data.WiggleDataset

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        File outFile = new File(fullout);
        assertTrue(outFile.exists());
        assertTrue(outFile.canRead());

        WiggleParser parser = new WiggleParser(new ResourceLocator(fullout));
        WiggleDataset wgs = parser.parse();
        assertEquals(3, wgs.getChromosomes().length);
        for(String chr: new String[]{"chr1", "chr3", "chr7"}){
            assertNotNull(wgs.getData(null, chr));
        }

        BufferedReader reader = new BufferedReader(new FileReader(outFile));
        String line = reader.readLine();
        assertTrue(line.contains("wiggle_0"));
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                File outFile = new File(fullout);
                assertTrue(outFile.exists());
                assertTrue(outFile.canRead());

                ResourceLocator locator = new ResourceLocator(fullout);
                WiggleDataset ds = (new WiggleParser(locator, IgvTools.loadGenome(hg18id))).parse();

                //We miss a few alignments with this option sometimes,
                //so it doesn't total up the same
                if (!opt.contains("strands=first")) {
                    float[] linetotals = getLineTotals(fullout);
                    rowTotals.put(opt, linetotals);
                }

                if (query) {
                    assertEquals(1, ds.getChromosomes().length);
                    assertEquals(chr, ds.getChromosomes()[0]);

                    int[] starts = ds.getStartLocations(chr);
                    for (Integer act_start : starts) {
                        assertTrue(act_start + " is outside range", act_start >= start - winsize && act_start < end + winsize);
                    }
                }
            }
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            e.printStackTrace();
        }
        Assume.assumeTrue(genome != null);


        WiggleDataset ds = (new WiggleParser(new ResourceLocator(wigPath), genome)).parse();
        DatasetDataSource wigSource = new DatasetDataSource(wigPath, ds, genome);


        TDFReader tdfReader = TDFReader.getReader(tdfPath);
        TDFDataSource tdfSource = new TDFDataSource(tdfReader, 0, tdfPath, genome);
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Related Classes of org.broad.igv.data.WiggleDataset

  • org.broad.igv.tdf.TDFRegressionTests
  • org.broad.igv.tools.IGVToolsCountTest
  • org.broad.igv.track.TrackProperties
  • org.broad.igv.util.ArrayHeapIntSorter
  • org.broad.igv.util.collections.FloatArrayList
  • org.broad.igv.util.collections.IntArrayList
  • org.broad.igv.util.IntComparator
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