List of usage examples for java.io PrintStream PrintStream
public PrintStream(File file) throws FileNotFoundException
From source file:io.anserini.search.SearchWebCollection.java
public static void main(String[] args) throws Exception { SearchArgs searchArgs = new SearchArgs(); CmdLineParser parser = new CmdLineParser(searchArgs, ParserProperties.defaults().withUsageWidth(90)); try {//from ww w . j av a2 s .c om parser.parseArgument(args); } catch (CmdLineException e) { System.err.println(e.getMessage()); parser.printUsage(System.err); System.err.println("Example: SearchWebCollection" + parser.printExample(OptionHandlerFilter.REQUIRED)); return; } LOG.info("Reading index at " + searchArgs.index); Directory dir; if (searchArgs.inmem) { LOG.info("Using MMapDirectory with preload"); dir = new MMapDirectory(Paths.get(searchArgs.index)); ((MMapDirectory) dir).setPreload(true); } else { LOG.info("Using default FSDirectory"); dir = FSDirectory.open(Paths.get(searchArgs.index)); } Similarity similarity = null; if (searchArgs.ql) { LOG.info("Using QL scoring model"); similarity = new LMDirichletSimilarity(searchArgs.mu); } else if (searchArgs.bm25) { LOG.info("Using BM25 scoring model"); similarity = new BM25Similarity(searchArgs.k1, searchArgs.b); } else { LOG.error("Error: Must specify scoring model!"); System.exit(-1); } RerankerCascade cascade = new RerankerCascade(); boolean useQueryParser = false; if (searchArgs.rm3) { cascade.add(new Rm3Reranker(new EnglishAnalyzer(), FIELD_BODY, "src/main/resources/io/anserini/rerank/rm3/rm3-stoplist.gov2.txt")); useQueryParser = true; } else { cascade.add(new IdentityReranker()); } FeatureExtractors extractors = null; if (searchArgs.extractors != null) { extractors = FeatureExtractors.loadExtractor(searchArgs.extractors); } if (searchArgs.dumpFeatures) { PrintStream out = new PrintStream(searchArgs.featureFile); Qrels qrels = new Qrels(searchArgs.qrels); cascade.add(new WebCollectionLtrDataGenerator(out, qrels, extractors)); } Path topicsFile = Paths.get(searchArgs.topics); if (!Files.exists(topicsFile) || !Files.isRegularFile(topicsFile) || !Files.isReadable(topicsFile)) { throw new IllegalArgumentException( "Topics file : " + topicsFile + " does not exist or is not a (readable) file."); } TopicReader tr = (TopicReader) Class .forName("io.anserini.search.query." + searchArgs.topicReader + "TopicReader") .getConstructor(Path.class).newInstance(topicsFile); SortedMap<Integer, String> topics = tr.read(); final long start = System.nanoTime(); SearchWebCollection searcher = new SearchWebCollection(searchArgs.index); searcher.search(topics, searchArgs.output, similarity, searchArgs.hits, cascade, useQueryParser, searchArgs.keepstop); searcher.close(); final long durationMillis = TimeUnit.MILLISECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS); LOG.info("Total " + topics.size() + " topics searched in " + DurationFormatUtils.formatDuration(durationMillis, "HH:mm:ss")); }
From source file:edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance.java
/** * This program does the pairwise alignment between each pair of sequences, * reports a summary of the average distances and the stdev at each rank. * @param args/*from www .ja v a2 s . c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { String trainseqFile = null; String taxFile = null; PrintStream outStream = null; AlignmentMode mode = AlignmentMode.overlap; boolean show_alignment = false; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("show_alignment")) { show_alignment = true; } if (line.hasOption("alignment-mode")) { String m = line.getOptionValue("alignment-mode").toLowerCase(); mode = AlignmentMode.valueOf(m); } if (args.length != 3) { throw new Exception("wrong arguments"); } args = line.getArgs(); trainseqFile = args[0]; taxFile = args[1]; outStream = new PrintStream(new File(args[2])); } catch (Exception e) { System.err.println("Command Error: " + e.getMessage()); new HelpFormatter().printHelp(80, " [options] trainseqFile taxonFile outFile", "", options, ""); return; } PairwiseSeqDistance theObj = new PairwiseSeqDistance(trainseqFile, taxFile, mode, show_alignment); theObj.printSummary(outStream); }
From source file:edu.oregonstate.eecs.mcplan.ml.LinearDiscriminantAnalysis.java
public static void main(final String[] args) throws FileNotFoundException { final File root = new File("test/LinearDiscriminantAnalysis"); root.mkdirs();/*from ww w. j a v a 2 s . c om*/ final int seed = 42; final int N = 30; final double shrinkage = 1e-6; final RandomGenerator rng = new MersenneTwister(seed); final Pair<ArrayList<double[]>, int[]> dataset = Datasets.twoVerticalGaussian2D(rng, N); final ArrayList<double[]> data = dataset.first; final int[] label = dataset.second; final int Nlabels = 2; final int[] shuffle_idx = Fn.linspace(0, Nlabels * N); Fn.shuffle(rng, shuffle_idx); final ArrayList<double[]> shuffled = new ArrayList<double[]>(); final int[] shuffled_label = new int[label.length]; for (int i = 0; i < data.size(); ++i) { shuffled.add(Fn.copy(data.get(shuffle_idx[i]))); shuffled_label[i] = label[shuffle_idx[i]]; } final Csv.Writer data_writer = new Csv.Writer(new PrintStream(new File(root, "data.csv"))); for (final double[] v : data) { for (int i = 0; i < v.length; ++i) { data_writer.cell(v[i]); } data_writer.newline(); } data_writer.close(); System.out.println("[Training]"); // final KernelPrincipalComponentsAnalysis<RealVector> kpca // = new KernelPrincipalComponentsAnalysis<RealVector>( shuffled, new RadialBasisFunctionKernel( 0.5 ), 1e-6 ); final LinearDiscriminantAnalysis lda = new LinearDiscriminantAnalysis(shuffled, shuffled_label, Nlabels, shrinkage); System.out.println("[Finished]"); for (final RealVector ev : lda.eigenvectors) { System.out.println(ev); } System.out.println("Transformed data:"); final LinearDiscriminantAnalysis.Transformer transformer = lda.makeTransformer(); final Csv.Writer transformed_writer = new Csv.Writer(new PrintStream(new File(root, "transformed.csv"))); for (final double[] u : data) { final RealVector uvec = new ArrayRealVector(u); System.out.println(uvec); final RealVector v = transformer.transform(uvec); System.out.println("-> " + v); for (int i = 0; i < v.getDimension(); ++i) { transformed_writer.cell(v.getEntry(i)); } transformed_writer.newline(); } transformed_writer.close(); }
From source file:com.act.lcms.AnimateNetCDFAroundMass.java
public static void main(String[] args) throws Exception { if (args.length < 7 || !areNCFiles(Arrays.copyOfRange(args, 5, args.length))) { throw new RuntimeException( "Needs: \n" + "(1) mass value, e.g., 132.0772 \n" + "(2) time value, e.g., 39.2, (seconds), \n" + "(3) minimum Mz Precision, 0.04 \n" + "(4) max z axis, e.g., 20000 \n" + "(5) prefix for .data and rendered .pdf \n" + "(6..) 2 or more NetCDF .nc files"); }/*from w w w . ja va 2 s . c o m*/ Double mz = Double.parseDouble(args[0]); Double time = Double.parseDouble(args[1]); Double minMzPrecision = Double.parseDouble(args[2]); Double maxZAxis = Double.parseDouble(args[3]); String outPrefix = args[4]; // the mz values go from 50-950, we start with a big window and exponentially narrow down double mzWin = 100; // time values go from 0-450, we start with a big window and exponentially narrow down double timeWin = 50; // the factor by which to zoom in every step (has to be >1, a value of 2 is good) double factor = 1.2; // the animation frame count int frame = 1; AnimateNetCDFAroundMass c = new AnimateNetCDFAroundMass(); String[] netCDFFnames = Arrays.copyOfRange(args, 5, args.length); List<List<XYZ>> spectra = c.getSpectra(netCDFFnames, time, timeWin, mz, mzWin); for (List<XYZ> s : spectra) { System.out.format("%d xyz datapoints in (initial narrowed) spectra\n", s.size()); } String[] labels = new String[netCDFFnames.length]; for (int i = 0; i < labels.length; i++) labels[i] = "Dataset: " + i; // you could set labels to netCDFFnames to get precise labels on the graphs Gnuplotter plotter = new Gnuplotter(); String fmt = "png"; List<String> outImgFiles = new ArrayList<>(), outDataFiles = new ArrayList<>(); while (mzWin > minMzPrecision) { // exponentially narrow windows down mzWin /= factor; timeWin /= factor; List<List<XYZ>> windowedSpectra = c.getSpectraInWindowAll(spectra, time, timeWin, mz, mzWin); String frameid = String.format("%03d", frame); String outPDF = outPrefix + frameid + "." + fmt; String outDATA = outPrefix + frameid + ".data"; outImgFiles.add(outPDF); outDataFiles.add(outDATA); frame++; // Write data output to outfile PrintStream out = new PrintStream(new FileOutputStream(outDATA)); // print out the spectra to outDATA for (List<XYZ> windowOfSpectra : windowedSpectra) { for (XYZ xyz : windowOfSpectra) { out.format("%.4f\t%.4f\t%.4f\n", xyz.time, xyz.mz, xyz.intensity); out.flush(); } // delimit this dataset from the rest out.print("\n\n"); } // close the .data out.close(); // render outDATA to outPDF using gnuplot plotter.plotMulti3D(outDATA, outPDF, fmt, labels, maxZAxis); } String outImgs = outPrefix + "*." + fmt; plotter.makeAnimatedGIF(outImgs, outPrefix + ".gif"); // all the frames are now in the animated gif, remove the intermediate files for (String f : outDataFiles) new File(f).delete(); for (String f : outImgFiles) new File(f).delete(); }
From source file:master.utilities.PopulationFunctionFromJSON.java
/** * Main method for debugging./*from ww w. j av a 2s . c o m*/ * * @param args * @throws java.lang.Exception */ public static void main(String[] args) throws Exception { PopulationFunctionFromJSON instance = new PopulationFunctionFromJSON(); instance.initByName("fileName", "/home/tim/work/articles/volzpaper/SimulatedData/SIR_1000sims.json", "popSizeExpression", "(I-1)/(2*0.00075*S)", "origin", new RealParameter("66.5499977474"), "trajNum", 1, "popSizeStart", 0.0, "popSizeEnd", 0.0); // Write pop sizes and intensities out PrintStream outf = new PrintStream("test.txt"); outf.println("t N intensity invIntensity"); double dt = 66.5499977474 / 1000; for (int i = 0; i <= 1000; i++) { double t = dt * i; double N = instance.getPopSize(t); double intensity = instance.getIntensity(t); double invIntensity = instance.getInverseIntensity(intensity); outf.format("%g %g %g %g\n", t, N, intensity, invIntensity); } outf.println(); }
From source file:AwsConsoleApp.java
public static void main(String[] args) throws Exception { System.out.println("==========================================="); System.out.println("Welcome to the AWS VPN connection creator"); System.out.println("==========================================="); init();//from w ww . j a v a 2 s . c o m List<String> CIDRblocks = new ArrayList<String>(); String vpnType = null; String vpnGatewayId = null; String customerGatewayId = null; String customerGatewayInfoPath = null; String routes = null; options.addOption("h", "help", false, "show help."); options.addOption("vt", "vpntype", true, "Set vpn tunnel type e.g. (ipec.1)"); options.addOption("vgw", "vpnGatewayId", true, "Set AWS VPN Gateway ID e.g. (vgw-eca54d85)"); options.addOption("cgw", "customerGatewayId", true, "Set AWS Customer Gateway ID e.g. (cgw-c16e87a8)"); options.addOption("r", "staticroutes", true, "Set static routes e.g. cutomer subnet 10.77.77.0/24"); options.addOption("vi", "vpninfo", true, "path to vpn info file c:\\temp\\customerGatewayInfo.xml"); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; // Parse command line options try { cmd = parser.parse(options, args); if (cmd.hasOption("h")) help(); if (cmd.hasOption("vt")) { log.log(Level.INFO, "Using cli argument -vt=" + cmd.getOptionValue("vt")); vpnType = cmd.getOptionValue("vt"); // Whatever you want to do with the setting goes here } else { log.log(Level.SEVERE, "Missing vt option"); help(); } if (cmd.hasOption("vgw")) { log.log(Level.INFO, "Using cli argument -vgw=" + cmd.getOptionValue("vgw")); vpnGatewayId = cmd.getOptionValue("vgw"); } else { log.log(Level.SEVERE, "Missing vgw option"); help(); } if (cmd.hasOption("cgw")) { log.log(Level.INFO, "Using cli argument -cgw=" + cmd.getOptionValue("cgw")); customerGatewayId = cmd.getOptionValue("cgw"); } else { log.log(Level.SEVERE, "Missing cgw option"); help(); } if (cmd.hasOption("r")) { log.log(Level.INFO, "Using cli argument -r=" + cmd.getOptionValue("r")); routes = cmd.getOptionValue("r"); String[] routeItems = routes.split(","); CIDRblocks = Arrays.asList(routeItems); } else { log.log(Level.SEVERE, "Missing r option"); help(); } if (cmd.hasOption("vi")) { log.log(Level.INFO, "Using cli argument -vi=" + cmd.getOptionValue("vi")); customerGatewayInfoPath = cmd.getOptionValue("vi"); } else { log.log(Level.SEVERE, "Missing vi option"); help(); } } catch (ParseException e) { log.log(Level.SEVERE, "Failed to parse comand line properties", e); help(); } /* * Amazon VPC * Create and delete VPN tunnel to customer VPN hardware */ try { //String vpnType = "ipsec.1"; //String vpnGatewayId = "vgw-eca54d85"; //String customerGatewayId = "cgw-c16e87a8"; //List<String> CIDRblocks = new ArrayList<String>(); //CIDRblocks.add("10.77.77.0/24"); //CIDRblocks.add("172.16.1.0/24"); //CIDRblocks.add("172.18.1.0/24"); //CIDRblocks.add("10.66.66.0/24"); //CIDRblocks.add("10.8.1.0/24"); //String customerGatewayInfoPath = "c:\\temp\\customerGatewayInfo.xml"; Boolean staticRoutesOnly = true; List<String> connectionIds = new ArrayList<String>(); List<String> connectionIdList = new ArrayList<String>(); connectionIdList = vpnExists(connectionIds); if (connectionIdList.size() == 0) { CreateVpnConnectionRequest vpnReq = new CreateVpnConnectionRequest(vpnType, customerGatewayId, vpnGatewayId); CreateVpnConnectionResult vpnRes = new CreateVpnConnectionResult(); VpnConnectionOptionsSpecification vpnspec = new VpnConnectionOptionsSpecification(); vpnspec.setStaticRoutesOnly(staticRoutesOnly); vpnReq.setOptions(vpnspec); System.out.println("Creating VPN connection"); vpnRes = ec2.createVpnConnection(vpnReq); String vpnConnId = vpnRes.getVpnConnection().getVpnConnectionId(); String customerGatewayInfo = vpnRes.getVpnConnection().getCustomerGatewayConfiguration(); //System.out.println("Customer Gateway Info:" + customerGatewayInfo); // Write Customer Gateway Info to file System.out.println("Writing Customer Gateway Info to file:" + customerGatewayInfoPath); try (PrintStream out = new PrintStream(new FileOutputStream(customerGatewayInfoPath))) { out.print(customerGatewayInfo); } System.out.println("Creating VPN routes"); for (String destCIDR : CIDRblocks) { CreateVpnConnectionRouteRequest routeReq = new CreateVpnConnectionRouteRequest(); CreateVpnConnectionRouteResult routeRes = new CreateVpnConnectionRouteResult(); routeReq.setDestinationCidrBlock(destCIDR); routeReq.setVpnConnectionId(vpnConnId); routeRes = ec2.createVpnConnectionRoute(routeReq); } // Parse XML file File file = new File(customerGatewayInfoPath); DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); Document document = db.parse(customerGatewayInfoPath); XPathFactory xPathfactory = XPathFactory.newInstance(); XPath xpath = xPathfactory.newXPath(); XPathExpression exprGetipAddress = xpath .compile("/vpn_connection/ipsec_tunnel/vpn_gateway/tunnel_outside_address/ip_address"); NodeList vpnGateway = (NodeList) exprGetipAddress.evaluate(document, XPathConstants.NODESET); if (vpnGateway != null) { for (int i = 0; i < vpnGateway.getLength(); i++) { String vpnGatewayIP = vpnGateway.item(i).getTextContent(); System.out .println("AWS vpnGatewayIP for tunnel " + Integer.toString(i) + " " + vpnGatewayIP); } } System.out.println("=============================================="); XPathExpression exprGetKey = xpath.compile("/vpn_connection/ipsec_tunnel/ike/pre_shared_key"); NodeList presharedKeyList = (NodeList) exprGetKey.evaluate(document, XPathConstants.NODESET); if (presharedKeyList != null) { for (int i = 0; i < presharedKeyList.getLength(); i++) { String pre_shared_key = presharedKeyList.item(i).getTextContent(); System.out.println( "AWS pre_shared_key for tunnel " + Integer.toString(i) + " " + pre_shared_key); } } System.out.println("Creating VPN creation completed!"); } else { boolean yn; Scanner scan = new Scanner(System.in); System.out.println("Enter yes or no to delete VPN connection: "); String input = scan.next(); String answer = input.trim().toLowerCase(); while (true) { if (answer.equals("yes")) { yn = true; break; } else if (answer.equals("no")) { yn = false; System.exit(0); } else { System.out.println("Sorry, I didn't catch that. Please answer yes/no"); } } // Delete all existing VPN connections System.out.println("Deleting AWS VPN connection(s)"); for (String vpnConID : connectionIdList) { DeleteVpnConnectionResult delVPNres = new DeleteVpnConnectionResult(); DeleteVpnConnectionRequest delVPNreq = new DeleteVpnConnectionRequest(); delVPNreq.setVpnConnectionId(vpnConID); delVPNres = ec2.deleteVpnConnection(delVPNreq); System.out.println("Successfully deleted AWS VPN conntion: " + vpnConID); } } } catch (AmazonServiceException ase) { System.out.println("Caught Exception: " + ase.getMessage()); System.out.println("Reponse Status Code: " + ase.getStatusCode()); System.out.println("Error Code: " + ase.getErrorCode()); System.out.println("Request ID: " + ase.getRequestId()); } }
From source file:Main.java
/** * Creates a no-op print stream./*from w w w. j a v a2s. c o m*/ */ public static PrintStream nopPrintStream() { return new PrintStream(nopOuputStream()); }
From source file:Main.java
public static void append(File aFile, String content) { try {//from w ww .j a v a 2 s. c o m PrintStream p = new PrintStream(new BufferedOutputStream(new FileOutputStream(aFile, true))); p.println(content); p.close(); } catch (Exception e) { e.printStackTrace(); System.err.println(aFile); } }
From source file:Main.java
public static void resultToFile(String path) throws FileNotFoundException { File file = new File(path); PrintStream printStream = new PrintStream(new FileOutputStream(file)); PrintStream out = printStream; System.setOut(out);/*from w ww .ja v a2 s . c o m*/ }
From source file:Main.java
private static String getStringFromException(Throwable e) { String result = ""; ByteArrayOutputStream bos = new ByteArrayOutputStream(); PrintStream ps = new PrintStream(bos); e.printStackTrace(ps);//w ww. j a v a 2 s . c o m try { result = bos.toString("utf-8"); } catch (UnsupportedEncodingException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } return result; }