/** * Called to set inital parameters. It is required that this be called * prior to writing the file */ @Override public void setTrackParameters(TrackType trackType, String trackLine, String[] trackNames) throws IOException { if (trackLine != null) { System.out.println(trackLine); } if (outputFile != null && writer == null) { writer = new TDFWriter(outputFile, genome.getId(), trackType, trackLine, trackNames, windowFunctions, compressed); nTracks = trackNames.length; // Convert genome coordinates from bp to kbp int genomeLength = (int) (genome.getLength() / 1000); genomeZoom = new Zoom(Globals.CHR_ALL, 0, genomeLength); TDFGroup rootGroup = writer.getRootGroup(); rootGroup.setAttribute("genome", genome.getId()); rootGroup.setAttribute("maxZoom", String.valueOf(nZoom)); } }
/** * Called to set initial parameters. It is required that this be called * prior to writing the file */ public void setTrackParameters(TrackType trackType, String trackLine, String[] trackNames, boolean computeWholeGenome) { if (trackLine != null) { log.info(trackLine); } if (outputFile != null && writer == null) { writer = new TDFWriter(outputFile, genome.getId(), trackType, trackLine, trackNames, windowFunctions, compressed); nTracks = trackNames.length; // Convert genome coordinates from bp to kbp if (computeWholeGenome) { int genomeLength = (int) (genome.getNominalLength() / 1000); genomeZoom = new Zoom(Globals.CHR_ALL, 0, genomeLength); } TDFGroup rootGroup = writer.getRootGroup(); rootGroup.setAttribute("genome", genome.getId()); rootGroup.setAttribute("maxZoom", String.valueOf(nZoom)); } }
writer.getRootGroup().setAttribute("chromosomes", chrString.toString()); writer.getRootGroup().setAttribute(entry.getKey(), entry.getValue()); group.setAttribute(TDFGroup.USE_PERCENTILE_AUTOSCALING, "true"); for (WindowFunction wf : allDataFunctions) { group.setAttribute(wf.getDisplayName(), String.valueOf(allDataStats.getValue(wf)));
writer.getRootGroup().setAttribute(TDFWriter.CHROMOSOMES, chrString.toString()); writer.getRootGroup().setAttribute(entry.getKey(), entry.getValue()); group.setAttribute(TDFGroup.USE_PERCENTILE_AUTOSCALING, "true"); for (WindowFunction wf : allDataFunctions) { group.setAttribute(wf.getValue(), String.valueOf(allDataStats.getValue(wf)));
/** * Test of createGroup method, of class IBFWriter. */ @Test public void testCreateGroup() { File testFile = new File("test1.tdf"); testFile.deleteOnExit(); String groupName = "/chr1"; TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false); TDFGroup group = writer.createGroup(groupName); group.setAttribute("attKey", "attValue"); group.setAttribute("attKey2", "attValue2"); writer.closeFile(); TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath()); group = reader.getGroup(groupName); assertEquals(groupName, group.getName()); assertEquals(2, group.attributes.size()); assertEquals("attValue", group.attributes.get("attKey")); assertEquals("attValue2", group.attributes.get("attKey2")); reader.close(); }