List of usage examples for java.util List size
int size();
From source file:com.lenovo.tensorhusky.common.utils.Shell.java
public static void main(String[] args) throws IOException { List<String> command = new ArrayList<String>(); command.add("ping"); command.add("-a"); command.add("baidu.com"); ShellCommandExecutor exe = new ShellCommandExecutor(command.toArray(new String[command.size()])); exe.execute();/* w ww . j a va2 s . co m*/ System.out.println(exe.getOutput()); }
From source file:diffhunter.DiffHunter.java
/** * @param args the command line arguments * @throws org.apache.commons.cli.ParseException * @throws java.io.IOException// w w w .ja va 2 s. c om */ public static void main(String[] args) throws ParseException, IOException { //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString(); // TODO code application logic here /*args = new String[] { "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData" };*/ /*args = new String[] { "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData" };*/ Options options = new Options(); // add t option options.addOption("i", "index", false, "Indexing BED files."); options.addOption("b", "bed", true, "bed file to be indexed"); options.addOption("o", "output", true, "Folder that the index/comparison file will be created."); options.addOption("r", "reference", true, "Reference annotation file to be used for indexing"); options.addOption("c", "compare", false, "Finding differences between two conditions"); options.addOption("1", "first", true, "First sample index location"); options.addOption("2", "second", true, "Second sample index location"); options.addOption("w", "window", true, "Length of window for identifying differences"); options.addOption("s", "sliding", true, "Length of sliding"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); boolean indexing = false; boolean comparing = false; //Indexing! if (cmd.hasOption("i")) { //if(cmd.hasOption("1")) //System.err.println("sasan"); //System.out.println("sasa"); indexing = true; } else if (cmd.hasOption("c")) { //System.err.println(""); comparing = true; } else { //System.err.println("Option is not deteced."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } //Indexing is selected // if (indexing == true) { //Since indexing is true. //User have to provide file for indexing. if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String bedfile_ = cmd.getOptionValue("b"); String reference_file = cmd.getOptionValue("r"); String folder_loc = cmd.getOptionValue("o"); String sample_name = FilenameUtils.getBaseName(bedfile_); try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB( Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) { Indexer indexing_ = new Indexer(reference_file); indexing_.Make_Index(B2, bedfile_, Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString()); B2.close(); } } else if (comparing == true) { if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1") || cmd.hasOption("2"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String folder_loc = cmd.getOptionValue("o"); int window_ = Integer.parseInt(cmd.getOptionValue("w")); //int window_=600; int slide_ = Integer.parseInt(cmd.getOptionValue("s")); String first = cmd.getOptionValue("1").replace("_BDB", ""); String second = cmd.getOptionValue("2").replace("_BDB", ""); String reference_file = cmd.getOptionValue("r"); //String folder_loc=cmd.getOptionValue("o"); String sample_name_first = FilenameUtils.getBaseName(first); String sample_name_second = FilenameUtils.getBaseName(second); Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first); Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second); List<String> first_condition_genes = Files .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath()) .collect(Collectors.toList()); List<String> second_condition_genes = Files .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath()) .collect(Collectors.toList()); System.out.println("First and second condition are loaded!!! "); List<String> intersection_ = new ArrayList<>(first_condition_genes); intersection_.retainAll(second_condition_genes); BufferedWriter output = new BufferedWriter( new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt") .toAbsolutePath().toString(), false)); List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>()); Worker_New worker_class = new Worker_New(); worker_class.Read_Reference(reference_file); while (!intersection_.isEmpty()) { List<String> selected_genes = new ArrayList<>(); //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));} //else selected_genes.addAll(intersection_.subList(0, 10000)); if (intersection_.size() <= intersection_.size()) { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } else { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } intersection_.removeAll(selected_genes); //System.out.println("Intersection count is:"+intersection_.size()); //final List<Result_Window> resultssss_=new ArrayList<>(); IntStream.range(0, selected_genes.size()).parallel().forEach(i -> { System.out.println(selected_genes.get(i) + "\tprocessing......"); String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2"; int start = worker_class.dic_genes.get(gene_of_interest).start_loc; int end = worker_class.dic_genes.get(gene_of_interest).end_loc; Map<Integer, Integer> first_ = Collections.EMPTY_MAP; try { first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } Map<Integer, Integer> second_ = Collections.EMPTY_MAP; try { second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_); List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_); //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i)); // System.out.println("top_window_first_Count\t"+top_windows_first.size()); // System.out.println("top_window_second_Count\t"+top_windows_second.size()); if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) { return; } List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, sample_name_first, sample_name_second, 0.01); if (!res_temp.isEmpty()) { final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01)); } //System.out.println(selected_genes.get(i)+"\tprocessed."); }); /*selected_genes.parallelStream().forEach(i -> { });*/ List<Double> pvals = new ArrayList<>(); for (int i = 0; i < final_results.size(); i++) { pvals.add(final_results.get(i).p_value); } List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals); System.out.println("Writing to file..."); output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR"); output.newLine(); for (int i = 0; i < final_results.size(); i++) { Result_Window item = final_results.get(i); output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } /* for (Result_Window item : final_results) { output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } */ final_results.clear(); } output.close(); } System.out.println("Done."); }
From source file:com.amazonaws.services.kinesis.leases.impl.LeaseCoordinatorExerciser.java
public static void main(String[] args) throws InterruptedException, DependencyException, InvalidStateException, ProvisionedThroughputException, IOException { int numCoordinators = 9; int numLeases = 73; int leaseDurationMillis = 10000; int epsilonMillis = 100; AWSCredentialsProvider creds = new DefaultAWSCredentialsProviderChain(); AmazonDynamoDBClient ddb = new AmazonDynamoDBClient(creds); ILeaseManager<KinesisClientLease> leaseManager = new KinesisClientLeaseManager("nagl_ShardProgress", ddb); if (leaseManager.createLeaseTableIfNotExists(10L, 50L)) { LOG.info("Waiting for newly created lease table"); if (!leaseManager.waitUntilLeaseTableExists(10, 300)) { LOG.error("Table was not created in time"); return; }//from www . j a v a 2 s.c o m } CWMetricsFactory metricsFactory = new CWMetricsFactory(creds, "testNamespace", 30 * 1000, 1000); final List<LeaseCoordinator<KinesisClientLease>> coordinators = new ArrayList<LeaseCoordinator<KinesisClientLease>>(); for (int i = 0; i < numCoordinators; i++) { String workerIdentifier = "worker-" + Integer.toString(i); LeaseCoordinator<KinesisClientLease> coord = new LeaseCoordinator<KinesisClientLease>(leaseManager, workerIdentifier, leaseDurationMillis, epsilonMillis, metricsFactory); coordinators.add(coord); } leaseManager.deleteAll(); for (int i = 0; i < numLeases; i++) { KinesisClientLease lease = new KinesisClientLease(); lease.setLeaseKey(Integer.toString(i)); lease.setCheckpoint(new ExtendedSequenceNumber("checkpoint")); leaseManager.createLeaseIfNotExists(lease); } final JFrame frame = new JFrame("Test Visualizer"); frame.setPreferredSize(new Dimension(800, 600)); final JPanel panel = new JPanel(new GridLayout(coordinators.size() + 1, 0)); final JLabel ticker = new JLabel("tick"); panel.add(ticker); frame.getContentPane().add(panel); final Map<String, JLabel> labels = new HashMap<String, JLabel>(); for (final LeaseCoordinator<KinesisClientLease> coord : coordinators) { JPanel coordPanel = new JPanel(); coordPanel.setLayout(new BoxLayout(coordPanel, BoxLayout.X_AXIS)); final Button button = new Button("Stop " + coord.getWorkerIdentifier()); button.setMaximumSize(new Dimension(200, 50)); button.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { if (coord.isRunning()) { coord.stop(); button.setLabel("Start " + coord.getWorkerIdentifier()); } else { try { coord.start(); } catch (LeasingException e) { LOG.error(e); } button.setLabel("Stop " + coord.getWorkerIdentifier()); } } }); coordPanel.add(button); JLabel label = new JLabel(); coordPanel.add(label); labels.put(coord.getWorkerIdentifier(), label); panel.add(coordPanel); } frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); new Thread() { // Key is lease key, value is green-ness as a value from 0 to 255. // Great variable name, huh? private Map<String, Integer> greenNesses = new HashMap<String, Integer>(); // Key is lease key, value is last owning worker private Map<String, String> lastOwners = new HashMap<String, String>(); @Override public void run() { while (true) { for (LeaseCoordinator<KinesisClientLease> coord : coordinators) { String workerIdentifier = coord.getWorkerIdentifier(); JLabel label = labels.get(workerIdentifier); List<KinesisClientLease> asgn = new ArrayList<KinesisClientLease>(coord.getAssignments()); Collections.sort(asgn, new Comparator<KinesisClientLease>() { @Override public int compare(KinesisClientLease arg0, KinesisClientLease arg1) { return arg0.getLeaseKey().compareTo(arg1.getLeaseKey()); } }); StringBuilder builder = new StringBuilder(); builder.append("<html>"); builder.append(workerIdentifier).append(":").append(asgn.size()).append(" "); for (KinesisClientLease lease : asgn) { String leaseKey = lease.getLeaseKey(); String lastOwner = lastOwners.get(leaseKey); // Color things green when they switch owners, decay the green-ness over time. Integer greenNess = greenNesses.get(leaseKey); if (greenNess == null || lastOwner == null || !lastOwner.equals(lease.getLeaseOwner())) { greenNess = 200; } else { greenNess = Math.max(0, greenNess - 20); } greenNesses.put(leaseKey, greenNess); lastOwners.put(leaseKey, lease.getLeaseOwner()); builder.append(String.format("<font color=\"%s\">%03d</font>", String.format("#00%02x00", greenNess), Integer.parseInt(leaseKey))).append(" "); } builder.append("</html>"); label.setText(builder.toString()); label.revalidate(); label.repaint(); } if (ticker.getText().equals("tick")) { ticker.setText("tock"); } else { ticker.setText("tick"); } try { Thread.sleep(200); } catch (InterruptedException e) { } } } }.start(); frame.pack(); frame.setVisible(true); for (LeaseCoordinator<KinesisClientLease> coord : coordinators) { coord.start(); } }
From source file:com.samtech.piv.ChinaNameTool.java
public static void main(String[] args) { ChinaNameTool tool = ChinaNameTool.getInstance(); System.out.println(tool.containSurName("")); List ls = new ArrayList(); ls.add("1 12344 11111"); ls.add("2vds"); ls.add("3vds"); ls.add("41111"); ls.add("5sdfs"); ls.add("6-"); ls.add("7,"); ls.add("8*"); ls.add("9");// w ww. j a v a2 s . com ls.add("10!"); ls.add("test"); ls.add(""); ls.add("??"); ls.add("??"); ls.add("????123456789"); ls.add("????123456789"); ls.add("YZ??,7842423921250"); ls.add("????7842423461567??"); ls.add("YZ?"); ls.add("YZC0906090012009"); for (int i = 0; i < ls.size(); i++) { String input = (String) ls.get(i); System.out.println(input + "=====" + tool.findChinaName(input)); } System.out.println("*************************"); for (int i = 0; i < ls.size(); i++) { String input = (String) ls.get(i); String[] names = tool.findChinaNames(input); if (names != null && names.length > 0) { String r = input + "====="; for (int j = 0; j < names.length; j++) { r = r + "," + names[j]; } System.out.println(r); } else { System.out.println(input + "=====null"); } } }
From source file:math2605.gn_qua.java
/** * @param args the command line arguments *//*from w w w. j a v a2 s. com*/ public static void main(String[] args) { //get file name System.out.println("Please enter a file name:"); Scanner scanner = new Scanner(System.in); String fileName = scanner.nextLine(); List<String[]> pairs = new ArrayList<>(); //get coordinate pairs and add to arraylist try { BufferedReader br = new BufferedReader(new FileReader(fileName)); String line; while ((line = br.readLine()) != null) { String[] pair = line.split(","); pairs.add(pair); } br.close(); } catch (Exception e) { System.out.println(e.getMessage()); } System.out.println("Please enter the value of a:"); double a = scanner.nextInt(); System.out.println("Please enter the value of b:"); double b = scanner.nextInt(); System.out.println("Please enter the value of c:"); double c = scanner.nextInt(); //init B, vector with 3 coordinates RealMatrix B = new Array2DRowRealMatrix(3, 1); B.setEntry(0, 0, a); B.setEntry(1, 0, b); B.setEntry(2, 0, c); System.out.println("Please enter the number of iteration for the Gauss-newton:"); //init N, number of iterations int N = scanner.nextInt(); //init r, vector of residuals RealMatrix r = new Array2DRowRealMatrix(pairs.size(), 1); setR(pairs, a, b, c, r); //init J, Jacobian of r RealMatrix J = new Array2DRowRealMatrix(pairs.size(), 3); setJ(pairs, a, b, c, r, J); System.out.println("J"); System.out.println(J); System.out.println("r"); System.out.println(r); RealMatrix sub = findQR(J, r); for (int i = N; i > 0; i--) { B = B.subtract(sub); double B0 = B.getEntry(0, 0); double B1 = B.getEntry(1, 0); double B2 = B.getEntry(2, 0); //CHANGE ABC TO USE B0, B1, B2 setR(pairs, B0, B1, B2, r); setJ(pairs, B0, B1, B2, r, J); } System.out.println("B"); System.out.println(B.toString()); }
From source file:com.act.lcms.db.io.ExportStandardIonResultsFromDB.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());// w w w .ja va 2 s . c om } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(ExportStandardIonResultsFromDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(ExportStandardIonResultsFromDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } try (DB db = DB.openDBFromCLI(cl)) { List<String> chemicalNames = new ArrayList<>(); if (cl.hasOption(OPTION_CONSTRUCT)) { // Extract the chemicals in the pathway and their product masses, then look up info on those chemicals List<Pair<ChemicalAssociatedWithPathway, Double>> productMasses = Utils .extractMassesForChemicalsAssociatedWithConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT)); for (Pair<ChemicalAssociatedWithPathway, Double> pair : productMasses) { chemicalNames.add(pair.getLeft().getChemical()); } } if (cl.hasOption(OPTION_CHEMICALS)) { chemicalNames.addAll(Arrays.asList(cl.getOptionValues(OPTION_CHEMICALS))); } if (chemicalNames.size() == 0) { System.err.format("No chemicals can be found from the input query.\n"); System.exit(-1); } List<String> standardIonHeaderFields = new ArrayList<String>() { { add(STANDARD_ION_HEADER_FIELDS.CHEMICAL.name()); add(STANDARD_ION_HEADER_FIELDS.BEST_ION_FROM_ALGO.name()); add(STANDARD_ION_HEADER_FIELDS.MANUAL_PICK.name()); add(STANDARD_ION_HEADER_FIELDS.AUTHOR.name()); add(STANDARD_ION_HEADER_FIELDS.DIAGNOSTIC_PLOTS.name()); add(STANDARD_ION_HEADER_FIELDS.NOTE.name()); } }; String outAnalysis; if (cl.hasOption(OPTION_OUTPUT_PREFIX)) { outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + TSV_FORMAT; } else { outAnalysis = String.join("-", chemicalNames) + "." + TSV_FORMAT; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); TSVWriter<String, String> resultsWriter = new TSVWriter<>(standardIonHeaderFields); resultsWriter.open(new File(outAnalysis)); // For each chemical, create a TSV row and a corresponding diagnostic plot for (String chemicalName : chemicalNames) { List<String> graphLabels = new ArrayList<>(); List<Double> yMaxList = new ArrayList<>(); String outData = plottingDirectory + "/" + chemicalName + ".data"; String outImg = plottingDirectory + "/" + chemicalName + ".pdf"; // For each diagnostic plot, open a new file stream. try (FileOutputStream fos = new FileOutputStream(outData)) { List<StandardIonResult> getResultByChemicalName = StandardIonResult.getByChemicalName(db, chemicalName); if (getResultByChemicalName != null && getResultByChemicalName.size() > 0) { // PART 1: Get the best metlin ion across all standard ion results for a given chemical String bestGlobalMetlinIon = AnalysisHelper .scoreAndReturnBestMetlinIonFromStandardIonResults(getResultByChemicalName, new HashMap<>(), true, true); // PART 2: Plot all the graphs related to the chemical. The plots are structured as follows: // // Page 1: All graphs (water, MeOH, Yeast) for Global ion picked (best ion among ALL standard ion runs for // the given chemical) by the algorithm // Page 2: All graphs for M+H // Page 3: All graphs for Local ions picked (best ion within a SINGLE standard ion run) + negative controls // for Yeast. // // Each page is demarcated by a blank graph. // Arrange results based on media Map<String, List<StandardIonResult>> categories = StandardIonResult .categorizeListOfStandardWellsByMedia(db, getResultByChemicalName); // This set contains all the best metlin ions corresponding to all the standard ion runs. Set<String> bestLocalIons = new HashSet<>(); bestLocalIons.add(bestGlobalMetlinIon); bestLocalIons.add(DEFAULT_ION); for (StandardIonResult result : getResultByChemicalName) { bestLocalIons.add(result.getBestMetlinIon()); } // We sort the best local ions are follows: // 1) Global best ion spectra 2) M+H spectra 3) Local best ion spectra List<String> bestLocalIonsArray = new ArrayList<>(bestLocalIons); Collections.sort(bestLocalIonsArray, new Comparator<String>() { @Override public int compare(String o1, String o2) { if (o1.equals(bestGlobalMetlinIon) && !o2.equals(bestGlobalMetlinIon)) { return -1; } else if (o1.equals(DEFAULT_ION) && !o2.equals(bestGlobalMetlinIon)) { return -1; } else { return 1; } } }); // This variable stores the index of the array at which all the remaining spectra are contained in one // page. This happens right after the M+H ion spectra. Integer combineAllSpectraIntoPageThreeFromIndex = 0; for (int i = 0; i < bestLocalIonsArray.size(); i++) { if (bestLocalIonsArray.get(i).equals(DEFAULT_ION)) { combineAllSpectraIntoPageThreeFromIndex = i + 1; } } for (int i = 0; i < bestLocalIonsArray.size(); i++) { String ion = bestLocalIonsArray.get(i); for (Map.Entry<String, List<StandardIonResult>> mediaToListOfIonResults : categories .entrySet()) { for (StandardIonResult result : mediaToListOfIonResults.getValue()) { // For every standard ion result, we plot the best global metlin ion and M+H. These plots are in the // pages 1 and 2. For all page 3 (aka miscellaneous spectra), we only plot the best local ion // corresponding to it's spectra and not some other graph's spectra. In the below condition, // we reach the page 3 case with not the same best ion as the spectra, in which case we just continue // and not draw anything on the page. if (i >= combineAllSpectraIntoPageThreeFromIndex && !(result.getBestMetlinIon().equals(ion))) { continue; } StandardWell positiveWell = StandardWell.getInstance().getById(db, result.getStandardWellId()); String positiveControlChemical = positiveWell.getChemical(); ScanData<StandardWell> encapsulatedDataForPositiveControl = AnalysisHelper .getScanDataForWell(db, lcmsDir, positiveWell, positiveControlChemical, positiveControlChemical); Set<String> singletonSet = Collections.singleton(ion); String additionalInfo = generateAdditionalLabelInformation(positiveWell, result, ion); List<String> labels = AnalysisHelper .writeScanData(fos, lcmsDir, MAX_INTENSITY, encapsulatedDataForPositiveControl, false, false, singletonSet) .stream().map(label -> label + additionalInfo) .collect(Collectors.toList()); yMaxList.add(encapsulatedDataForPositiveControl.getMs1ScanResults() .getMaxIntensityForIon(ion)); List<String> negativeLabels = null; // Only do the negative control in the miscellaneous page (page 3) and if the well is in yeast media. if (mediaToListOfIonResults.getKey() .equals(StandardWell.MEDIA_TYPE.YEAST.name()) && (i >= combineAllSpectraIntoPageThreeFromIndex && (result.getBestMetlinIon().equals(ion)))) { //TODO: Change the representative negative well to one that displays the highest noise in the future. // For now, we just use the first index among the negative wells. int representativeIndex = 0; StandardWell representativeNegativeControlWell = StandardWell.getInstance() .getById(db, result.getNegativeWellIds().get(representativeIndex)); ScanData encapsulatedDataForNegativeControl = AnalysisHelper .getScanDataForWell(db, lcmsDir, representativeNegativeControlWell, positiveWell.getChemical(), representativeNegativeControlWell.getChemical()); String negativePlateAdditionalInfo = generateAdditionalLabelInformation( representativeNegativeControlWell, null, null); negativeLabels = AnalysisHelper.writeScanData(fos, lcmsDir, MAX_INTENSITY, encapsulatedDataForNegativeControl, false, false, singletonSet) .stream().map(label -> label + negativePlateAdditionalInfo) .collect(Collectors.toList()); yMaxList.add(encapsulatedDataForNegativeControl.getMs1ScanResults() .getMaxIntensityForIon(ion)); } graphLabels.addAll(labels); if (negativeLabels != null) { graphLabels.addAll(negativeLabels); } } } // Add a blank graph to demarcate pages. if (i < combineAllSpectraIntoPageThreeFromIndex) { graphLabels.addAll(AnalysisHelper.writeScanData(fos, lcmsDir, 0.0, BLANK_SCAN, false, false, new HashSet<>())); yMaxList.add(0.0d); } } // We need to pass the yMax values as an array to the Gnuplotter. Double fontScale = null; if (cl.hasOption(FONT_SCALE)) { try { fontScale = Double.parseDouble(cl.getOptionValue(FONT_SCALE)); } catch (IllegalArgumentException e) { System.err.format("Argument for font-scale must be a floating point number.\n"); System.exit(1); } } Double[] yMaxes = yMaxList.toArray(new Double[yMaxList.size()]); Gnuplotter plotter = fontScale == null ? new Gnuplotter() : new Gnuplotter(fontScale); plotter.plot2D(outData, outImg, graphLabels.toArray(new String[graphLabels.size()]), "time", null, "intensity", "pdf", null, null, yMaxes, outImg + ".gnuplot"); Map<String, String> row = new HashMap<>(); row.put(STANDARD_ION_HEADER_FIELDS.CHEMICAL.name(), chemicalName); row.put(STANDARD_ION_HEADER_FIELDS.BEST_ION_FROM_ALGO.name(), bestGlobalMetlinIon); row.put(STANDARD_ION_HEADER_FIELDS.DIAGNOSTIC_PLOTS.name(), outImg); resultsWriter.append(row); resultsWriter.flush(); } } } resultsWriter.flush(); resultsWriter.close(); } }
From source file:net.kolola.msgparsercli.MsgParseCLI.java
public static void main(String[] args) { // Parse options OptionParser parser = new OptionParser("f:a:bi?*"); OptionSet options = parser.parse(args); // Get the filename if (!options.has("f")) { System.err.print("Specify a msg file with the -f option"); System.exit(0);/*w w w. ja va2 s .com*/ } File file = new File((String) options.valueOf("f")); MsgParser msgp = new MsgParser(); Message msg = null; try { msg = msgp.parseMsg(file); } catch (UnsupportedOperationException | IOException e) { System.err.print("File does not exist or is not a valid msg file"); //e.printStackTrace(); System.exit(1); } // Show info (as JSON) if (options.has("i")) { Map<String, Object> data = new HashMap<String, Object>(); String date; try { Date st = msg.getClientSubmitTime(); date = st.toString(); } catch (Exception g) { try { date = msg.getDate().toString(); } catch (Exception e) { date = "[UNAVAILABLE]"; } } data.put("date", date); data.put("subject", msg.getSubject()); data.put("from", "\"" + msg.getFromName() + "\" <" + msg.getFromEmail() + ">"); data.put("to", "\"" + msg.getToRecipient().toString()); String cc = ""; for (RecipientEntry r : msg.getCcRecipients()) { if (cc.length() > 0) cc.concat("; "); cc.concat(r.toString()); } data.put("cc", cc); data.put("body_html", msg.getBodyHTML()); data.put("body_rtf", msg.getBodyRTF()); data.put("body_text", msg.getBodyText()); // Attachments List<Map<String, String>> atts = new ArrayList<Map<String, String>>(); for (Attachment a : msg.getAttachments()) { HashMap<String, String> info = new HashMap<String, String>(); if (a instanceof FileAttachment) { FileAttachment fa = (FileAttachment) a; info.put("type", "file"); info.put("filename", fa.getFilename()); info.put("size", Long.toString(fa.getSize())); } else { info.put("type", "message"); } atts.add(info); } data.put("attachments", atts); JSONObject json = new JSONObject(data); try { System.out.print(json.toString(4)); } catch (JSONException e) { e.printStackTrace(); } } // OR return an attachment in BASE64 else if (options.has("a")) { Integer anum = Integer.parseInt((String) options.valueOf("a")); Encoder b64 = Base64.getEncoder(); List<Attachment> atts = msg.getAttachments(); if (atts.size() <= anum) { System.out.print("Attachment " + anum.toString() + " does not exist"); } Attachment att = atts.get(anum); if (att instanceof FileAttachment) { FileAttachment fatt = (FileAttachment) att; System.out.print(b64.encodeToString(fatt.getData())); } else { System.err.print("Attachment " + anum.toString() + " is a message - That's not implemented yet :("); } } // OR print the message body else if (options.has("b")) { System.out.print(msg.getConvertedBodyHTML()); } else { System.err.print( "Specify either -i to return msg information or -a <num> to print an attachment as a BASE64 string"); } }
From source file:com.lightboxtechnologies.nsrl.OCSVTest.java
public static void main(String[] args) throws IOException { final String mfg_filename = args[0]; final String os_filename = args[1]; final String prod_filename = args[2]; final String hash_filename = args[3]; final LineTokenizer tok = new OpenCSVLineTokenizer(); final RecordLoader loader = new RecordLoader(); final ErrorConsumer err = new ErrorConsumer() { public void consume(BadDataException e, long linenum) { System.err.println("malformed record, line " + linenum); e.printStackTrace();/*ww w . j a va 2s. c o m*/ } }; // read manufacturer, OS, product data final Map<String, MfgData> mfg = new HashMap<String, MfgData>(); final Map<String, OSData> os = new HashMap<String, OSData>(); final Map<Integer, List<ProdData>> prod = new HashMap<Integer, List<ProdData>>(); SmallTableLoader.load(mfg_filename, mfg, os_filename, os, prod_filename, prod, tok, err); // read hash data final RecordConsumer<HashData> hcon = new RecordConsumer<HashData>() { public void consume(HashData hd) { /* System.out.print(hd); for (ProdData pd : prod.get(hd.prod_code)) { System.out.print(pd); final MfgData pmd = mfg.get(pd.mfg_code); System.out.print(pmd); } final OSData osd = os.get(hd.os_code); System.out.print(osd); final MfgData osmd = mfg.get(osd.mfg_code); System.out.print(osmd); System.out.println(""); */ /* final Hex hex = new Hex(); String sha1 = null; String md5 = null; String crc32 = null; try { sha1 = (String) hex.encode((Object) hd.sha1); md5 = (String) hex.encode((Object) hd.md5); crc32 = (String) hex.encode((Object) hd.crc32); } catch (EncoderException e) { throw new RuntimeException(e); } */ final ObjectMapper mapper = new ObjectMapper(); final String sha1 = Hex.encodeHexString(hd.sha1); final String md5 = Hex.encodeHexString(hd.md5); final String crc32 = Hex.encodeHexString(hd.crc32); final Map<String, Object> hd_m = new HashMap<String, Object>(); hd_m.put("sha1", sha1); hd_m.put("md5", md5); hd_m.put("crc32", crc32); hd_m.put("name", hd.name); hd_m.put("size", hd.size); hd_m.put("special_code", hd.special_code); final OSData osd = os.get(hd.os_code); final MfgData osmfgd = mfg.get(osd.mfg_code); final Map<String, Object> os_m = new HashMap<String, Object>(); os_m.put("name", osd.name); os_m.put("version", osd.version); os_m.put("manufacturer", osmfgd.name); hd_m.put("os", os_m); final List<Map<String, Object>> pl_l = new ArrayList<Map<String, Object>>(); for (ProdData pd : prod.get(hd.prod_code)) { if (!osd.code.equals(pd.os_code)) { // os code mismatch /* System.err.println( "Hash record OS code == " + osd.code + " != " + pd.os_code + " == product record OS code" ); */ continue; } final Map<String, Object> prod_m = new HashMap<String, Object>(); prod_m.put("name", pd.name); prod_m.put("version", pd.version); prod_m.put("language", pd.language); prod_m.put("app_type", pd.app_type); prod_m.put("os_code", pd.os_code); final MfgData md = mfg.get(pd.mfg_code); prod_m.put("manufacturer", md.name); pl_l.add(prod_m); } if (pl_l.size() > 1) { System.err.println(hd.prod_code); } hd_m.put("products", pl_l); try { mapper.writeValue(System.out, hd_m); } catch (IOException e) { // should be impossible throw new IllegalStateException(e); } } }; final RecordProcessor<HashData> hproc = new HashRecordProcessor(); final LineHandler hlh = new DefaultLineHandler<HashData>(tok, hproc, hcon, err); InputStream zin = null; try { // zin = new GZIPInputStream(new FileInputStream(hash_filename)); zin = new FileInputStream(hash_filename); loader.load(zin, hlh); zin.close(); } finally { IOUtils.closeQuietly(zin); } System.out.println(); /* for (Map.Entry<String,String> e : mfg.entrySet()) { System.out.println(e.getKey() + " = " + e.getValue()); } for (Map.Entry<String,OSData> e : os.entrySet()) { System.out.println(e.getKey() + " = " + e.getValue()); } for (Map.Entry<Integer,List<ProdData>> e : prod.entrySet()) { System.out.println(e.getKey() + " = " + e.getValue()); } */ }
From source file:com.g2inc.scap.library.domain.SCAPContentManager.java
/** * A main method only used for testing//from ww w. ja v a 2 s.c o m * * @param args Command-line arguments * */ public static void main(String[] args) throws Exception { BasicConfigurator.configure(); LOG.trace("SchemaParser starting, schemaVersion =" + args[0] + ", xsd File=" + args[1]); File xsdFile = new File(args[1]); if (!xsdFile.exists()) { LOG.error("Usage: java SchemaParser <name of xsd file>"); } SCAPDocumentTypeEnum version = SCAPDocumentTypeEnum.valueOf(args[0]); SCAPContentManager mgr = SCAPContentManager.getInstance(new File(args[1])); // schema-related data should now be populated List<String> platformTypes = mgr.getValidPlatforms(version); LOG.trace("STARTING PLATFORMS"); for (int i = 0; i < platformTypes.size(); i++) { LOG.trace(platformTypes.get(i)); } String[] platforms = { "windows", "independent" }; List<NameDoc> list = null; Iterator<NameDoc> iter = null; LOG.trace("STARTING TESTS"); list = mgr.getValidTestTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc testName = iter.next(); LOG.trace("\t" + testName); } LOG.trace("STARTING OBJECTS"); list = mgr.getValidObjectTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc objName = iter.next(); LOG.trace("\t" + objName); LOG.trace("STARTING OBJECT ENTITIES FOR " + objName.getName()); List<OvalEntity> entityList = mgr.getValidObjectEntityTypes(version, "windows", objName.getName()); if (entityList != null && entityList.size() > 0) { for (int i = 0; i < entityList.size(); i++) { LOG.trace("\t\t" + entityList.get(i).toString()); } } } LOG.trace("STARTING STATES"); list = mgr.getValidStateTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc stateName = iter.next(); LOG.trace("\t" + stateName); LOG.trace("STARTING STATE ENTITIES FOR " + stateName.getName()); List<OvalEntity> entityList = mgr.getValidStateEntityTypes(version, "windows", stateName.getName()); if (entityList != null && entityList.size() > 0) { for (int i = 0; i < entityList.size(); i++) { LOG.trace("\t\t" + entityList.get(i).toString()); } } } }
From source file:edu.byu.nlp.al.app.CrowdsourcingActiveMeasurement.java
public static void main(String[] args) throws InterruptedException, IOException { // parse CLI arguments ArgumentValues opts = new ArgumentParser(CrowdsourcingActiveMeasurement.class).parseArgs(args); if (labelingStrategy.toString().contains("LDA")) { Preconditions.checkArgument(numTopics > 0, "LDA-based strategies require numTopics>0"); }/* w w w. ja va 2s . c o m*/ Preconditions.checkArgument(evalPoint > 0 || measEvalPoint > 0, "evalPoint must be greater than 0"); if (new File(basedir).exists()) { Preconditions.checkArgument(new File(basedir).isDirectory(), "basedir must be a directory " + basedir); } Preconditions.checkArgument(annotateTopKChoices > 0, "--annotate-top-k-choices must be greater than 0"); // this generator deals with data creation (so that all runs with the same annotation strategy // settings get the same datasets, regardless of the algorithm run on them) RandomGenerator dataRnd = new MersenneTwister(dataSeed); RandomGenerator algRnd = new MersenneTwister(algorithmSeed); // Read in chains of parameter settings (if any). // Each file is assumed to represent a single chain. List<SerializableCrowdsourcingState> initializationChains = Lists.newArrayList(); for (String chainFile : opts.getPositionalArgs()) { initializationChains.add(SerializableCrowdsourcingState.deserializeFrom(chainFile)); } // aggregate chains (this is calculating max marginal val of variables according to chains) initializationChains = (initializationChains.size() == 0) ? null : initializationChains; SerializableCrowdsourcingState initializationState = SerializableCrowdsourcingState .majorityVote(initializationChains, algRnd); // ensure encosing // open IO streams PrintWriter debugOut = prepareOutput(debugFile, nullWriter()); PrintWriter annotationsOut = prepareOutput(annotationsFile, nullWriter()); PrintWriter tabularPredictionsOut = prepareOutput(tabularFile, nullWriter()); PrintWriter resultsOut = prepareOutput(resultsFile, new PrintWriter(System.out)); PrintWriter serializeOut = prepareOutput(serializeToFile, nullWriter()); // pass on to the main program CrowdsourcingActiveMeasurement.run(args, debugOut, annotationsOut, tabularPredictionsOut, resultsOut, serializeOut, initializationState, dataRnd, algRnd); }