List of usage examples for java.io PrintWriter close
public void close()
From source file:csv.parser.CSVParser.java
@SuppressWarnings("resource") public static void main(String[] args) throws Exception { String file_to_parse;//from w w w. j ava 2 s. c o m String[] val_array; file_to_parse = "./input/E-library-data-3.csv"; //Build reader instance //Read CSV file CSVReader reader = new CSVReader(new FileReader(file_to_parse), ';', '"', 1); //Read all rows at once List<String[]> allRows = reader.readAll(); // Read CSV line by line and use the string array as you want for (String[] row : allRows) { for (int i = 0; i < row.length; i++) { //Removing all newlines, tabs and '&' characters(invalid XML character) row[i] = row[i].replaceAll("(\\r|\\n|\\r\\n)+", " "); row[i] = row[i].replaceAll(System.getProperty("line.separator"), "; "); row[i] = row[i].replaceAll("&", "and"); } System.out.println(Arrays.toString(row)); } //Get the input fields List<String[]> map = getMap(); String[] field; //Numbering for folders, folderNum is incremented for each new file long folderNum; folderNum = 0; for (String[] row : allRows) { //Creating new folder File file1 = new File("./output//newdir//folder" + folderNum + ""); file1.mkdirs(); //Creating content file PrintWriter writer_content = new PrintWriter("./output//newdir//folder" + folderNum + "//contents", "UTF-16"); //Creating metadata_lrmi.xml PrintWriter writer_lrmi = new PrintWriter( "./output//newdir//folder" + folderNum + "//metadata_lrmi.xml", "UTF-16"); //Creating content.xml PrintWriter writer = new PrintWriter("./output//newdir//folder" + folderNum + "//content.xml", "UTF-16"); writer.println("<?xml version=\"1.0\" encoding=\"utf-16\" standalone=\"no\"?>"); writer.println("<dublin_core schema=\"dc\">"); writer_lrmi.println("<?xml version=\"1.0\" encoding=\"utf-16\" standalone=\"no\"?>"); writer_lrmi.println("<dublin_core shema=\"lrmi\">"); for (int i = 0; i < row.length; i++) { //After snooping data, we have to change these setting for each new csv file, as the data fileds are many times mismatched //These if-else statements take care of mismatched steps. if (i == 43) { continue; } else if (i == 43) { field = map.get(42); } else if (i == 44) { field = map.get(43); } else if (i == 45 || i == 46) { continue; } else { field = map.get(i); } //Separate multiple values val_array = parseVal(row[i]); // if (val_array.length == 0) { // continue; // } PrintWriter useWriter = writer; if (field[0].equals("lrmi")) { useWriter = writer_lrmi; } switch (field.length) { case 2: writeXML(useWriter, field[1], "", val_array); break; case 3: writeXML(useWriter, field[1], field[2], val_array); break; default: } } folderNum++; writer.println("</dublin_core>"); writer_lrmi.println("</dublin_core>"); writer.close(); writer_lrmi.close(); writer_content.close(); } }
From source file:lambertmrev.LambertMRev.java
/** * @param args the command line arguments *///w ww .j a va 2s . c o m public static void main(String[] args) { // Want to test the Lambert class so you can specify the number of revs for which to compute //System.out.print("this is the frames tutorial \n"); try { Frame inertialFrame = FramesFactory.getEME2000(); TimeScale utc = TimeScalesFactory.getTAI(); AbsoluteDate initialDate = new AbsoluteDate(2004, 01, 01, 23, 30, 00.000, utc); double mu = 3.986004415e+14; double a = 24396159; // semi major axis in meters double e = 0.72831215; // eccentricity double i = Math.toRadians(7); // inclination double omega = Math.toRadians(180); // perigee argument double raan = Math.toRadians(261); // right ascension of ascending node double lM = 0; // mean anomaly Orbit initialOrbit = new KeplerianOrbit(a, e, i, omega, raan, lM, PositionAngle.MEAN, inertialFrame, initialDate, mu); //KeplerianPropagator kepler = new KeplerianPropagator(initialOrbit); // set geocentric positions Vector3D r1 = new Vector3D(-6.88999e3, 3.92763e4, 2.67053e3); Vector3D r2 = new Vector3D(-3.41458e4, 2.05328e4, 3.44315e3); Vector3D r1_site = new Vector3D(4.72599e3, 1.26633e3, 4.07799e3); Vector3D r2_site = new Vector3D(4.70819e3, 1.33099e3, 4.07799e3); // get the topocentric positions Vector3D top1 = Transform.geo2radec(r1.scalarMultiply(1000), r1_site.scalarMultiply(1000)); Vector3D top2 = Transform.geo2radec(r2.scalarMultiply(1000), r2_site.scalarMultiply(1000)); // time of flight in seconds double tof = 3 * 3600; // propagate to 0 and tof Lambert test = new Lambert(); boolean cw = false; int multi_revs = 1; RealMatrix v1_mat; Random randomGenerator = new Random(); PrintWriter out_a = new PrintWriter("out_java_a.txt"); PrintWriter out_e = new PrintWriter("out_java_e.txt"); PrintWriter out_rho1 = new PrintWriter("out_java_rho1.txt"); PrintWriter out_rho2 = new PrintWriter("out_java_rho2.txt"); // start the loop double A, Ecc, rho1, rho2, tof_hyp; long time1 = System.nanoTime(); for (int ll = 0; ll < 1e6; ll++) { rho1 = top1.getZ() / 1000 + 1e-3 * randomGenerator.nextGaussian() * top1.getZ() / 1000; rho2 = top2.getZ() / 1000 + 1e-3 * randomGenerator.nextGaussian() * top2.getZ() / 1000; //tof_hyp = FastMath.abs(tof + 0.1*3600 * randomGenerator.nextGaussian()); // from topo to geo Vector3D r1_hyp = Transform.radec2geo(top1.getX(), top1.getY(), rho1, r1_site); Vector3D r2_hyp = Transform.radec2geo(top2.getX(), top2.getY(), rho2, r2_site); // System.out.println(r1_hyp.scalarMultiply(1000).getNorm()); // System.out.println(r2_hyp.scalarMultiply(1000).getNorm()); // System.out.println(tof/3600); test.lambert_problem(r1_hyp.scalarMultiply(1000), r2_hyp.scalarMultiply(1000), tof, mu, cw, multi_revs); v1_mat = test.get_v1(); Vector3D v1 = new Vector3D(v1_mat.getEntry(0, 0), v1_mat.getEntry(0, 1), v1_mat.getEntry(0, 2)); // System.out.println(v1); PVCoordinates rv1 = new PVCoordinates(r1_hyp.scalarMultiply(1000), v1); Orbit orbit_out = new KeplerianOrbit(rv1, inertialFrame, initialDate, mu); A = orbit_out.getA(); Ecc = orbit_out.getE(); // System.out.println(ll + " - " +A); out_a.println(A); out_e.println(Ecc); out_rho1.println(rho1); out_rho2.println(rho2); } long time2 = System.nanoTime(); long timeTaken = time2 - time1; out_a.close(); out_e.close(); out_rho1.close(); out_rho2.close(); System.out.println("Time taken " + timeTaken / 1000 / 1000 + " milli secs"); // get the truth test.lambert_problem(r1.scalarMultiply(1000), r2.scalarMultiply(1000), tof, mu, cw, multi_revs); v1_mat = test.get_v1(); Vector3D v1 = new Vector3D(v1_mat.getEntry(0, 0), v1_mat.getEntry(0, 1), v1_mat.getEntry(0, 2)); PVCoordinates rv1 = new PVCoordinates(r1.scalarMultiply(1000), v1); Orbit orbit_out = new KeplerianOrbit(rv1, inertialFrame, initialDate, mu); //System.out.println(orbit_out.getA()); } catch (FileNotFoundException ex) { Logger.getLogger(LambertMRev.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:com.adobe.aem.demomachine.Json2Csv.java
public static void main(String[] args) throws IOException { String inputFile1 = null;//from w w w.ja v a2 s.co m String inputFile2 = null; String outputFile = null; HashMap<String, String> hmReportSuites = new HashMap<String, String>(); // Command line options for this tool Options options = new Options(); options.addOption("c", true, "Filename 1"); options.addOption("r", true, "Filename 2"); options.addOption("o", true, "Filename 3"); CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("c")) { inputFile1 = cmd.getOptionValue("c"); } if (cmd.hasOption("r")) { inputFile2 = cmd.getOptionValue("r"); } if (cmd.hasOption("o")) { outputFile = cmd.getOptionValue("o"); } if (inputFile1 == null || inputFile1 == null || outputFile == null) { System.exit(-1); } } catch (ParseException ex) { logger.error(ex.getMessage()); } // List of customers and report suites for these customers String sInputFile1 = readFile(inputFile1, Charset.defaultCharset()); sInputFile1 = sInputFile1.replaceAll("ObjectId\\(\"([0-9a-z]*)\"\\)", "\"$1\""); // Processing the list of report suites for each customer try { JSONArray jCustomers = new JSONArray(sInputFile1.trim()); for (int i = 0, size = jCustomers.length(); i < size; i++) { JSONObject jCustomer = jCustomers.getJSONObject(i); Iterator<?> keys = jCustomer.keys(); String companyName = null; while (keys.hasNext()) { String key = (String) keys.next(); if (key.equals("company")) { companyName = jCustomer.getString(key); } } keys = jCustomer.keys(); while (keys.hasNext()) { String key = (String) keys.next(); if (key.equals("report_suites")) { JSONArray jReportSuites = jCustomer.getJSONArray(key); for (int j = 0, rSize = jReportSuites.length(); j < rSize; j++) { hmReportSuites.put(jReportSuites.getString(j), companyName); System.out.println(jReportSuites.get(j) + " for company " + companyName); } } } } // Creating the out put file PrintWriter writer = new PrintWriter(outputFile, "UTF-8"); writer.println("\"" + "Customer" + "\",\"" + "ReportSuite ID" + "\",\"" + "Number of Documents" + "\",\"" + "Last Updated" + "\""); // Processing the list of SOLR collections String sInputFile2 = readFile(inputFile2, Charset.defaultCharset()); sInputFile2 = sInputFile2.replaceAll("NumberLong\\(\"([0-9a-z]*)\"\\)", "\"$1\""); JSONObject jResults = new JSONObject(sInputFile2.trim()); JSONArray jCollections = jResults.getJSONArray("result"); for (int i = 0, size = jCollections.length(); i < size; i++) { JSONObject jCollection = jCollections.getJSONObject(i); String id = null; String number = null; String lastupdate = null; Iterator<?> keys = jCollection.keys(); while (keys.hasNext()) { String key = (String) keys.next(); if (key.equals("_id")) { id = jCollection.getString(key); } } keys = jCollection.keys(); while (keys.hasNext()) { String key = (String) keys.next(); if (key.equals("noOfDocs")) { number = jCollection.getString(key); } } keys = jCollection.keys(); while (keys.hasNext()) { String key = (String) keys.next(); if (key.equals("latestUpdateDate")) { lastupdate = jCollection.getString(key); } } Date d = new Date(Long.parseLong(lastupdate)); System.out.println(hmReportSuites.get(id) + "," + id + "," + number + "," + lastupdate + "," + new SimpleDateFormat("MM-dd-yyyy").format(d)); writer.println("\"" + hmReportSuites.get(id) + "\",\"" + id + "\",\"" + number + "\",\"" + new SimpleDateFormat("MM-dd-yyyy").format(d) + "\""); } writer.close(); } catch (JSONException e) { // TODO Auto-generated catch block e.printStackTrace(); } }
From source file:com.medicaid.mmis.util.DataLoader.java
/** * The main function, imports the files given as arguments. * // w w w . ja va 2 s . com * @param args the file names * @throws IOException for read/write errors * @throws PortalServiceException for any other errors */ public static void main(String[] args) throws IOException, PortalServiceException { if (args.length != 2) { System.out.println("2 file path arguments are required."); return; } PropertyConfigurator.configure("log4j.properties"); logger = Logger.getLogger(DataLoader.class); LookupServiceBean lookupBean = new LookupServiceBean(); EntityManagerFactory emf = Persistence.createEntityManagerFactory("cms-data-load"); EntityManager em = emf.createEntityManager(); lookupBean.setEm(em); DataLoader loader = new DataLoader(); loader.setLookup(lookupBean); SequenceGeneratorBean sequence = new SequenceGeneratorBean(); sequence.setEm(em); ProviderEnrollmentServiceBean enrollmentBean = new ProviderEnrollmentServiceBean(); enrollmentBean.setEm(em); enrollmentBean.setSequence(sequence); enrollmentBean.setLookupService(lookupBean); loader.setEnrollmentService(enrollmentBean); long processId = sequence.getNextValue("PROCESS_ID"); System.out.println("Started process id " + processId); BufferedReader br = null; PrintWriter accepted = null; PrintWriter rejected = null; try { System.out.println("Processing file 1..."); File success = new File("accepted_1_" + processId + ".txt"); File failure = new File("rejected_1_" + processId + ".txt"); success.createNewFile(); failure.createNewFile(); accepted = new PrintWriter(success); rejected = new PrintWriter(failure); br = new BufferedReader(new FileReader(args[0])); String line = null; int total = 0; int errors = 0; while ((line = br.readLine()) != null) { total++; try { em.getTransaction().begin(); loader.readProviderFile(new ByteArrayInputStream(line.getBytes())); em.getTransaction().commit(); accepted.println(line); logger.info("Commit row " + total); } catch (PortalServiceException e) { rejected.println(line); em.getTransaction().rollback(); errors++; logger.error("Rollback row " + total + " :" + e.getMessage()); } } accepted.flush(); accepted.close(); rejected.flush(); rejected.close(); br.close(); System.out.println("Total records read: " + total); System.out.println("Total rejected: " + errors); System.out.println("Processing file 2..."); success = new File("accepted_2_" + processId + ".txt"); failure = new File("rejected_2_" + processId + ".txt"); success.createNewFile(); failure.createNewFile(); accepted = new PrintWriter(success); rejected = new PrintWriter(failure); br = new BufferedReader(new FileReader(args[1])); line = null; total = 0; errors = 0; while ((line = br.readLine()) != null) { total++; try { em.getTransaction().begin(); Map<String, OwnershipInformation> owners = loader .readWS000EXT2OWNBEN(new ByteArrayInputStream(line.getBytes())); for (Map.Entry<String, OwnershipInformation> entry : owners.entrySet()) { enrollmentBean.addBeneficialOwners(entry.getKey(), entry.getValue()); } em.getTransaction().commit(); accepted.println(line); logger.info("Commit row " + total); } catch (PortalServiceException e) { rejected.println(line); em.getTransaction().rollback(); errors++; logger.error("Rollback row " + total + " :" + e.getMessage()); } } accepted.flush(); rejected.flush(); System.out.println("Total records read: " + total); System.out.println("Total rejected: " + errors); } finally { if (br != null) { br.close(); } if (accepted != null) { accepted.close(); } if (rejected != null) { rejected.close(); } } }
From source file:com.galois.fiveui.HeadlessRunner.java
/** * @param args list of headless run description filenames * @throws IOException//from w ww . j av a2s.co m * @throws URISyntaxException * @throws ParseException */ @SuppressWarnings("static-access") public static void main(final String[] args) throws IOException, URISyntaxException, ParseException { // Setup command line options Options options = new Options(); Option help = new Option("h", "print this help message"); Option output = OptionBuilder.withArgName("outfile").hasArg().withDescription("write output to file") .create("o"); Option report = OptionBuilder.withArgName("report directory").hasArg() .withDescription("write HTML reports to given directory").create("r"); options.addOption(output); options.addOption(report); options.addOption("v", false, "verbose output"); options.addOption("vv", false, "VERY verbose output"); options.addOption(help); // Parse command line options CommandLineParser parser = new GnuParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.err.println("Command line option parsing failed. Reason: " + e.getMessage()); System.exit(1); } // Display help if requested if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("headless <input file 1> [<input file 2> ...]", options); System.exit(1); } // Set logging levels BasicConfigurator.configure(); Logger fiveuiLogger = Logger.getLogger("com.galois.fiveui"); Logger rootLogger = Logger.getRootLogger(); if (cmd.hasOption("v")) { fiveuiLogger.setLevel(Level.DEBUG); rootLogger.setLevel(Level.ERROR); } else if (cmd.hasOption("vv")) { fiveuiLogger.setLevel(Level.DEBUG); rootLogger.setLevel(Level.DEBUG); } else { fiveuiLogger.setLevel(Level.ERROR); rootLogger.setLevel(Level.ERROR); } // Setup output file if requested PrintWriter outStream = null; if (cmd.hasOption("o")) { String outfile = cmd.getOptionValue("o"); try { outStream = new PrintWriter(new BufferedWriter(new FileWriter(outfile))); } catch (IOException e) { System.err.println("Could not open outfile for writing: " + cmd.getOptionValue("outfile")); System.exit(1); } } else { outStream = new PrintWriter(new BufferedWriter(new PrintWriter(System.out))); } // Setup HTML reports directory before the major work happens in case we // have to throw an exception. PrintWriter summaryFile = null; PrintWriter byURLFile = null; PrintWriter byRuleFile = null; if (cmd.hasOption("r")) { String repDir = cmd.getOptionValue("r"); try { File file = new File(repDir); if (!file.exists()) { file.mkdir(); logger.info("report directory created: " + repDir); } else { logger.info("report directory already exists!"); } summaryFile = new PrintWriter(new FileWriter(repDir + File.separator + "summary.html")); byURLFile = new PrintWriter(new FileWriter(repDir + File.separator + "byURL.html")); byRuleFile = new PrintWriter(new FileWriter(repDir + File.separator + "byRule.html")); } catch (IOException e) { System.err.println("could not open report directory / files for writing"); System.exit(1); } } // Major work: process input files ImmutableList<Result> results = null; for (String in : cmd.getArgs()) { HeadlessRunDescription descr = HeadlessRunDescription.parse(in); logger.debug("invoking headless run..."); BatchRunner runner = new BatchRunner(); results = runner.runHeadless(descr); logger.debug("runHeadless returned " + results.size() + " results"); // write results to the output stream as we go for (Result result : results) { outStream.println(result.toString()); } outStream.flush(); } outStream.close(); // Write report files if requested if (cmd.hasOption("r") && results != null) { Reporter kermit = new Reporter(results); summaryFile.write(kermit.getSummary()); summaryFile.close(); byURLFile.write(kermit.getByURL()); byURLFile.close(); byRuleFile.write(kermit.getByRule()); byRuleFile.close(); } }
From source file:edu.isi.karma.research.modeling.ModelLearner_LOD.java
public static void main(String[] args) throws Exception { ServletContextParameterMap contextParameters = ContextParametersRegistry.getInstance().getDefault(); contextParameters.setParameterValue(ContextParameter.USER_CONFIG_DIRECTORY, "/Users/mohsen/karma/config"); OntologyManager ontologyManager = new OntologyManager(contextParameters.getId()); File ff = new File(Params.ONTOLOGY_DIR); File[] files = ff.listFiles(); if (files == null) { logger.error("no ontology to import at " + ff.getAbsolutePath()); return;/*from ww w .j ava2 s.co m*/ } for (File f : files) { if (f.getName().endsWith(".owl") || f.getName().endsWith(".rdf") || f.getName().endsWith(".n3") || f.getName().endsWith(".ttl") || f.getName().endsWith(".xml")) { logger.info("Loading ontology file: " + f.getAbsolutePath()); ontologyManager.doImport(f, "UTF-8"); } } ontologyManager.updateCache(); String outputPath = Params.OUTPUT_DIR; String graphPath = Params.GRAPHS_DIR; FileUtils.cleanDirectory(new File(graphPath)); List<SemanticModel> semanticModels = ModelReader.importSemanticModelsFromJsonFiles(Params.MODEL_DIR, Params.MODEL_MAIN_FILE_EXT); ModelLearner_LOD modelLearner = null; boolean onlyGenerateSemanticTypeStatistics = false; boolean onlyUseOntology = false; boolean useCorrectType = false; int numberOfCandidates = 4; boolean onlyEvaluateInternalLinks = false; int maxPatternSize = 3; if (onlyGenerateSemanticTypeStatistics) { getStatistics(semanticModels); return; } String filePath = Params.RESULTS_DIR + "temp/"; String filename = ""; filename += "lod-results"; filename += useCorrectType ? "-correct" : "-k=" + numberOfCandidates; filename += onlyUseOntology ? "-ontology" : "-p" + maxPatternSize; filename += onlyEvaluateInternalLinks ? "-internal" : "-all"; filename += ".csv"; PrintWriter resultFile = new PrintWriter(new File(filePath + filename)); resultFile.println("source \t p \t r \t t \n"); for (int i = 0; i < semanticModels.size(); i++) { // for (int i = 0; i <= 10; i++) { // int i = 1; { int newSourceIndex = i; SemanticModel newSource = semanticModels.get(newSourceIndex); logger.info("======================================================"); logger.info(newSource.getName() + "(#attributes:" + newSource.getColumnNodes().size() + ")"); System.out.println(newSource.getName() + "(#attributes:" + newSource.getColumnNodes().size() + ")"); logger.info("======================================================"); SemanticModel correctModel = newSource; List<ColumnNode> columnNodes = correctModel.getColumnNodes(); List<Node> steinerNodes = new LinkedList<Node>(columnNodes); String graphName = graphPath + "lod" + Params.GRAPH_FILE_EXT; if (onlyUseOntology) { modelLearner = new ModelLearner_LOD(new GraphBuilder(ontologyManager, false), steinerNodes); } else if (new File(graphName).exists()) { // read graph from file try { logger.info("loading the graph ..."); DirectedWeightedMultigraph<Node, DefaultLink> graph = GraphUtil.importJson(graphName); modelLearner = new ModelLearner_LOD(new GraphBuilderTopK(ontologyManager, graph), steinerNodes); } catch (Exception e) { e.printStackTrace(); resultFile.close(); return; } } else { logger.info("building the graph ..."); // create and save the graph to file // GraphBuilder_Popularity b = new GraphBuilder_Popularity(ontologyManager, // Params.LOD_OBJECT_PROPERIES_FILE, // Params.LOD_DATA_PROPERIES_FILE); GraphBuilder_LOD_Pattern b = new GraphBuilder_LOD_Pattern(ontologyManager, Params.PATTERNS_DIR, maxPatternSize); modelLearner = new ModelLearner_LOD(b.getGraphBuilder(), steinerNodes); } long start = System.currentTimeMillis(); List<SortableSemanticModel> hypothesisList = modelLearner.hypothesize(useCorrectType, numberOfCandidates); long elapsedTimeMillis = System.currentTimeMillis() - start; float elapsedTimeSec = elapsedTimeMillis / 1000F; List<SortableSemanticModel> topHypotheses = null; if (hypothesisList != null) { // for (SortableSemanticModel sss : hypothesisList) { // ModelEvaluation mmm = sss.evaluate(correctModel); // System.out.println(mmm.getPrecision() + ", " + mmm.getRecall()); // } topHypotheses = hypothesisList.size() > 10 ? hypothesisList.subList(0, 10) : hypothesisList; } Map<String, SemanticModel> models = new TreeMap<String, SemanticModel>(); ModelEvaluation me; models.put("1-correct model", correctModel); if (topHypotheses != null) for (int k = 0; k < topHypotheses.size(); k++) { SortableSemanticModel m = topHypotheses.get(k); me = m.evaluate(correctModel, onlyEvaluateInternalLinks, false); String label = "candidate " + k + "\n" + // (m.getSteinerNodes() == null ? "" : m.getSteinerNodes().getScoreDetailsString()) + "link coherence:" + (m.getLinkCoherence() == null ? "" : m.getLinkCoherence().getCoherenceValue()) + "\n"; label += (m.getSteinerNodes() == null || m.getSteinerNodes().getCoherence() == null) ? "" : "node coherence:" + m.getSteinerNodes().getCoherence().getCoherenceValue() + "\n"; label += "confidence:" + m.getConfidenceScore() + "\n"; label += m.getSteinerNodes() == null ? "" : "mapping score:" + m.getSteinerNodes().getScore() + "\n"; label += "cost:" + roundDecimals(m.getCost(), 6) + "\n" + // "-distance:" + me.getDistance() + "-precision:" + me.getPrecision() + "-recall:" + me.getRecall(); models.put(label, m); if (k == 0) { // first rank model System.out.println("precision: " + me.getPrecision() + ", recall: " + me.getRecall() + ", time: " + elapsedTimeSec); logger.info("precision: " + me.getPrecision() + ", recall: " + me.getRecall() + ", time: " + elapsedTimeSec); String s = newSource.getName() + "\t" + me.getPrecision() + "\t" + me.getRecall() + "\t" + elapsedTimeSec; resultFile.println(s); } } String outName = outputPath + newSource.getName() + Params.GRAPHVIS_OUT_DETAILS_FILE_EXT; GraphVizUtil.exportSemanticModelsToGraphviz(models, newSource.getName(), outName, GraphVizLabelType.LocalId, GraphVizLabelType.LocalUri, true, true); } resultFile.close(); }
From source file:com.zimbra.cs.account.AttributeManagerUtil.java
public static void main(String[] args) throws IOException, ServiceException { CliUtil.toolSetup();// w ww .j ava 2 s .co m CommandLine cl = parseArgs(args); if (!cl.hasOption('a')) usage("no action specified"); String actionStr = cl.getOptionValue('a'); Action action = null; try { action = Action.valueOf(actionStr); } catch (IllegalArgumentException iae) { usage("unknown action: " + actionStr); } AttributeManager am = null; if (action != Action.dump && action != Action.listAttrs) { if (!cl.hasOption('i')) usage("no input attribute xml files specified"); am = new AttributeManager(cl.getOptionValue('i')); if (am.hasErrors()) { ZimbraLog.misc.warn(am.getErrors()); System.exit(1); } } OutputStream os = System.out; if (cl.hasOption('o')) { os = new FileOutputStream(cl.getOptionValue('o')); } PrintWriter pw = new PrintWriter(new BufferedWriter(new OutputStreamWriter(os, "utf8"))); AttributeManagerUtil amu = new AttributeManagerUtil(am); switch (action) { case dump: LdapProv.getInst().dumpLdapSchema(pw); break; case generateDefaultCOSLdif: amu.generateDefaultCOSLdif(pw); break; case generateDefaultExternalCOSLdif: amu.generateDefaultExternalCOSLdif(pw); break; case generateGetters: amu.generateGetters(cl.getOptionValue('c'), cl.getOptionValue('r')); break; case generateGlobalConfigLdif: amu.generateGlobalConfigLdif(pw); break; case generateLdapSchema: if (!cl.hasOption('t')) { usage("no schema template specified"); } amu.generateLdapSchema(pw, cl.getOptionValue('t')); break; case generateMessageProperties: amu.generateMessageProperties(cl.getOptionValue('r')); break; case generateProvisioning: amu.generateProvisioningConstants(cl.getOptionValue('r')); break; case generateSchemaLdif: amu.generateSchemaLdif(pw); break; case listAttrs: amu.listAttrs(pw, cl.getOptionValues('c'), cl.getOptionValues('n'), cl.getOptionValues('f')); break; } pw.close(); }
From source file:id3Crawler.java
public static void main(String[] args) throws IOException { //Input for the directory to be searched. System.out.println("Please enter a directory: "); Scanner scanner = new Scanner(System.in); String input = scanner.nextLine(); //Start a timer to calculate runtime startTime = System.currentTimeMillis(); System.out.println("Starting scan..."); //Files for output PrintWriter pw1 = new PrintWriter(new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/Song.txt")); PrintWriter pw2 = new PrintWriter(new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/Artist.txt")); PrintWriter pw3 = new PrintWriter(new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/Album.txt")); PrintWriter pw4 = new PrintWriter( new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/PerformedBy.txt")); PrintWriter pw5 = new PrintWriter( new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/TrackOf.txt")); PrintWriter pw6 = new PrintWriter( new FileWriter("C:/Users/gbob3_000/Desktop/id3CrawlerOutput/CreatedBy.txt")); //This is used for creating IDs for artists, songs, albums. int idCounter = 0; //This is used to prevent duplicate artists String previousArtist = " "; String currentArtist;/*from w ww. j a va 2 s . c o m*/ int artistID = 0; //This is used to prevent duplicate albums String previousAlbum = " "; String currentAlbum; int albumID = 0; //This array holds valid extensions to iterate through String[] extensions = new String[] { "mp3" }; //iterate through all files in a directory Iterator<File> it = FileUtils.iterateFiles(new File(input), extensions, true); while (it.hasNext()) { //open the next file File file = it.next(); //instantiate an mp3file object with the opened file MP3 song = GetMP3(file); //pass the song through SongInfo and return the required information SongInfo info = new SongInfo(song); //This is used to prevent duplicate artists/albums currentArtist = info.getArtistInfo(); currentAlbum = info.getAlbumInfo(); //Append the song information to the end of a text file pw1.println(idCounter + "\t" + info.getTitleInfo()); //This prevents duplicates of artists if (!(currentArtist.equals(previousArtist))) { pw2.println(idCounter + "\t" + info.getArtistInfo()); previousArtist = currentArtist; artistID = idCounter; } //This prevents duplicates of albums if (!(currentAlbum.equals(previousAlbum))) { pw3.println(idCounter + "\t" + info.getAlbumInfo()); previousAlbum = currentAlbum; albumID = idCounter; //This formats the IDs for a "CreatedBy" relationship table pw6.println(artistID + "\t" + albumID); } //This formats the IDs for a "PerformedBy" relationship table pw4.println(idCounter + "\t" + artistID); //This formats the IDs for a "TrackOf" relationship table pw5.println(idCounter + "\t" + albumID); idCounter++; songCounter++; } scanner.close(); pw1.close(); pw2.close(); pw3.close(); pw4.close(); pw5.close(); pw6.close(); System.out.println("Scan took " + ((System.currentTimeMillis() - startTime) / 1000.0) + " seconds to scan " + songCounter + " items!"); }
From source file:edu.msu.cme.rdp.readseq.utils.SequenceTrimmer.java
public static void main(String[] args) throws IOException { Options options = new Options(); options.addOption("r", "ref-seq", true, "Trim points are given as positions in a reference sequence from this file"); options.addOption("i", "inclusive", false, "Trim points are inclusive"); options.addOption("l", "length", true, "Minimum length of sequence after trimming"); options.addOption("f", "filled-ratio", true, "Minimum ratio of filled model positions of sequence after trimming"); options.addOption("o", "out", true, "Write sequences to directory (default=cwd)"); options.addOption("s", "stats", true, "Write stats to file"); PrintWriter statsOut = new PrintWriter(new NullWriter()); boolean inclusive = false; int minLength = 0; int minTrimmedLength = 0; int maxNs = 0; int maxTrimNs = 0; int trimStart = 0; int trimStop = 0; Sequence refSeq = null;/*from w ww . j a v a2s .c o m*/ float minFilledRatio = 0; int expectedModelPos = -1; String[] inputFiles = null; File outdir = new File("."); try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("ref-seq")) { refSeq = readRefSeq(new File(line.getOptionValue("ref-seq"))); } if (line.hasOption("inclusive")) { inclusive = true; } if (line.hasOption("length")) { minLength = Integer.valueOf(line.getOptionValue("length")); } if (line.hasOption("filled-ratio")) { minFilledRatio = Float.valueOf(line.getOptionValue("filled-ratio")); } if (line.hasOption("out")) { outdir = new File(line.getOptionValue("out")); if (!outdir.isDirectory()) { outdir = outdir.getParentFile(); System.err.println("Output option is not a directory, using " + outdir + " instead"); } } if (line.hasOption("stats")) { statsOut = new PrintWriter(line.getOptionValue("stats")); } args = line.getArgs(); if (args.length < 3) { throw new Exception("Unexpected number of arguments"); } trimStart = Integer.parseInt(args[0]); trimStop = Integer.parseInt(args[1]); inputFiles = Arrays.copyOfRange(args, 2, args.length); if (refSeq != null) { expectedModelPos = SeqUtils.getMaskedBySeqString(refSeq.getSeqString()).length(); trimStart = translateCoord(trimStart, refSeq, CoordType.seq, CoordType.model); trimStop = translateCoord(trimStop, refSeq, CoordType.seq, CoordType.model); } } catch (Exception e) { new HelpFormatter().printHelp("SequenceTrimmer <trim start> <trim stop> <aligned file> ...", options); System.err.println("Error: " + e.getMessage()); } System.err.println("Starting sequence trimmer"); System.err.println("* Input files: " + Arrays.asList(inputFiles)); System.err.println("* Minimum Length: " + minLength); System.err.println("* Trim point inclusive?: " + inclusive); System.err.println("* Trim points: " + trimStart + "-" + trimStop); System.err.println("* Min filled ratio: " + minFilledRatio); System.err.println("* refSeq: " + ((refSeq == null) ? "model" : refSeq.getSeqName() + " " + refSeq.getDesc())); Sequence seq; SeqReader reader; TrimStats stats; writeStatsHeader(statsOut); FastaWriter seqWriter; File in; for (String infile : inputFiles) { in = new File(infile); reader = new SequenceReader(in); seqWriter = new FastaWriter(new File(outdir, "trimmed_" + in.getName())); while ((seq = reader.readNextSequence()) != null) { if (seq.getSeqName().startsWith("#")) { seqWriter.writeSeq(seq.getSeqName(), "", trimMetaSeq(seq.getSeqString(), trimStart, trimStop)); continue; } stats = getStats(seq, trimStart, trimStop); boolean passed = didSeqPass(stats, minLength, minTrimmedLength, maxNs, maxTrimNs, minFilledRatio); writeStats(statsOut, seq.getSeqName(), stats, passed); if (passed) { seqWriter.writeSeq(seq.getSeqName(), seq.getDesc(), new String(stats.trimmedBases)); } } reader.close(); seqWriter.close(); } statsOut.close(); }
From source file:microbiosima.SelectiveMicrobiosima.java
/** * @param args//from w ww .j a v a 2 s. c o m * the command line arguments * @throws java.io.FileNotFoundException * @throws java.io.UnsupportedEncodingException */ public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException { int populationSize = 500;//Integer.parseInt(parameters[1]); int microSize = 1000;//Integer.parseInt(parameters[2]); int numberOfSpecies = 150;//Integer.parseInt(parameters[3]); int numberOfGeneration = 10000; int Ngene = 10; int numberOfObservation = 100; int numberOfReplication = 10; double Ngenepm = 5; double pctEnv = 0; double pctPool = 0; double msCoeff = 1; double hsCoeff = 1; boolean HMS_or_TMS = true; 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(6).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, (5) number of total traits, (6)number of traits per microbe" + " [default: 500 1000 150 10000 10 5]"); 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" + " msCoeff Parameter related to microbe selection strength\n" + " hsCoeff Parameter related to host selection strength\n" + " HMS_or_TMS String HMS or TMS to specify host-mediated or trait-mediated microbe selection\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 != 5) { System.out.println( "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. 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]); msCoeff = Double.parseDouble(pct_config[2]); hsCoeff = Double.parseDouble(pct_config[3]); if (pct_config[4].equals("HMS")) HMS_or_TMS = true; if (pct_config[4].equals("TMS")) HMS_or_TMS = false; 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 (msCoeff < 1) { System.out.println( "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff=" + msCoeff + ")! EXIT"); System.exit(3); } if (hsCoeff < 1) { System.out.println( "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff=" + hsCoeff + ")! EXIT"); System.exit(3); } if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) { System.out.println( "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS=" + pct_config[4] + ")! 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]); Ngene = Integer.parseInt(configs[4]); Ngenepm = Double.parseDouble(configs[5]); if (Ngenepm > Ngene) { System.out.println( "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT"); System.exit(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\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ") .append(Ngenepm).append("\n"); System.out.println(sb.toString()); double[] environment = new double[numberOfSpecies]; for (int i = 0; i < numberOfSpecies; i++) { environment[i] = 1 / (double) numberOfSpecies; } int[] fitnessToHost = new int[Ngene]; int[] fitnessToMicrobe = new int[Ngene]; for (int rep = 0; rep < numberOfReplication; rep++) { String prefix = "" + (rep + 1) + "_"; String sufix; if (HMS_or_TMS) sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt"; else sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".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))); PrintWriter file7 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix))); PrintWriter file8 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix))); PrintWriter file9 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix))); PrintWriter file10 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix))); PrintWriter file11 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix))); PrintWriter file12 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix))); for (int i = 0; i < Ngene; i++) { fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1; fitnessToHost[i] = MathUtil.getNextInt(2) - 1; } MathUtil.setSeed(rep % numberOfReplication); SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm, msCoeff, fitnessToHost, fitnessToMicrobe); MathUtil.setSeed(); SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize, pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS); while (population.getNumberOfGeneration() < numberOfGeneration) { population.sumSpecies(); if (population.getNumberOfGeneration() % numberOfObservation == 0) { //file1.print(population.gammaDiversity(false)); //file2.print(population.alphaDiversity(false)); //file1.print("\t"); //file2.print("\t"); 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()); file7.print(population.averageHostFitness()); file7.print("\t"); file7.println(population.varianceHostFitness()); file8.println(population.cosOfMH()); file9.println(population.printOutHFitness()); file10.println(population.printOutMFitness()); file11.println(population.printBacteriaContents()); } population.getNextGen(); } for (SelectiveIndividual host : population.getIndividuals()) { file12.println(host.printBacteriaContents()); } file1.close(); file2.close(); file3.close(); file4.close(); file5.close(); file6.close(); file7.close(); file8.close(); file9.close(); file10.close(); file11.close(); file12.close(); } catch (IOException e) { e.printStackTrace(); } } }