List of usage examples for java.io PrintWriter PrintWriter
public PrintWriter(File file) throws FileNotFoundException
From source file:at.tuwien.ifs.feature.evaluation.SimilarityRetrievalWriter.java
public static void main(String[] args) throws SOMToolboxException, IOException { // register and parse all options JSAPResult config = OptionFactory.parseResults(args, OPTIONS); File inputVectorFile = config.getFile("inputVectorFile"); String outputDirStr = AbstractOptionFactory.getFilePath(config, "outputDirectory"); File outputDirBase = new File(outputDirStr); outputDirBase.mkdirs();/*ww w . ja v a 2 s . co m*/ String metricName = config.getString("metric"); DistanceMetric metric = AbstractMetric.instantiateNice(metricName); int neighbours = config.getInt("numberNeighbours"); int startIndex = config.getInt("startIndex"); int numberItems = config.getInt("numberItems", -1); try { SOMLibSparseInputData data = new SOMLibSparseInputData(inputVectorFile.getAbsolutePath()); int endIndex = data.numVectors(); if (numberItems != -1) { if (startIndex + numberItems > endIndex) { System.out.println("Specified number of items (" + numberItems + ") exceeds maximum (" + data.numVectors() + "), limiting to " + (endIndex - startIndex) + "."); } else { endIndex = startIndex + numberItems; } } StdErrProgressWriter progress = new StdErrProgressWriter(endIndex - startIndex, "processing vector "); // SortedSet<InputDistance> distances; for (int inputDatumIndex = startIndex; inputDatumIndex < endIndex; inputDatumIndex++) { InputDatum inputDatum = data.getInputDatum(inputDatumIndex); String inputLabel = inputDatum.getLabel(); if (inputDatumIndex == -1) { throw new IllegalArgumentException( "Input with label '" + inputLabel + "' not found in vector file '" + inputVectorFile + "'; possible labels are: " + StringUtils.toString(data.getLabels(), 15)); } File outputDir = new File(outputDirBase, inputLabel.charAt(2) + "/" + inputLabel.charAt(3) + "/" + inputLabel.charAt(4)); outputDir.mkdirs(); File outputFile = new File(outputDir, inputLabel + ".txt"); boolean fileExistsAndValid = false; if (outputFile.exists()) { // check if it the valid data String linesInvalid = ""; int validLineCount = 0; ArrayList<String> lines = FileUtils.readLinesAsList(outputFile.getAbsolutePath()); for (String string : lines) { if (string.trim().length() == 0) { continue; } String[] parts = string.split("\t"); if (parts.length != 2) { linesInvalid += "Line '" + string + "' invalid - contains " + parts.length + " elements.\n"; } else if (!NumberUtils.isNumber(parts[1])) { linesInvalid = "Line '" + string + "' invalid - 2nd part is not a number.\n"; } else { validLineCount++; } } if (validLineCount != neighbours) { linesInvalid = "Not enough valid lines; expected " + neighbours + ", found " + validLineCount + ".\n"; } fileExistsAndValid = true; if (org.apache.commons.lang.StringUtils.isNotBlank(linesInvalid)) { System.out.println("File " + outputFile.getAbsolutePath() + " exists, but is not valid:\n" + linesInvalid); } } if (fileExistsAndValid) { Logger.getLogger("at.tuwien.ifs.feature.evaluation").finer( "File " + outputFile.getAbsolutePath() + " exists and is valid; not recomputing"); } else { PrintWriter p = new PrintWriter(outputFile); SmallestElementSet<InputDistance> distances = data.getNearestDistances(inputDatumIndex, neighbours, metric); for (InputDistance inputDistance : distances) { p.println(inputDistance.getInput().getLabel() + "\t" + inputDistance.getDistance()); } p.close(); } progress.progress(); } } catch (IllegalArgumentException e) { System.out.println(e.getMessage() + ". Aborting."); System.exit(-1); } }
From source file:com.kappaware.logtrawler.Main.java
@SuppressWarnings("static-access") static public void main(String[] argv) throws Throwable { Config config;// ww w .j av a 2 s . c o m Options options = new Options(); options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("config-file") .withDescription("JSON configuration file").create("c")); options.addOption(OptionBuilder.hasArg().withArgName("folder").withLongOpt("folder") .withDescription("Folder to monitor").create("f")); options.addOption(OptionBuilder.hasArg().withArgName("exclusion").withLongOpt("exclusion") .withDescription("Exclusion regex").create("x")); options.addOption(OptionBuilder.hasArg().withArgName("adminEndpoint").withLongOpt("admin-endpoint") .withDescription("Endpoint for admin REST").create("e")); options.addOption(OptionBuilder.hasArg().withArgName("outputFlow").withLongOpt("output-flow") .withDescription("Target to post result on").create("o")); options.addOption(OptionBuilder.hasArg().withArgName("hostname").withLongOpt("hostname") .withDescription("This hostname").create("h")); options.addOption(OptionBuilder.withLongOpt("displayDot").withDescription("Display Dot").create("d")); options.addOption(OptionBuilder.hasArg().withArgName("mimeType").withLongOpt("mime-type") .withDescription("Valid MIME type").create("m")); options.addOption(OptionBuilder.hasArg().withArgName("allowedAdmin").withLongOpt("allowedAdmin") .withDescription("Allowed admin network").create("a")); options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("gen-config-file") .withDescription("Generate JSON configuration file").create("g")); options.addOption(OptionBuilder.hasArg().withArgName("maxBatchSize").withLongOpt("max-batch-size") .withDescription("Max JSON batch (array) size").create("b")); CommandLineParser clParser = new BasicParser(); CommandLine line; String configFile = null; try { // parse the command line argument line = clParser.parse(options, argv); if (line.hasOption("c")) { configFile = line.getOptionValue("c"); config = Json.fromJson(Config.class, new BufferedReader(new InputStreamReader(new FileInputStream(configFile)))); } else { config = new Config(); } if (line.hasOption("f")) { String[] fs = line.getOptionValues("f"); // Get the first agent (Create it if needed) if (config.getAgents() == null || config.getAgents().size() == 0) { Config.Agent agent = new Config.Agent("default"); config.addAgent(agent); } Config.Agent agent = config.getAgents().iterator().next(); for (String f : fs) { agent.addFolder(new Config.Agent.Folder(f, false)); } } if (line.hasOption("e")) { String e = line.getOptionValue("e"); config.setAdminEndpoint(e); } if (line.hasOption("o")) { String[] es = line.getOptionValues("o"); if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { for (String s : es) { agent.addOuputFlow(s); } } } } if (line.hasOption("h")) { String e = line.getOptionValue("h"); config.setHostname(e); } if (line.hasOption("x")) { if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { if (agent.getFolders() != null) { for (Folder folder : agent.getFolders()) { String[] exs = line.getOptionValues("x"); for (String ex : exs) { folder.addExcludedPath(ex); } } } } } } if (line.hasOption("m")) { if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { String[] exs = line.getOptionValues("m"); for (String ex : exs) { agent.addLogMimeType(ex); } } } } if (line.hasOption("a")) { String[] exs = line.getOptionValues("a"); for (String ex : exs) { config.addAdminAllowedNetwork(ex); } } if (line.hasOption("d")) { config.setDisplayDot(true); } if (line.hasOption("b")) { Integer i = getIntegerParameter(line, "b"); if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { agent.setOutputMaxBatchSize(i); } } } config.setDefault(); if (line.hasOption("g")) { String fileName = line.getOptionValue("g"); PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fileName, false))); out.println(Json.toJson(config, true)); out.flush(); out.close(); System.exit(0); } } catch (ParseException exp) { // oops, something went wrong usage(options, exp.getMessage()); return; } try { // Check config if (config.getAgents() == null || config.getAgents().size() < 1) { throw new ConfigurationException("At least one folder to monitor must be provided!"); } Map<String, AgentHandler> agentHandlerByName = new HashMap<String, AgentHandler>(); for (Config.Agent agent : config.getAgents()) { agentHandlerByName.put(agent.getName(), new AgentHandler(agent)); } if (!Utils.isNullOrEmpty(config.getAdminEndpoint())) { new AdminServer(config, agentHandlerByName); } } catch (ConfigurationException e) { log.error(e.toString()); System.exit(1); } catch (Throwable t) { log.error("Error in main", t); System.exit(2); } }
From source file:eu.fbk.utils.lsa.util.Anvur.java
public static void main(String[] args) throws Exception { String logConfig = System.getProperty("log-config"); if (logConfig == null) { logConfig = "log-config.txt"; }//from w ww. j av a2 s . c o m PropertyConfigurator.configure(logConfig); /* if (args.length != 2) { log.println("Usage: java -mx512M eu.fbk.utils.lsa.util.Anvur in-file out-dir"); System.exit(1); } File l = new File(args[1]); if (!l.exists()) { l.mkdir(); } List<String[]> list = readText(new File(args[0])); String oldCategory = ""; for (int i=0;i<list.size();i++) { String[] s = list.get(i); if (!oldCategory.equals(s[0])) { File f = new File(args[1] + File.separator + s[0]); boolean b = f.mkdir(); logger.debug(f + " created " + b); } File g = new File(args[1] + File.separator + s[0] + File.separator + s[1] + ".txt"); logger.debug("writing " + g + "..."); PrintWriter pw = new PrintWriter(new FileWriter(g)); //pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2])); if (s.length == 5) { pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2] + " " + s[4].replace('_', ' '))); } else { pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2])); } pw.flush(); pw.close(); } // end for i */ if (args.length != 7) { System.out.println(args.length); System.out.println( "Usage: java -mx2G eu.fbk.utils.lsa.util.Anvur input threshold size dim idf in-file-csv fields\n\n"); System.exit(1); } // DecimalFormat dec = new DecimalFormat("#.00"); File Ut = new File(args[0] + "-Ut"); File Sk = new File(args[0] + "-S"); File r = new File(args[0] + "-row"); File c = new File(args[0] + "-col"); File df = new File(args[0] + "-df"); double threshold = Double.parseDouble(args[1]); int size = Integer.parseInt(args[2]); int dim = Integer.parseInt(args[3]); boolean rescaleIdf = Boolean.parseBoolean(args[4]); //"author_check"0, "authors"1, "title"2, "year"3, "pubtype"4, "publisher"5, "journal"6, "volume"7, "number"8, "pages"9, "abstract"10, "nauthors", "citedby" String[] labels = { "author_check", "authors", "title", "year", "pubtype", "publisher", "journal", "volume", "number", "pages", "abstract", "nauthors", "citedby" //author_id authors title year pubtype publisher journal volume number pages abstract nauthors citedby }; String name = buildName(labels, args[6]); File bwf = new File(args[5] + name + "-bow.txt"); PrintWriter bw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bwf), "UTF-8"))); File bdf = new File(args[5] + name + "-bow.csv"); PrintWriter bd = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bdf), "UTF-8"))); File lwf = new File(args[5] + name + "-ls.txt"); PrintWriter lw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(lwf), "UTF-8"))); File ldf = new File(args[5] + name + "-ls.csv"); PrintWriter ld = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(ldf), "UTF-8"))); File blwf = new File(args[5] + name + "-bow+ls.txt"); PrintWriter blw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(blwf), "UTF-8"))); File bldf = new File(args[5] + name + "-bow+ls.csv"); PrintWriter bld = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bldf), "UTF-8"))); File logf = new File(args[5] + name + ".log"); PrintWriter log = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(logf), "UTF-8"))); //System.exit(0); LSM lsm = new LSM(Ut, Sk, r, c, df, dim, rescaleIdf); LSSimilarity lss = new LSSimilarity(lsm, size); List<String[]> list = readText(new File(args[5])); // author_check authors title year pubtype publisher journal volume number pages abstract nauthors citedby //header for (int i = 0; i < list.size(); i++) { String[] s1 = list.get(i); String t1 = s1[0].toLowerCase(); bw.print("\t"); lw.print("\t"); blw.print("\t"); bw.print(i + "(" + s1[0] + ")"); lw.print(i + "(" + s1[0] + ")"); blw.print(i + "(" + s1[0] + ")"); } // end for i bw.print("\n"); lw.print("\n"); blw.print("\n"); for (int i = 0; i < list.size(); i++) { logger.info(i + "\t"); String[] s1 = list.get(i); String t1 = buildText(s1, args[6]); BOW bow1 = new BOW(t1); logger.info(bow1); Vector d1 = lsm.mapDocument(bow1); d1.normalize(); log.println("d1:" + d1); Vector pd1 = lsm.mapPseudoDocument(d1); pd1.normalize(); log.println("pd1:" + pd1); Vector m1 = merge(pd1, d1); log.println("m1:" + m1); // write the orginal line for (int j = 0; j < s1.length; j++) { bd.print(s1[j]); bd.print("\t"); ld.print(s1[j]); ld.print("\t"); bld.print(s1[j]); bld.print("\t"); } // write the bow, ls, and bow+ls vectors bd.println(d1); ld.println(pd1); bld.println(m1); bw.print(i + "(" + s1[0] + ")"); lw.print(i + "(" + s1[0] + ")"); blw.print(i + "(" + s1[0] + ")"); for (int j = 0; j < i + 1; j++) { bw.print("\t"); lw.print("\t"); blw.print("\t"); } // end for j for (int j = i + 1; j < list.size(); j++) { logger.info(i + "\t" + j); String[] s2 = list.get(j); String t2 = buildText(s2, args[6]); BOW bow2 = new BOW(t2); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t1:" + t1); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t2:" + t2); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow1:" + bow1); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow2:" + bow2); Vector d2 = lsm.mapDocument(bow2); d2.normalize(); log.println("d2:" + d2); Vector pd2 = lsm.mapPseudoDocument(d2); pd2.normalize(); log.println("pd2:" + pd2); Vector m2 = merge(pd2, d2); log.println("m2:" + m2); float cosVSM = d1.dotProduct(d2) / (float) Math.sqrt(d1.dotProduct(d1) * d2.dotProduct(d2)); float cosLSM = pd1.dotProduct(pd2) / (float) Math.sqrt(pd1.dotProduct(pd1) * pd2.dotProduct(pd2)); float cosBOWLSM = m1.dotProduct(m2) / (float) Math.sqrt(m1.dotProduct(m1) * m2.dotProduct(m2)); bw.print("\t"); bw.print(dec.format(cosVSM)); lw.print("\t"); lw.print(dec.format(cosLSM)); blw.print("\t"); blw.print(dec.format(cosBOWLSM)); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow\t" + cosVSM); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") ls:\t" + cosLSM); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow+ls:\t" + cosBOWLSM); } bw.print("\n"); lw.print("\n"); blw.print("\n"); } // end for i logger.info("wrote " + bwf); logger.info("wrote " + bwf); logger.info("wrote " + bdf); logger.info("wrote " + lwf); logger.info("wrote " + ldf); logger.info("wrote " + blwf); logger.info("wrote " + bldf); logger.info("wrote " + logf); ld.close(); bd.close(); bld.close(); bw.close(); lw.close(); blw.close(); log.close(); }
From source file:edu.uga.cs.fluxbuster.FluxbusterCLI.java
/** * The main method.//www . jav a 2s .co m * * @param args the command line arguments */ public static void main(String[] args) { GnuParser parser = new GnuParser(); Options opts = FluxbusterCLI.initializeOptions(); CommandLine cli; try { cli = parser.parse(opts, args); if (cli.hasOption('?')) { throw new ParseException(null); } if (validateDate(cli.getOptionValue('d')) && validateDate(cli.getOptionValue('e'))) { if (log.isInfoEnabled()) { StringBuffer arginfo = new StringBuffer("\n"); arginfo.append("generate-clusters: " + cli.hasOption('g') + "\n"); arginfo.append("calc-features: " + cli.hasOption('f') + "\n"); arginfo.append("calc-similarity: " + cli.hasOption('s') + "\n"); arginfo.append("classify-clusters: " + cli.hasOption('c') + "\n"); arginfo.append("start-date: " + cli.getOptionValue('d') + "\n"); arginfo.append("end-date: " + cli.getOptionValue('e') + "\n"); log.info(arginfo.toString()); } try { boolean clus = true, feat = true, simil = true, clas = true; if (cli.hasOption('g') || cli.hasOption('f') || cli.hasOption('s') || cli.hasOption('c')) { if (!cli.hasOption('g')) { clus = false; } if (!cli.hasOption('f')) { feat = false; } if (!cli.hasOption('s')) { simil = false; } if (!cli.hasOption('c')) { clas = false; } } DBInterfaceFactory.init(); SimpleDateFormat df = new SimpleDateFormat("yyyyMMdd"); Date logdate = df.parse(cli.getOptionValue('d')); long startTime = logdate.getTime() / 1000; long endTime = df.parse(cli.getOptionValue('e')).getTime() / 1000; if (clus) { ClusterGenerator cg = new ClusterGenerator(); List<DomainCluster> clusters = cg.generateClusters(startTime, endTime, true); cg.storeClusters(clusters, logdate); } if (feat) { FeatureCalculator calc = new FeatureCalculator(); calc.updateFeatures(logdate); } if (simil) { ClusterSimilarityCalculator calc2 = new ClusterSimilarityCalculator(); calc2.updateClusterSimilarities(logdate); } if (clas) { Classifier calc3 = new Classifier(); calc3.updateClusterClasses(logdate, 30); } } catch (Exception e) { if (log.isFatalEnabled()) { log.fatal("", e); } } finally { DBInterfaceFactory.shutdown(); } } else { throw new ParseException(null); } } catch (ParseException e1) { PrintWriter writer = new PrintWriter(System.out); HelpFormatter usageFormatter = new HelpFormatter(); usageFormatter.printHelp(writer, 80, "fluxbuster", "If none of the options g, f, s, c are specified " + "then the program will execute as if all of them " + "have been specified. Otherwise, the program will " + "only execute the options specified.", opts, 0, 2, ""); writer.close(); } }
From source file:com.metadave.kash.KashConsole.java
public static void main(String[] args) throws IOException { CommandLine commandLine = processArgs(args); ConsoleReader reader = new ConsoleReader(); reader.setBellEnabled(false);//from w w w.j av a 2 s . c o m reader.setExpandEvents(false); // TODO: look into this // TODO: Pasting in text with tabs prints out a ton of completions //reader.addCompleter(new jline.console.completer.StringsCompleter(keywords)); String line; PrintWriter out = new PrintWriter(System.out); KashRuntimeContext ctx = new KashRuntimeContext(); if (!commandLine.hasOption("nosignals")) { ConsoleSignalHander.install("INT", ctx); } boolean nextLinePrompt = false; ANSIBuffer buf = new ANSIBuffer(); buf.setAnsiEnabled(!commandLine.hasOption("nocolor")); buf.blue("Welcome to Kash\n"); buf.blue("(c) 2015 Dave Parfitt\n"); System.out.println(buf.toString()); if (!commandLine.hasOption("noconfig")) { String config = null; try { config = readConfig(); } catch (Exception e) { e.printStackTrace(); } if (config != null && !config.trim().isEmpty()) { processInput(config, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); } } // if (commandLine.hasOption("infile")) { // String filename = commandLine.getOptionValue("infile"); // readInputFile(filename, ctx); // ctx.getActionListener().term(); // System.exit(0); // } StringBuffer lines = new StringBuffer(); ANSIBuffer ansiprompt = new ANSIBuffer(); ansiprompt.setAnsiEnabled(true); ansiprompt.green("> "); String prompt = ansiprompt.toString(!commandLine.hasOption("nocolor")); boolean inHereDoc = false; while ((line = reader.readLine(nextLinePrompt ? "" : prompt)) != null) { out.flush(); String chunks[] = line.split(" "); String consoleCommandCheck = chunks[0].toLowerCase().trim(); if (consoleOnlyCommands.containsKey(consoleCommandCheck)) { consoleOnlyCommands.get(consoleCommandCheck).run(line, reader); continue; } if (line.contains("~%~") && !line.contains("\\~%~")) { inHereDoc = !inHereDoc; } if (!line.trim().endsWith(";")) { nextLinePrompt = true; lines.append(line); lines.append("\n"); } else if (line.trim().endsWith(";") && !inHereDoc) { lines.append(line); String input = lines.toString(); nextLinePrompt = false; processInput(input, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); lines = new StringBuffer(); } else if (inHereDoc) { lines.append(line); lines.append("\n"); } } }
From source file:com.metadave.eql.EQLConsole.java
public static void main(String[] args) throws IOException { CommandLine commandLine = processArgs(args); ConsoleReader reader = new ConsoleReader(); reader.setBellEnabled(false);/*from ww w.j av a 2 s . com*/ reader.setExpandEvents(false); // TODO: look into this // TODO: Pasting in text with tabs prints out a ton of completions //reader.addCompleter(new jline.console.completer.StringsCompleter(keywords)); String line; PrintWriter out = new PrintWriter(System.out); RuntimeContext ctx = new RuntimeContext(); if (!commandLine.hasOption("nosignals")) { ConsoleSignalHander.install("INT", ctx); } boolean nextLinePrompt = false; ANSIBuffer buf = new ANSIBuffer(); buf.setAnsiEnabled(!commandLine.hasOption("nocolor")); buf.blue("Welcome to EQL\n"); buf.blue("(c) 2015 Dave Parfitt\n"); System.out.println(buf.toString()); if (!commandLine.hasOption("noconfig")) { String config = null; try { config = readConfig(); } catch (Exception e) { e.printStackTrace(); } if (config != null && !config.trim().isEmpty()) { processInput(config, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); } } // if (commandLine.hasOption("infile")) { // String filename = commandLine.getOptionValue("infile"); // readInputFile(filename, ctx); // ctx.getActionListener().term(); // System.exit(0); // } StringBuffer lines = new StringBuffer(); ANSIBuffer ansiprompt = new ANSIBuffer(); ansiprompt.setAnsiEnabled(true); ansiprompt.green("> "); String prompt = ansiprompt.toString(!commandLine.hasOption("nocolor")); boolean inHereDoc = false; while ((line = reader.readLine(nextLinePrompt ? "" : prompt)) != null) { out.flush(); String chunks[] = line.split(" "); String consoleCommandCheck = chunks[0].toLowerCase().trim(); if (consoleOnlyCommands.containsKey(consoleCommandCheck)) { consoleOnlyCommands.get(consoleCommandCheck).run(line, reader); continue; } if (line.contains("~%~") && !line.contains("\\~%~")) { inHereDoc = !inHereDoc; } if (!line.trim().endsWith(";")) { nextLinePrompt = true; lines.append(line); lines.append("\n"); } else if (line.trim().endsWith(";") && !inHereDoc) { lines.append(line); String input = lines.toString(); nextLinePrompt = false; processInput(input, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); lines = new StringBuffer(); } else if (inHereDoc) { lines.append(line); lines.append("\n"); } } }
From source file:microbiosima.Microbiosima.java
/** * @param args//from ww w. jav a2 s . co m * the command line arguments * @throws java.io.FileNotFoundException * @throws java.io.UnsupportedEncodingException */ public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException { //Init with default values int populationSize = 500; int microSize = 1000; int numberOfSpecies = 150; int numberOfGeneration = 10000; int numberOfObservation = 100; int numberOfReplication = 1; double pctEnv = 0; double pctPool = 0; Options options = new Options(); Option help = new Option("h", "help", false, "print this message"); Option version = new Option("v", "version", false, "print the version information and exit"); options.addOption(help); options.addOption(version); options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS") .desc("Number generation for observation [default: 100]").build()); options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP") .desc("Number of replication [default: 1]").build()); Builder C = Option.builder("c").longOpt("config").numberOfArgs(4).argName("Pop Micro Spec Gen") .desc("Four Parameters in the following orders: " + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation" + " [default: 500 1000 150 10000]"); options.addOption(C.build()); HelpFormatter formatter = new HelpFormatter(); String syntax = "microbiosima pctEnv pctPool"; String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n" + "required arguments:\n" + " pctEnv Percentage of environmental acquisition\n" + " pctPool Percentage of pooled environmental component\n" + "\noptional arguments:\n"; String footer = "\n"; formatter.setWidth(80); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); String[] pct_config = cmd.getArgs(); if (cmd.hasOption("h") || args.length == 0) { formatter.printHelp(syntax, header, options, footer, true); System.exit(0); } if (cmd.hasOption("v")) { System.out.println("Microbiosima " + VERSION); System.exit(0); } if (pct_config.length != 2) { System.out.println("ERROR! Required exactly two argumennts for pct_env and pct_pool. It got " + pct_config.length + ": " + Arrays.toString(pct_config)); formatter.printHelp(syntax, header, options, footer, true); System.exit(3); } else { pctEnv = Double.parseDouble(pct_config[0]); pctPool = Double.parseDouble(pct_config[1]); if (pctEnv < 0 || pctEnv > 1) { System.out.println( "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv=" + pctEnv + ")! EXIT"); System.exit(3); } if (pctPool < 0 || pctPool > 1) { System.out.println( "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool=" + pctPool + ")! EXIT"); System.exit(3); } } if (cmd.hasOption("config")) { String[] configs = cmd.getOptionValues("config"); populationSize = Integer.parseInt(configs[0]); microSize = Integer.parseInt(configs[1]); numberOfSpecies = Integer.parseInt(configs[2]); numberOfGeneration = Integer.parseInt(configs[3]); } if (cmd.hasOption("obs")) { numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs")); } if (cmd.hasOption("rep")) { numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep")); } } catch (ParseException e) { e.printStackTrace(); System.exit(3); } StringBuilder sb = new StringBuilder(); sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize) .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ") .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration) .append("\n\tNumber generation for observation: ").append(numberOfObservation) .append("\n\tNumber of replication: ").append(numberOfReplication).append("\n"); System.out.println(sb.toString()); // System.exit(3); // LogNormalDistribution lgd=new LogNormalDistribution(0,1); // environment=lgd.sample(150); // double environment_sum=0; // for (int i=0;i<No;i++){ // environment_sum+=environment[i]; // } // for (int i=0;i<No;i++){ // environment[i]/=environment_sum; // } double[] environment = new double[numberOfSpecies]; for (int i = 0; i < numberOfSpecies; i++) { environment[i] = 1 / (double) numberOfSpecies; } for (int rep = 0; rep < numberOfReplication; rep++) { String prefix = "" + (rep + 1) + "_"; String sufix = "_E" + pctEnv + "_P" + pctPool + ".txt"; System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix); try { PrintWriter file1 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix))); PrintWriter file2 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix))); PrintWriter file3 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix))); PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix))); PrintWriter file5 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix))); PrintWriter file6 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix))); Population population = new Population(microSize, environment, populationSize, pctEnv, pctPool, 0, 0); while (population.getNumberOfGeneration() < numberOfGeneration) { population.sumSpecies(); if (population.getNumberOfGeneration() % numberOfObservation == 0) { file1.println(population.gammaDiversity(true)); file2.println(population.alphaDiversity(true)); file3.print(population.betaDiversity(true)); file3.print("\t"); file3.println(population.BrayCurtis(true)); file4.println(population.printOut()); file5.println(population.interGenerationDistance()); file6.println(population.environmentPopulationDistance()); } population.getNextGen(); } file1.close(); file2.close(); file3.close(); file4.close(); file5.close(); file6.close(); } catch (IOException e) { e.printStackTrace(); } } }
From source file:CSVWriter.java
/** * Test driver//w w w . ja v a 2 s.c o m * * @param args [0]: The name of the file. */ static public void main(String[] args) { try { // write out a test file PrintWriter pw = new PrintWriter(new FileWriter(args[0])); CSVWriter csv = new CSVWriter(pw, false, ',', System.getProperty("line.separator")); csv.writeCommentln("This is a test csv-file: '" + args[0] + "'"); csv.write("abc"); csv.write("def"); csv.write("g h i"); csv.write("jk,l"); csv.write("m\"n\'o "); csv.writeln(); csv.write("m\"n\'o "); csv.write(" "); csv.write("a"); csv.write("x,y,z"); csv.write("x;y;z"); csv.writeln(); csv.writeln(new String[] { "This", "is", "an", "array." }); csv.close(); } catch (IOException e) { e.printStackTrace(); System.out.println(e.getMessage()); } }
From source file:mitm.common.tools.CreateCA.java
public static void main(String[] args) throws Exception { PropertyConfigurator.configure("conf/log4j.properties"); if (args.length != 1) { System.err.println("p12 file expected."); return;//from w w w . ja va 2 s. c o m } System.out.println("Please enter your password: "); ConsoleReader consoleReader = new ConsoleReader(new FileInputStream(FileDescriptor.in), new PrintWriter(System.err)); String password = consoleReader.readLine(new Character('*')); CreateCA createCA = new CreateCA(); File p12File = new File(args[0]); createCA.generateCA(password, p12File); System.out.println("CA generated and written to " + p12File.getAbsolutePath()); }
From source file:ServeurFTP.java
public static void main(String[] args) { String server1, username1, password1, file1; String server2, username2, password2, file2; String[] parts;//from ww w . j a va 2s .com int port1 = 0, port2 = 0; FTPClient ftp1, ftp2; ProtocolCommandListener listener; if (args.length < 8) { System.err.println("Usage: ftp <host1> <user1> <pass1> <file1> <host2> <user2> <pass2> <file2>"); System.exit(1); } server1 = args[0]; parts = server1.split(":"); if (parts.length == 2) { server1 = parts[0]; port1 = Integer.parseInt(parts[1]); } username1 = args[1]; password1 = args[2]; file1 = args[3]; server2 = args[4]; parts = server2.split(":"); if (parts.length == 2) { server2 = parts[0]; port2 = Integer.parseInt(parts[1]); } username2 = args[5]; password2 = args[6]; file2 = args[7]; listener = new PrintCommandListener(new PrintWriter(System.out), true); ftp1 = new FTPClient(); ftp1.addProtocolCommandListener(listener); ftp2 = new FTPClient(); ftp2.addProtocolCommandListener(listener); try { int reply; if (port1 > 0) { ftp1.connect(server1, port1); } else { ftp1.connect(server1); } System.out.println("Connected to " + server1 + "."); reply = ftp1.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp1.disconnect(); System.err.println("FTP server1 refused connection."); System.exit(1); } } catch (IOException e) { if (ftp1.isConnected()) { try { ftp1.disconnect(); } catch (IOException f) { // do nothing } } System.err.println("Could not connect to server1."); e.printStackTrace(); System.exit(1); } try { int reply; if (port2 > 0) { ftp2.connect(server2, port2); } else { ftp2.connect(server2); } System.out.println("Connected to " + server2 + "."); reply = ftp2.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp2.disconnect(); System.err.println("FTP server2 refused connection."); System.exit(1); } } catch (IOException e) { if (ftp2.isConnected()) { try { ftp2.disconnect(); } catch (IOException f) { // do nothing } } System.err.println("Could not connect to server2."); e.printStackTrace(); System.exit(1); } __main: try { if (!ftp1.login(username1, password1)) { System.err.println("Could not login to " + server1); break __main; } if (!ftp2.login(username2, password2)) { System.err.println("Could not login to " + server2); break __main; } // Let's just assume success for now. ftp2.enterRemotePassiveMode(); ftp1.enterRemoteActiveMode(InetAddress.getByName(ftp2.getPassiveHost()), ftp2.getPassivePort()); // Although you would think the store command should be sent to server2 // first, in reality, ftp servers like wu-ftpd start accepting data // connections right after entering passive mode. Additionally, they // don't even send the positive preliminary reply until after the // transfer is completed (in the case of passive mode transfers). // Therefore, calling store first would hang waiting for a preliminary // reply. if (ftp1.remoteRetrieve(file1) && ftp2.remoteStoreUnique(file2)) { // if(ftp1.remoteRetrieve(file1) && ftp2.remoteStore(file2)) { // We have to fetch the positive completion reply. ftp1.completePendingCommand(); ftp2.completePendingCommand(); } else { System.err.println("Couldn't initiate transfer. Check that filenames are valid."); break __main; } } catch (IOException e) { e.printStackTrace(); System.exit(1); } finally { try { if (ftp1.isConnected()) { ftp1.logout(); ftp1.disconnect(); } } catch (IOException e) { // do nothing } try { if (ftp2.isConnected()) { ftp2.logout(); ftp2.disconnect(); } } catch (IOException e) { // do nothing } } }