static void calculateEigenvector(String file, String chr, int binsize) throws IOException { if (!file.endsWith("hic")) { System.err.println("Only 'hic' files are supported"); System.exit(-1); } // Load the expected density function, if it exists. Map<Integer, DensityFunction> zoomToDensityMap = null; String densityFile = file + ".densities"; if (FileUtils.resourceExists(densityFile)) { InputStream is = null; try { is = ParsingUtils.openInputStream(densityFile); zoomToDensityMap = DensityUtil.readDensities(is); } finally { if (is != null) is.close(); } } else { System.err.println("Densities file doesn't exist"); System.exit(-1); } SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file); Dataset dataset = (new DatasetReader(ss)).read(); Chromosome[] tmp = dataset.getChromosomes(); Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>(); for (Chromosome c : tmp) { chromosomeMap.put(c.getName(), c); } if (!chromosomeMap.containsKey(chr)) { System.err.println("Unknown chromosome: " + chr); System.exit(-1); } int zoomIdx = 0; boolean found = false; for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) { if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) { found = true; break; } } if (!found) { System.err.println("Unknown bin size: " + binsize); System.exit(-1); } Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr), chromosomeMap.get(chr)); MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx); final DensityFunction df = zoomToDensityMap.get(zd.getZoom()); double[] eigenvector = zd.computeEigenvector(df, 0); for (double ev : eigenvector) System.out.print(ev + " "); System.out.println(); }