public static void dumpTile(String ibfFile, String dsName, int tileNumber) { TDFReader reader = TDFReader.getReader(ibfFile); TDFDataset ds = reader.getDataset(dsName); TDFTile tile = reader.readTile(ds, tileNumber); if (tile == null) { System.out.println("Null tile: " + dsName + " [" + tileNumber + "]"); } else { dumpTileData(reader, "", tile, System.out); } }
TDFTile tile = reader.readTile(ds, i); if (tile != null) { System.out.print(" " + i);
synchronized TDFTile getTile(int t) { String key = getName() + "_" + t; TDFTile tile = null; if (!cache.containsKey(key)) { tile = reader.readTile(this, t); cache.put(key, tile); } else { tile = cache.get(key); } return tile; }
synchronized TDFTile getTile(int t) { String key = getName() + "_" + t; TDFTile tile = null; if (!cache.containsKey(key)) { tile = reader.readTile(this, t); cache.put(key, tile); } else { tile = cache.get(key); } return tile; }
TDFTile tile = reader.readTile(ds, tileNumber); if (tile == null) { System.out.println("Null tile: " + dsName + " [" + tileNumber + "]");
TDFTile tile = reader.readTile(ds, tileNumber); if (tile == null) {
@Test public void testReader() throws Exception { String url = "http://data.broadinstitute.org/igvdata/encode/hg18/broadHistone/SignalK562H3k4me3.tdf"; TDFReader reader = new TDFReader(new ResourceLocator(url)); int version = reader.getVersion(); assertEquals(3, version); assertTrue(reader.compressed); String [] trackNames = reader.getTrackNames(); int nTracks = trackNames.length; assertEquals(1, nTracks); String trackName = trackNames[0]; assertEquals(trackName, "SignalK562H3k4me3.wig.gz"); Set<String> chrNames = reader.getChromosomeNames(); int nChromosomes = chrNames.size(); assertEquals(24, nChromosomes); String datasetName = "/chr1/z0/mean"; TDFDataset dataset = reader.getDataset(datasetName); assertEquals(datasetName, dataset.getName()); TDFTile tile = reader.readTile(dataset, 0); assertNotNull(tile); } }
assertEquals("value2", ds.getAttribute("attr2")); TDFTile dsTile = reader.readTile(ds, 0);