private void loadAnnotations(String annotationFilename) { try { LineIterator lines = new LineIterator(new FastBufferedReader(new FileReader(annotationFilename))); for (MutableString line : lines.allLines()) { if (line.startsWith("#")) continue; String tokens[] = line.toString().split("\t"); final String chromosome = tokens[0]; int position = Integer.parseInt(tokens[1]); // convert to zero-based position used by goby/variationanalysis: position -= 1; Int2ObjectAVLTreeMap<Annotation> perPositionMap = annotations.getOrDefault(chromosome, new Int2ObjectAVLTreeMap<>()); Annotation a = new Annotation(); a.position = position; a.toBase = tokens.length >= 3 ? tokens[2] : null; a.frequency = tokens.length >= 4 ? Float.parseFloat(tokens[3]) : null; perPositionMap.put(position, a); annotations.put(chromosome, perPositionMap); } } catch (FileNotFoundException e) { throw new RuntimeException("Unable to find annotation filename:" + annotationFilename, e); } }
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
if (jsapResult.userSpecified("loadAll")) lineIterator = ((LineIterator)lineIterator).allLines().iterator();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done(); } else collection = new FileLinesCollection(stringFile, encoding.toString(), zipped);
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();