writer.getRootGroup().setAttribute("chromosomes", chrString.toString()); writer.getRootGroup().setAttribute(entry.getKey(), entry.getValue());
writer.getRootGroup().setAttribute(TDFWriter.CHROMOSOMES, chrString.toString()); writer.getRootGroup().setAttribute(entry.getKey(), entry.getValue());
/** * 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)); } }