List of usage examples for java.io BufferedReader BufferedReader
public BufferedReader(Reader in)
From source file:com.genentech.chemistry.openEye.apps.SDFMCSSSphereExclusion.java
public static void main(String... args) throws IOException { CommandLineParser parser = new PosixParser(); CommandLine cmd = null;//ww w . j a va 2s . c om try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } // the only reason not to match centroids in reverse order id if // a non-centroid is to be assigned to multiple centroids boolean printSphereMatchCount = cmd.hasOption("printSphereMatchCount"); boolean reverseMatch = !cmd.hasOption("checkSpheresInOrder") && !printSphereMatchCount; boolean printAll = cmd.hasOption("printAll") || printSphereMatchCount; double radius = Double.parseDouble(cmd.getOptionValue("radius")); String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String refFile = cmd.getOptionValue("ref"); SimComparatorFactory<OEMolBase, OEMolBase, SimComparator<OEMolBase>> compFact; compFact = getComparatorFactory(cmd); SphereExclusion<OEMolBase, SimComparator<OEMolBase>> alg = new SphereExclusion<OEMolBase, SimComparator<OEMolBase>>( compFact, refFile, outFile, radius, reverseMatch, printSphereMatchCount, printAll); alg.run(inFile); alg.close(); }
From source file:edu.mit.fss.examples.TDRSSFederate.java
/** * The main method. This configures the Orekit data path, creates the * SaudiComsat federate objects and launches the associated graphical user * interface./* ww w. ja v a 2 s . co m*/ * * @param args the arguments * @throws RTIexception the RTI exception * @throws URISyntaxException */ public static void main(String[] args) throws RTIexception, URISyntaxException { BasicConfigurator.configure(); logger.debug("Setting Orekit data path."); System.setProperty(DataProvidersManager.OREKIT_DATA_PATH, new File(TDRSSFederate.class.getResource("/orekit-data.zip").toURI()).getAbsolutePath()); logger.trace("Creating federate instance."); final TDRSSFederate federate = new TDRSSFederate(); logger.trace("Setting minimum step duration and time step."); long timeStep = 60 * 1000, minimumStepDuration = 100; federate.setMinimumStepDuration(minimumStepDuration); federate.setTimeStep(timeStep); logger.debug("Loading TLE data from file."); final List<Component> panels = new ArrayList<Component>(); for (String satName : Arrays.asList("TDRS 3", "TDRS 5", "TDRS 6", "TDRS 7", "TDRS 8", "TDRS 9", "TDRS 10", "TDRS 11")) { try { BufferedReader br = new BufferedReader(new InputStreamReader( federate.getClass().getClassLoader().getResourceAsStream("edu/mit/fss/examples/data.tle"))); while (br.ready()) { if (br.readLine().matches(".*" + satName + ".*")) { logger.debug("Found " + satName + " data."); logger.trace("Adding " + satName + " supplier space system."); SpaceSystem system = new SpaceSystem(satName, new TLE(br.readLine(), br.readLine()), 5123e3); federate.addObject(system); panels.add(new SpaceSystemPanel(federate, system)); try { logger.trace("Setting inital time."); federate.setInitialTime(system.getInitialState().getDate() .toDate(TimeScalesFactory.getUTC()).getTime()); } catch (IllegalArgumentException | OrekitException e) { logger.error(e.getMessage()); e.printStackTrace(); } break; } } br.close(); } catch (IllegalArgumentException | OrekitException | IOException e) { e.printStackTrace(); logger.fatal(e); } } try { logger.trace("Adding WSGT ground station."); SurfaceSystem wsgt = new SurfaceSystem("WSGT", new GeodeticPoint(FastMath.toRadians(32.5007), FastMath.toRadians(-106.6086), 1474), new AbsoluteDate(), 5123e3, 5); federate.addObject(wsgt); panels.add(new SurfaceSystemPanel(federate, wsgt)); logger.trace("Adding STGT ground station."); SurfaceSystem stgt = new SurfaceSystem("STGT", new GeodeticPoint(FastMath.toRadians(32.5430), FastMath.toRadians(-106.6120), 1468), new AbsoluteDate(), 5123e3, 5); federate.addObject(stgt); panels.add(new SurfaceSystemPanel(federate, stgt)); logger.trace("Adding GRGT ground station."); SurfaceSystem grgt = new SurfaceSystem("GRGT", new GeodeticPoint(FastMath.toRadians(13.6148), FastMath.toRadians(144.8565), 142), new AbsoluteDate(), 5123e3, 5); federate.addObject(grgt); panels.add(new SurfaceSystemPanel(federate, grgt)); } catch (OrekitException e) { logger.error(e.getMessage()); e.printStackTrace(); } logger.debug("Launching the graphical user interface."); try { SwingUtilities.invokeAndWait(new Runnable() { @Override public void run() { MemberFrame frame = new MemberFrame(federate, new MultiComponentPanel(panels)); frame.pack(); frame.setVisible(true); } }); } catch (InvocationTargetException | InterruptedException e) { logger.error(e.getMessage()); e.printStackTrace(); } logger.trace("Setting federate name, type, and FOM path."); federate.getConnection().setFederateName("TDRSS"); federate.getConnection().setFederateType("FSS Supplier"); federate.getConnection().setFederationName("FSS"); federate.getConnection().setFomPath( new File(federate.getClass().getClassLoader().getResource("edu/mit/fss/hla/fss.xml").toURI()) .getAbsolutePath()); federate.getConnection().setOfflineMode(false); federate.connect(); }
From source file:de.citec.csra.elancsv.parser.SimpleParser.java
public static void main(String[] args) throws IOException, ParseException { Options opts = new Options(); opts.addOption("file", true, "Tab-separated ELAN export file to load."); opts.addOption("tier", true, "Tier to analyze. Optional: Append ::num to interpret annotations numerically."); opts.addOption("format", true, "How to read information from the file name. %V -> participant, %A -> annoatator, %C -> condition, e.g. \"%V - %A\""); opts.addOption("help", false, "Print this help and exit"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(opts, args); if (cmd.hasOption("help")) { helpExit(opts, "where OPTION includes:"); }/*from w w w . jav a2s . co m*/ String infile = cmd.getOptionValue("file"); if (infile == null) { helpExit(opts, "Error: no file given."); } String format = cmd.getOptionValue("format"); if (format == null) { helpExit(opts, "Error: no format given."); } String tier = cmd.getOptionValue("tier"); if (tier == null) { helpExit(opts, "Error: no tier given."); } // TODO count values in annotations (e.g. search all robot occurrences) String[] tn = tier.split("::"); boolean numeric = false; if (tn.length == 2 && tn[1].equals("num")) { numeric = true; tier = tn[0]; } format = "^" + format + "$"; format = format.replaceFirst("%V", "(?<V>.*?)"); format = format.replaceFirst("%A", "(?<A>.*?)"); format = format.replaceFirst("%C", "(?<C>.*?)"); Pattern pa = Pattern.compile(format); Map<String, Participant> participants = new HashMap<>(); BufferedReader br = new BufferedReader(new FileReader(infile)); String line; int lineno = 0; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); lineno++; if (parts.length < 5) { System.err.println("WARNING: line '" + lineno + "' too short '" + line + "'"); continue; } Annotation a = new Annotation(Long.valueOf(parts[ElanFormat.START.field]), Long.valueOf(parts[ElanFormat.STOP.field]), Long.valueOf(parts[ElanFormat.DURATION.field]), parts[ElanFormat.VALUE.field]); String tname = parts[ElanFormat.TIER.field]; String file = parts[ElanFormat.FILE.field].replaceAll(".eaf", ""); Matcher m = pa.matcher(file); String vp = file; String condition = "?"; String annotator = "?"; String participantID = vp; if (m.find()) { vp = m.group("V"); if (format.indexOf("<A>") > 0) { annotator = m.group("A"); } if (format.indexOf("<C>") > 0) { condition = m.group("C"); } } participantID = vp + ";" + annotator; if (!participants.containsKey(participantID)) { participants.put(participantID, new Participant(vp, condition, annotator)); } Participant p = participants.get(participantID); if (!p.tiers.containsKey(tname)) { p.tiers.put(tname, new Tier(tname)); } p.tiers.get(tname).annotations.add(a); } Map<String, Map<String, Number>> values = new HashMap<>(); Set<String> rownames = new HashSet<>(); String allCountKey = "c: all values"; String allDurationKey = "d: all values"; String allMeanKey = "m: all values"; for (Map.Entry<String, Participant> e : participants.entrySet()) { // System.out.println(e); Tier t = e.getValue().tiers.get(tier); String participantID = e.getKey(); if (!values.containsKey(participantID)) { values.put(participantID, new HashMap<String, Number>()); } Map<String, Number> row = values.get(participantID); //participant id if (t != null) { row.put(allCountKey, 0l); row.put(allDurationKey, 0l); row.put(allMeanKey, 0l); for (Annotation a : t.annotations) { long countAll = (long) row.get(allCountKey) + 1; long durationAll = (long) row.get(allDurationKey) + a.duration; long meanAll = durationAll / countAll; row.put(allCountKey, countAll); row.put(allDurationKey, durationAll); row.put(allMeanKey, meanAll); if (!numeric) { String countKey = "c: " + a.value; String durationKey = "d: " + a.value; String meanKey = "m: " + a.value; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(durationKey)) { row.put(durationKey, 0l); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } long count = (long) row.get(countKey) + 1; long duration = (long) row.get(durationKey) + a.duration; double mean = duration * 1.0 / count; row.put(countKey, count); row.put(durationKey, duration); row.put(meanKey, mean); rownames.add(countKey); rownames.add(durationKey); rownames.add(meanKey); } else { String countKey = "c: " + t.name; String sumKey = "s: " + t.name; String meanKey = "m: " + t.name; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(sumKey)) { row.put(sumKey, 0d); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } double d = 0; try { d = Double.valueOf(a.value); } catch (NumberFormatException ex) { } long count = (long) row.get(countKey) + 1; double sum = (double) row.get(sumKey) + d; double mean = sum / count; row.put(countKey, count); row.put(sumKey, sum); row.put(meanKey, mean); rownames.add(countKey); rownames.add(sumKey); rownames.add(meanKey); } } } } ArrayList<String> list = new ArrayList(rownames); Collections.sort(list); StringBuilder header = new StringBuilder("ID;Annotator;"); header.append(allCountKey); header.append(";"); header.append(allDurationKey); header.append(";"); header.append(allMeanKey); header.append(";"); for (String l : list) { header.append(l); header.append(";"); } System.out.println(header); for (Map.Entry<String, Map<String, Number>> e : values.entrySet()) { StringBuilder row = new StringBuilder(e.getKey()); row.append(";"); if (e.getValue().containsKey(allCountKey)) { row.append(e.getValue().get(allCountKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allDurationKey)) { row.append(e.getValue().get(allDurationKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allMeanKey)) { row.append(e.getValue().get(allMeanKey)); } else { row.append("0"); } row.append(";"); for (String l : list) { if (e.getValue().containsKey(l)) { row.append(e.getValue().get(l)); } else { row.append("0"); } row.append(";"); } System.out.println(row); } }
From source file:PlyBounder.java
public static void main(String[] args) { // Get the commandline arguments Options options = new Options(); // Available options Option plyPath = OptionBuilder.withArgName("dir").hasArg() .withDescription("directory containing input .ply files").create("plyPath"); Option boundingbox = OptionBuilder.withArgName("string").hasArg() .withDescription("bounding box in WKT notation").create("boundingbox"); Option outputPlyFile = OptionBuilder.withArgName("file").hasArg().withDescription("output PLY file name") .create("outputPlyFile"); options.addOption(plyPath);/* ww w .j a v a 2 s. c o m*/ options.addOption(boundingbox); options.addOption(outputPlyFile); String plydir = "."; String boundingboxstr = ""; String outputfilename = ""; CommandLineParser parser = new DefaultParser(); try { // parse the command line arguments CommandLine line = parser.parse(options, args); boundingboxstr = line.getOptionValue("boundingbox"); outputfilename = line.getOptionValue("outputPlyFile"); if (line.hasOption("plyPath")) { // print the value of block-size plydir = line.getOptionValue("plyPath"); System.out.println("Using plyPath=" + plydir); } else { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("PlyBounder", options); } //System.out.println( "plyPath=" + line.getOptionValue( "plyPath" ) ); } catch (ParseException exp) { System.err.println("Error getting arguments: " + exp.getMessage()); } // input directory // Get list of files File dir = new File(plydir); //System.out.println("Getting all files in " + dir.getCanonicalPath()); List<File> files = (List<File>) FileUtils.listFiles(dir, new String[] { "ply", "PLY" }, false); for (File file : files) { try { System.out.println("file=" + file.getCanonicalPath()); } catch (IOException e) { e.printStackTrace(); } } String sometempfile = "magweg.wkt"; String s = null; // Loop through .ply files in directory for (File file : files) { try { String cmdl[] = { "./ply-tool.py", "intersection", file.getCanonicalPath(), boundingboxstr, sometempfile }; //System.out.println("Running: " + Arrays.toString(cmdl)); Process p = Runtime.getRuntime().exec(cmdl); BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream())); BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream())); // read the output from the command System.out.println("cmdout:\n"); while ((s = stdInput.readLine()) != null) { System.out.println(s); } // read any errors from the attempted command System.out.println("cmderr:\n"); while ((s = stdError.readLine()) != null) { System.out.println(s); } } catch (IOException e) { e.printStackTrace(); } } // Write new .ply file //ply-tool write setfile outputPlyFile try { String cmdl = "./ply-tool.py write " + sometempfile + " " + outputfilename; System.out.println("Running: " + cmdl); Process p = Runtime.getRuntime().exec(cmdl); BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream())); BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream())); // read the output from the command System.out.println("cmdout:\n"); while ((s = stdInput.readLine()) != null) { System.out.println(s); } // read any errors from the attempted command System.out.println("cmderr:\n"); while ((s = stdError.readLine()) != null) { System.out.println(s); } } catch (IOException e) { e.printStackTrace(); } // Done System.out.println("Done"); }
From source file:edu.upenn.egricelab.AlignerBoost.FilterSAMAlignPE.java
public static void main(String[] args) { if (args.length == 0) { printUsage();/*ww w .j a v a 2s . c o m*/ return; } try { parseOptions(args); } catch (IllegalArgumentException e) { System.err.println("Error: " + e.getMessage()); printUsage(); return; } // Read in chrList, if specified if (chrFile != null) { chrFilter = new HashSet<String>(); try { BufferedReader chrFilterIn = new BufferedReader(new FileReader(chrFile)); String chr = null; while ((chr = chrFilterIn.readLine()) != null) chrFilter.add(chr); chrFilterIn.close(); if (verbose > 0) System.err.println( "Only looking at alignments on " + chrFilter.size() + " specified chromosomes"); } catch (IOException e) { System.err.println("Error: " + e.getMessage()); return; } } if (verbose > 0) { // Start the processMonitor processMonitor = new Timer(); // Start the ProcessStatusTask statusTask = new ProcessStatusTask(); // Schedule to show the status every 1 second processMonitor.scheduleAtFixedRate(statusTask, 0, statusFreq); } // Read in known SNP file, if specified if (knownSnpFile != null) { if (verbose > 0) System.err.println("Checking known SNPs from user specified VCF file"); knownVCF = new VCFFileReader(new File(knownSnpFile)); } SamReaderFactory readerFac = SamReaderFactory.makeDefault(); SAMFileWriterFactory writerFac = new SAMFileWriterFactory(); if (!isSilent) readerFac.validationStringency(ValidationStringency.LENIENT); // use LENIENT stringency else readerFac.validationStringency(ValidationStringency.SILENT); // use SILENT stringency SamReader in = readerFac.open(new File(inFile)); SAMFileHeader inHeader = in.getFileHeader(); if (inHeader.getGroupOrder() == GroupOrder.reference && inHeader.getSortOrder() == SortOrder.coordinate) System.err.println("Warning: Input file '" + inFile + "' might be sorted by coordinate and cannot be correctly processed!"); SAMFileHeader header = inHeader.clone(); // copy the inFile header as outFile header // Add new programHeader SAMProgramRecord progRec = new SAMProgramRecord(progName); progRec.setProgramName(progName); progRec.setProgramVersion(progVer); progRec.setCommandLine(StringUtils.join(" ", args)); header.addProgramRecord(progRec); //System.err.println(inFile + " groupOrder: " + in.getFileHeader().getGroupOrder() + " sortOrder: " + in.getFileHeader().getSortOrder()); // reset the orders header.setGroupOrder(groupOrder); header.setSortOrder(sortOrder); // write SAMHeader String prevID = null; SAMRecord prevRecord = null; List<SAMRecord> alnList = new ArrayList<SAMRecord>(); List<SAMRecordPair> alnPEList = null; // Estimate fragment length distribution by scan one-pass through the alignments SAMRecordIterator results = in.iterator(); if (!NO_ESTIMATE) { if (verbose > 0) { System.err.println("Estimating insert fragment size distribution ..."); statusTask.reset(); statusTask.setInfo("alignments scanned"); } long N = 0; double fragL_S = 0; // fragLen sum double fragL_SS = 0; // fragLen^2 sum while (results.hasNext()) { SAMRecord record = results.next(); if (verbose > 0) statusTask.updateStatus(); if (record.getFirstOfPairFlag() && !record.isSecondaryOrSupplementary()) { double fragLen = Math.abs(record.getInferredInsertSize()); if (fragLen != 0 && fragLen >= MIN_FRAG_LEN && fragLen <= MAX_FRAG_LEN) { // only consider certain alignments N++; fragL_S += fragLen; fragL_SS += fragLen * fragLen; } // stop estimate if already enough if (MAX_ESTIMATE_SCAN > 0 && N >= MAX_ESTIMATE_SCAN) break; } } if (verbose > 0) statusTask.finish(); // estimate fragment size if (N >= MIN_ESTIMATE_BASE) { // override command line values MEAN_FRAG_LEN = fragL_S / N; SD_FRAG_LEN = Math.sqrt((N * fragL_SS - fragL_S * fragL_S) / (N * (N - 1))); String estStr = String.format("Estimated fragment size distribution: N(%.1f, %.1f)", MEAN_FRAG_LEN, SD_FRAG_LEN); if (verbose > 0) System.err.println(estStr); // also add the estimation to comment header.addComment(estStr); } else { System.err.println( "Unable to estimate the fragment size distribution due to too few observed alignments"); System.err.println( "You have to specify the '--mean-frag-len' and '--sd-frag-len' on the command line and re-run this step"); statusTask.cancel(); processMonitor.cancel(); return; } // Initiate the normal model normModel = new NormalDistribution(MEAN_FRAG_LEN, SD_FRAG_LEN); // reset the iterator, if necessary if (in.type() == SamReader.Type.SAM_TYPE) { try { in.close(); } catch (IOException e) { System.err.println(e.getMessage()); } in = readerFac.open(new File(inFile)); } results.close(); results = in.iterator(); } // end of NO_ESTIMATE SAMFileWriter out = OUT_IS_SAM ? writerFac.makeSAMWriter(header, false, new File(outFile)) : writerFac.makeBAMWriter(header, false, new File(outFile)); // check each alignment again if (verbose > 0) { System.err.println("Filtering alignments ..."); statusTask.reset(); statusTask.setInfo("alignments processed"); } while (results.hasNext()) { SAMRecord record = results.next(); if (verbose > 0) statusTask.updateStatus(); String ID = record.getReadName(); // fix read and quality string for this read, if is a secondary hit from multiple hits, used for BWA alignment if (ID.equals(prevID) && record.getReadLength() == 0) SAMAlignFixer.fixSAMRecordRead(record, prevRecord); if (chrFilter != null && !chrFilter.contains(record.getReferenceName())) { prevID = ID; prevRecord = record; continue; } // fix MD:Z string for certain aligners with invalid format (i.e. seqAlto) if (fixMD) SAMAlignFixer.fixMisStr(record); // fix alignment, ignore if failed (unmapped or empty) if (!SAMAlignFixer.fixSAMRecord(record, knownVCF, DO_1DP)) { prevID = ID; prevRecord = record; continue; } if (!record.getReadPairedFlag()) { System.err.println("Error: alignment is not from a paired-end read at\n" + record.getSAMString()); out.close(); statusTask.cancel(); processMonitor.cancel(); return; } if (!ID.equals(prevID) && prevID != null || !results.hasNext()) { // a non-first new ID meet, or end of alignments // create alnPEList from filtered alnList alnPEList = createAlnPEListFromAlnList(alnList); //System.err.printf("%d alignments for %s transformed to %d alnPairs%n", alnList.size(), prevID, alnPEList.size()); int totalPair = alnPEList.size(); // filter highly unlikely PEhits filterPEHits(alnPEList, MIN_ALIGN_RATE, MIN_IDENTITY); // calculate posterior mapQ for each pair calcPEHitPostP(alnPEList, totalPair, MAX_HIT); // filter hits by mapQ if (MIN_MAPQ > 0) filterPEHits(alnPEList, MIN_MAPQ); // sort the list first with an anonymous class of comparator, with DESCREASING order Collections.sort(alnPEList, Collections.reverseOrder()); // control max-best if (MAX_BEST != 0 && alnPEList.size() > MAX_BEST) { // potential too much best hits int nBestStratum = 0; int bestMapQ = alnPEList.get(0).getPEMapQ(); // best mapQ from first PE for (SAMRecordPair pr : alnPEList) if (pr.getPEMapQ() == bestMapQ) nBestStratum++; else break; // stop searching for sorted list if (nBestStratum > MAX_BEST) alnPEList.clear(); } // filter alignments with auxiliary filters if (!MAX_SENSITIVITY) filterPEHits(alnPEList, MAX_SEED_MIS, MAX_SEED_INDEL, MAX_ALL_MIS, MAX_ALL_INDEL); // report remaining secondary alignments, up-to MAX_REPORT for (int i = 0; i < alnPEList.size() && (MAX_REPORT == 0 || i < MAX_REPORT); i++) { SAMRecordPair repPair = alnPEList.get(i); if (doUpdateBit) repPair.setNotPrimaryAlignmentFlags(i != 0); int nReport = MAX_REPORT == 0 ? Math.min(alnPEList.size(), MAX_REPORT) : alnPEList.size(); int nFiltered = alnPEList.size(); if (repPair.fwdRecord != null) { repPair.fwdRecord.setAttribute("NH", nReport); repPair.fwdRecord.setAttribute("XN", nFiltered); out.addAlignment(repPair.fwdRecord); } if (repPair.revRecord != null) { repPair.revRecord.setAttribute("NH", nReport); repPair.revRecord.setAttribute("XN", nFiltered); out.addAlignment(repPair.revRecord); } } // reset list alnList.clear(); alnPEList.clear(); } // update if (!ID.equals(prevID)) { prevID = ID; prevRecord = record; } alnList.add(record); } // end while try { in.close(); out.close(); } catch (IOException e) { System.err.println(e.getMessage()); } // Terminate the monitor task and monitor if (verbose > 0) { statusTask.cancel(); statusTask.finish(); processMonitor.cancel(); } }
From source file:com.cyberway.issue.net.PublicSuffixes.java
/** * Utility method for dumping a regex String, based on a published public * suffix list, which matches any SURT-form hostname up through the broadest * 'private' (assigned/sold) domain-segment. That is, for any of the * SURT-form hostnames...//w w w . j a v a2s.c o m * * com,example, com,example,www, com,example,california,www * * ...the regex will match 'com,example,'. * * @param args * @throws IOException */ public static void main(String args[]) throws IOException { String regex; if (args.length == 0 || "=".equals(args[0])) { // use bundled list regex = getTopmostAssignedSurtPrefixRegex(); } else { // use specified filename BufferedReader reader = new BufferedReader(new FileReader(args[0])); regex = getTopmostAssignedSurtPrefixRegex(reader); IOUtils.closeQuietly(reader); } boolean needsClose = false; BufferedWriter writer; if (args.length >= 2) { // writer to specified file writer = new BufferedWriter(new FileWriter(args[1])); needsClose = true; } else { // write to stdout writer = new BufferedWriter(new OutputStreamWriter(System.out)); } writer.append(regex); writer.flush(); if (needsClose) { writer.close(); } }
From source file:de.binfalse.jatter.App.java
/** * Run jatter's main./*from w w w . j a va 2 s . co m*/ * * @param args * the arguments * @throws Exception * the exception */ public static void main(String[] args) throws Exception { Options options = new Options(); Option conf = new Option("c", "config", true, "config file path"); conf.setRequired(false); options.addOption(conf); Option t = new Option("t", "template", false, "show a config template"); t.setRequired(false); options.addOption(t); Option v = new Option("v", "verbose", false, "print information messages"); v.setRequired(false); options.addOption(v); Option d = new Option("d", "debug", false, "print debugging messages incl stack traces"); d.setRequired(false); options.addOption(d); Option h = new Option("h", "help", false, "show help"); h.setRequired(false); options.addOption(h); CommandLineParser parser = new DefaultParser(); CommandLine cmd; try { cmd = parser.parse(options, args); if (cmd.hasOption("h")) throw new RuntimeException("showing the help page"); } catch (Exception e) { help(options, e.getMessage()); return; } if (cmd.hasOption("t")) { System.out.println(); BufferedReader br = new BufferedReader(new InputStreamReader( App.class.getClassLoader().getResourceAsStream("config.properties.template"))); while (br.ready()) System.out.println(br.readLine()); br.close(); System.exit(0); } if (cmd.hasOption("v")) LOGGER.setMinLevel(LOGGER.INFO); if (cmd.hasOption("d")) { LOGGER.setMinLevel(LOGGER.DEBUG); LOGGER.setLogStackTrace(true); } if (!cmd.hasOption("c")) help(options, "a config file is required for running jatter"); startJatter(cmd.getOptionValue("c")); }
From source file:com.interacciones.mxcashmarketdata.driver.client.DriverClient.java
public static void main(String[] args) throws Throwable { init(args);/*from w w w. j a v a 2 s . c o m*/ NioSocketConnector connector = new NioSocketConnector(); // Configure the service. connector.setConnectTimeoutMillis(CONNECT_TIMEOUT); if (USE_CUSTOM_CODEC) { connector.getFilterChain().addLast("codec", new ProtocolCodecFilter(new SumUpProtocolCodecFactory(false))); } else { connector.getFilterChain().addLast("codec", new ProtocolCodecFilter(new ObjectSerializationCodecFactory())); } int[] values = new int[] {}; connector.getFilterChain().addLast("logger", new LoggingFilter()); connector.setHandler(new ClientSessionHandler(values)); long time = System.currentTimeMillis(); IoSession session; for (;;) { try { System.out.println(host + " " + port + " " + fileTest); ConnectFuture future = connector.connect(new InetSocketAddress(host, port)); future.awaitUninterruptibly(); session = future.getSession(); File file = new File(fileTest); FileInputStream is = new FileInputStream(file); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); int data = br.read(); int count = 0; IoBuffer ib = IoBuffer.allocate(274); ib.setAutoExpand(true); boolean flagcount = false; while (data != -1) { data = br.read(); ib.put((byte) data); if (flagcount) { count++; } if (data == 13) { count = 1; flagcount = true; LOGGER.debug(ib.toString()); } if (count == 4) { ib.flip(); session.write(ib); ib = IoBuffer.allocate(274); ib.setAutoExpand(true); flagcount = false; count = 0; //Thread.sleep(500); } } break; } catch (RuntimeIoException e) { LOGGER.error("Failed to connect."); e.printStackTrace(); Thread.sleep(5000); } } time = System.currentTimeMillis() - time; LOGGER.info("Time " + time); // wait until the summation is done session.getCloseFuture().awaitUninterruptibly(); connector.dispose(); }
From source file:edu.cmu.lti.oaqa.knn4qa.apps.FilterVocabulary.java
public static void main(String[] args) { String optKeys[] = { IN_VOC_FILE_PARAM, OUT_VOC_FILE_PARAM, CommonParams.MEM_FWD_INDEX_PARAM, CommonParams.MAX_WORD_QTY_PARAM }; String optDescs[] = { IN_VOC_FILE_DESC, OUT_VOC_FILE_DESC, CommonParams.MEM_FWD_INDEX_DESC, CommonParams.MAX_WORD_QTY_DESC }; boolean hasArg[] = { true, true, true, true }; ParamHelper mParamHelper = null;//from w w w.j av a 2 s . co m try { mParamHelper = new ParamHelper(args, optKeys, optDescs, hasArg); CommandLine cmd = mParamHelper.getCommandLine(); String outputFile = cmd.getOptionValue(OUT_VOC_FILE_PARAM); if (null == outputFile) { UsageSpecify(OUT_VOC_FILE_DESC, mParamHelper.getOptions()); } String inputFile = cmd.getOptionValue(IN_VOC_FILE_PARAM); if (null == inputFile) { UsageSpecify(IN_VOC_FILE_DESC, mParamHelper.getOptions()); } int maxWordQty = Integer.MAX_VALUE; String tmpi = cmd.getOptionValue(CommonParams.MAX_WORD_QTY_PARAM); if (null != tmpi) { maxWordQty = Integer.parseInt(tmpi); } String memFwdIndxName = cmd.getOptionValue(CommonParams.MEM_FWD_INDEX_PARAM); if (null == memFwdIndxName) { UsageSpecify(CommonParams.MEM_FWD_INDEX_DESC, mParamHelper.getOptions()); } VocabularyFilterAndRecoder filter = new FrequentIndexWordFilterAndRecoder(memFwdIndxName, maxWordQty); BufferedReader finp = new BufferedReader( new InputStreamReader(CompressUtils.createInputStream(inputFile))); BufferedWriter fout = new BufferedWriter( new OutputStreamWriter(CompressUtils.createOutputStream(outputFile))); try { String line; int wordQty = 0; long addedQty = 0; long totalQty = 0; for (totalQty = 0; (line = finp.readLine()) != null;) { ++totalQty; // Skip empty lines line = line.trim(); if (line.isEmpty()) continue; GizaVocRec rec = new GizaVocRec(line); if (filter.checkWord(rec.mWord)) { rec.save(fout); addedQty++; } if (totalQty % REPORT_INTERVAL_QTY == 0) System.out.println(String.format( "Processed %d lines (%d source word entries) from '%s', added %d lines", totalQty, wordQty, inputFile, addedQty)); } } finally { finp.close(); fout.close(); } } catch (ParseException e) { Usage("Cannot parse arguments", mParamHelper != null ? mParamHelper.getOptions() : null); e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); System.err.println("Terminating due to an exception: " + e); System.exit(1); } }
From source file:smtpsend.java
/** * Example of how to extend the SMTPTransport class. * This example illustrates how to issue the XACT * command before the SMTPTransport issues the DATA * command./* w ww . j a v a 2s .c o m*/ * public static class SMTPExtension extends SMTPTransport { public SMTPExtension(Session session, URLName url) { super(session, url); // to check that we're being used System.out.println("SMTPExtension: constructed"); } protected synchronized OutputStream data() throws MessagingException { if (supportsExtension("XACCOUNTING")) issueCommand("XACT", 250); return super.data(); } } */ public static void main(String[] argv) { String to, subject = null, from = null, cc = null, bcc = null, url = null; String mailhost = null; String mailer = "smtpsend"; String file = null; String protocol = null, host = null, user = null, password = null; String record = null; // name of folder in which to record mail boolean debug = false; boolean verbose = false; boolean auth = false; String prot = "smtp"; BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); int optind; /* * Process command line arguments. */ for (optind = 0; optind < argv.length; optind++) { if (argv[optind].equals("-T")) { protocol = argv[++optind]; } else if (argv[optind].equals("-H")) { host = argv[++optind]; } else if (argv[optind].equals("-U")) { user = argv[++optind]; } else if (argv[optind].equals("-P")) { password = argv[++optind]; } else if (argv[optind].equals("-M")) { mailhost = argv[++optind]; } else if (argv[optind].equals("-f")) { record = argv[++optind]; } else if (argv[optind].equals("-a")) { file = argv[++optind]; } else if (argv[optind].equals("-s")) { subject = argv[++optind]; } else if (argv[optind].equals("-o")) { // originator from = argv[++optind]; } else if (argv[optind].equals("-c")) { cc = argv[++optind]; } else if (argv[optind].equals("-b")) { bcc = argv[++optind]; } else if (argv[optind].equals("-L")) { url = argv[++optind]; } else if (argv[optind].equals("-d")) { debug = true; } else if (argv[optind].equals("-v")) { verbose = true; } else if (argv[optind].equals("-A")) { auth = true; } else if (argv[optind].equals("-S")) { prot = "smtps"; } else if (argv[optind].equals("--")) { optind++; break; } else if (argv[optind].startsWith("-")) { System.out.println("Usage: smtpsend [[-L store-url] | [-T prot] [-H host] [-U user] [-P passwd]]"); System.out.println("\t[-s subject] [-o from-address] [-c cc-addresses] [-b bcc-addresses]"); System.out.println("\t[-f record-mailbox] [-M transport-host] [-d] [-a attach-file]"); System.out.println("\t[-v] [-A] [-S] [address]"); System.exit(1); } else { break; } } try { /* * Prompt for To and Subject, if not specified. */ if (optind < argv.length) { // XXX - concatenate all remaining arguments to = argv[optind]; System.out.println("To: " + to); } else { System.out.print("To: "); System.out.flush(); to = in.readLine(); } if (subject == null) { System.out.print("Subject: "); System.out.flush(); subject = in.readLine(); } else { System.out.println("Subject: " + subject); } /* * Initialize the JavaMail Session. */ Properties props = System.getProperties(); if (mailhost != null) props.put("mail." + prot + ".host", mailhost); if (auth) props.put("mail." + prot + ".auth", "true"); /* * Create a Provider representing our extended SMTP transport * and set the property to use our provider. * Provider p = new Provider(Provider.Type.TRANSPORT, prot, "smtpsend$SMTPExtension", "JavaMail demo", "no version"); props.put("mail." + prot + ".class", "smtpsend$SMTPExtension"); */ // Get a Session object Session session = Session.getInstance(props, null); if (debug) session.setDebug(true); /* * Register our extended SMTP transport. * session.addProvider(p); */ /* * Construct the message and send it. */ Message msg = new MimeMessage(session); if (from != null) msg.setFrom(new InternetAddress(from)); else msg.setFrom(); msg.setRecipients(Message.RecipientType.TO, InternetAddress.parse(to, false)); if (cc != null) msg.setRecipients(Message.RecipientType.CC, InternetAddress.parse(cc, false)); if (bcc != null) msg.setRecipients(Message.RecipientType.BCC, InternetAddress.parse(bcc, false)); msg.setSubject(subject); String text = collect(in); if (file != null) { // Attach the specified file. // We need a multipart message to hold the attachment. MimeBodyPart mbp1 = new MimeBodyPart(); mbp1.setText(text); MimeBodyPart mbp2 = new MimeBodyPart(); mbp2.attachFile(file); MimeMultipart mp = new MimeMultipart(); mp.addBodyPart(mbp1); mp.addBodyPart(mbp2); msg.setContent(mp); } else { // If the desired charset is known, you can use // setText(text, charset) msg.setText(text); } msg.setHeader("X-Mailer", mailer); msg.setSentDate(new Date()); // send the thing off /* * The simple way to send a message is this: * Transport.send(msg); * * But we're going to use some SMTP-specific features for * demonstration purposes so we need to manage the Transport * object explicitly. */ SMTPTransport t = (SMTPTransport) session.getTransport(prot); try { if (auth) t.connect(mailhost, user, password); else t.connect(); t.sendMessage(msg, msg.getAllRecipients()); } finally { if (verbose) System.out.println("Response: " + t.getLastServerResponse()); t.close(); } System.out.println("\nMail was sent successfully."); /* * Save a copy of the message, if requested. */ if (record != null) { // Get a Store object Store store = null; if (url != null) { URLName urln = new URLName(url); store = session.getStore(urln); store.connect(); } else { if (protocol != null) store = session.getStore(protocol); else store = session.getStore(); // Connect if (host != null || user != null || password != null) store.connect(host, user, password); else store.connect(); } // Get record Folder. Create if it does not exist. Folder folder = store.getFolder(record); if (folder == null) { System.err.println("Can't get record folder."); System.exit(1); } if (!folder.exists()) folder.create(Folder.HOLDS_MESSAGES); Message[] msgs = new Message[1]; msgs[0] = msg; folder.appendMessages(msgs); System.out.println("Mail was recorded successfully."); } } catch (Exception e) { /* * Handle SMTP-specific exceptions. */ if (e instanceof SendFailedException) { MessagingException sfe = (MessagingException) e; if (sfe instanceof SMTPSendFailedException) { SMTPSendFailedException ssfe = (SMTPSendFailedException) sfe; System.out.println("SMTP SEND FAILED:"); if (verbose) System.out.println(ssfe.toString()); System.out.println(" Command: " + ssfe.getCommand()); System.out.println(" RetCode: " + ssfe.getReturnCode()); System.out.println(" Response: " + ssfe.getMessage()); } else { if (verbose) System.out.println("Send failed: " + sfe.toString()); } Exception ne; while ((ne = sfe.getNextException()) != null && ne instanceof MessagingException) { sfe = (MessagingException) ne; if (sfe instanceof SMTPAddressFailedException) { SMTPAddressFailedException ssfe = (SMTPAddressFailedException) sfe; System.out.println("ADDRESS FAILED:"); if (verbose) System.out.println(ssfe.toString()); System.out.println(" Address: " + ssfe.getAddress()); System.out.println(" Command: " + ssfe.getCommand()); System.out.println(" RetCode: " + ssfe.getReturnCode()); System.out.println(" Response: " + ssfe.getMessage()); } else if (sfe instanceof SMTPAddressSucceededException) { System.out.println("ADDRESS SUCCEEDED:"); SMTPAddressSucceededException ssfe = (SMTPAddressSucceededException) sfe; if (verbose) System.out.println(ssfe.toString()); System.out.println(" Address: " + ssfe.getAddress()); System.out.println(" Command: " + ssfe.getCommand()); System.out.println(" RetCode: " + ssfe.getReturnCode()); System.out.println(" Response: " + ssfe.getMessage()); } } } else { System.out.println("Got Exception: " + e); if (verbose) e.printStackTrace(); } } }