List of usage examples for java.util Collections sort
@SuppressWarnings({ "unchecked", "rawtypes" })
public static <T> void sort(List<T> list, Comparator<? super T> c)
From source file:com.act.lcms.db.io.PrintConstructInfo.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/*from w w w.j a v a 2 s . c o m*/ } 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(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } 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); } try (DB db = DB.openDBFromCLI(cl)) { System.out.print("Loading/updating LCMS scan files into DB\n"); ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); String construct = cl.getOptionValue(OPTION_CONSTRUCT); List<LCMSWell> lcmsWells = LCMSWell.getInstance().getByConstructID(db, construct); Collections.sort(lcmsWells, new Comparator<LCMSWell>() { @Override public int compare(LCMSWell o1, LCMSWell o2) { return o1.getId().compareTo(o2.getId()); } }); Set<String> uniqueMSIDs = new HashSet<>(); Map<Integer, Plate> platesById = new HashMap<>(); System.out.format("\n\n-- Construct %s --\n\n", construct); List<ChemicalAssociatedWithPathway> pathwayChems = ChemicalAssociatedWithPathway.getInstance() .getChemicalsAssociatedWithPathwayByConstructId(db, construct); System.out.print("Chemicals associated with pathway:\n"); System.out.format(" %-8s%-15s%-45s\n", "index", "kind", "chemical"); for (ChemicalAssociatedWithPathway chem : pathwayChems) { System.out.format(" %-8d%-15s%-45s\n", chem.getIndex(), chem.getKind(), chem.getChemical()); } System.out.print("\nLCMS wells:\n"); System.out.format(" %-15s%-6s%-15s%-15s%-15s\n", "barcode", "well", "msid", "fed", "lcms_count"); for (LCMSWell well : lcmsWells) { uniqueMSIDs.add(well.getMsid()); Plate p = platesById.get(well.getPlateId()); if (p == null) { // TODO: migrate Plate to be a subclass of BaseDBModel. p = Plate.getPlateById(db, well.getPlateId()); platesById.put(p.getId(), p); } String chem = well.getChemical(); List<ScanFile> scanFiles = ScanFile.getScanFileByPlateIDRowAndColumn(db, p.getId(), well.getPlateRow(), well.getPlateColumn()); System.out.format(" %-15s%-6s%-15s%-15s%-15d\n", p.getBarcode(), well.getCoordinatesString(), well.getMsid(), chem == null || chem.isEmpty() ? "--" : chem, scanFiles.size()); System.out.flush(); } List<Integer> plateIds = Arrays.asList(platesById.keySet().toArray(new Integer[platesById.size()])); Collections.sort(plateIds); System.out.print("\nAppears in plates:\n"); for (Integer id : plateIds) { Plate p = platesById.get(id); System.out.format(" %s: %s\n", p.getBarcode(), p.getName()); } List<String> msids = Arrays.asList(uniqueMSIDs.toArray(new String[uniqueMSIDs.size()])); Collections.sort(msids); System.out.format("\nMSIDS: %s\n", StringUtils.join(msids, ", ")); Set<String> availableNegativeControls = new HashSet<>(); for (Map.Entry<Integer, Plate> entry : platesById.entrySet()) { List<LCMSWell> wells = LCMSWell.getInstance().getByPlateId(db, entry.getKey()); for (LCMSWell well : wells) { if (!construct.equals(well.getComposition())) { availableNegativeControls.add(well.getComposition()); } } } // Print available standards for each step w/ plate barcodes and coordinates. System.out.format("\nAvailable Standards:\n"); Map<Integer, Plate> plateCache = new HashMap<>(); for (ChemicalAssociatedWithPathway chem : pathwayChems) { List<StandardWell> matchingWells = StandardWell.getInstance().getStandardWellsByChemical(db, chem.getChemical()); for (StandardWell well : matchingWells) { if (!plateCache.containsKey(well.getPlateId())) { Plate p = Plate.getPlateById(db, well.getPlateId()); plateCache.put(p.getId(), p); } } Map<Integer, List<StandardWell>> standardWellsByPlateId = new HashMap<>(); for (StandardWell well : matchingWells) { List<StandardWell> plateWells = standardWellsByPlateId.get(well.getPlateId()); if (plateWells == null) { plateWells = new ArrayList<>(); standardWellsByPlateId.put(well.getPlateId(), plateWells); } plateWells.add(well); } List<Pair<String, Integer>> plateBarcodes = new ArrayList<>(plateCache.size()); for (Plate p : plateCache.values()) { if (p.getBarcode() == null) { plateBarcodes.add(Pair.of("(no barcode)", p.getId())); } else { plateBarcodes.add(Pair.of(p.getBarcode(), p.getId())); } } Collections.sort(plateBarcodes); System.out.format(" %s:\n", chem.getChemical()); for (Pair<String, Integer> barcodePair : plateBarcodes) { // TODO: hoist this whole sorting/translation step into a utility class. List<StandardWell> wells = standardWellsByPlateId.get(barcodePair.getRight()); if (wells == null) { // Don't print plates that don't apply to this chemical, which can happen because we're caching the plates. continue; } Collections.sort(wells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { int c = o1.getPlateRow().compareTo(o2.getPlateRow()); if (c != 0) return c; return o1.getPlateColumn().compareTo(o2.getPlateColumn()); } }); List<String> descriptions = new ArrayList<>(wells.size()); for (StandardWell well : wells) { descriptions.add(String.format("%s in %s%s", well.getCoordinatesString(), well.getMedia(), well.getConcentration() == null ? "" : String.format(" c. %f", well.getConcentration()))); } System.out.format(" %s: %s\n", barcodePair.getLeft(), StringUtils.join(descriptions, ", ")); } } List<String> negativeControlStrains = Arrays .asList(availableNegativeControls.toArray(new String[availableNegativeControls.size()])); Collections.sort(negativeControlStrains); System.out.format("\nAvailable negative controls: %s\n", StringUtils.join(negativeControlStrains, ",")); System.out.print("\n----------\n"); System.out.print("\n\n"); } }
From source file:de.tudarmstadt.ukp.experiments.dip.wp1.documents.Step6HITPreparator.java
public static void main(String[] args) throws Exception { // input dir - list of xml query containers // step5-linguistic-annotation/ System.err.println("Starting step 6 HIT Preparation"); File inputDir = new File(args[0]); // output dir File outputDir = new File(args[1]); if (outputDir.exists()) { outputDir.delete();/*from w ww . j a v a 2 s.co m*/ } outputDir.mkdir(); List<String> queries = new ArrayList<>(); // iterate over query containers int countClueWeb = 0; int countSentence = 0; for (File f : FileUtils.listFiles(inputDir, new String[] { "xml" }, false)) { QueryResultContainer queryResultContainer = QueryResultContainer .fromXML(FileUtils.readFileToString(f, "utf-8")); if (queries.contains(f.getName()) || queries.size() == 0) { // groups contain only non-empty documents Map<Integer, List<QueryResultContainer.SingleRankedResult>> groups = new HashMap<>(); // split to groups according to number of sentences for (QueryResultContainer.SingleRankedResult rankedResult : queryResultContainer.rankedResults) { if (rankedResult.originalXmi != null) { byte[] bytes = new BASE64Decoder() .decodeBuffer(new ByteArrayInputStream(rankedResult.originalXmi.getBytes())); JCas jCas = JCasFactory.createJCas(); XmiCasDeserializer.deserialize(new ByteArrayInputStream(bytes), jCas.getCas()); Collection<Sentence> sentences = JCasUtil.select(jCas, Sentence.class); int groupId = sentences.size() / 40; if (rankedResult.originalXmi == null) { System.err.println("Empty document: " + rankedResult.clueWebID); } else { if (!groups.containsKey(groupId)) { groups.put(groupId, new ArrayList<>()); } } //handle it groups.get(groupId).add(rankedResult); countClueWeb++; } } for (Map.Entry<Integer, List<QueryResultContainer.SingleRankedResult>> entry : groups.entrySet()) { Integer groupId = entry.getKey(); List<QueryResultContainer.SingleRankedResult> rankedResults = entry.getValue(); // make sure the results are sorted // DEBUG // for (QueryResultContainer.SingleRankedResult r : rankedResults) { // System.out.print(r.rank + "\t"); // } Collections.sort(rankedResults, (o1, o2) -> o1.rank.compareTo(o2.rank)); // iterate over results for one query and group for (int i = 0; i < rankedResults.size() && i < TOP_RESULTS_PER_GROUP; i++) { QueryResultContainer.SingleRankedResult rankedResult = rankedResults.get(i); QueryResultContainer.SingleRankedResult r = rankedResults.get(i); int rank = r.rank; MustacheFactory mf = new DefaultMustacheFactory(); Mustache mustache = mf.compile("template/template.html"); String queryId = queryResultContainer.qID; String query = queryResultContainer.query; // make the first letter uppercase query = query.substring(0, 1).toUpperCase() + query.substring(1); List<String> relevantInformationExamples = queryResultContainer.relevantInformationExamples; List<String> irrelevantInformationExamples = queryResultContainer.irrelevantInformationExamples; byte[] bytes = new BASE64Decoder() .decodeBuffer(new ByteArrayInputStream(rankedResult.originalXmi.getBytes())); JCas jCas = JCasFactory.createJCas(); XmiCasDeserializer.deserialize(new ByteArrayInputStream(bytes), jCas.getCas()); List<generators.Sentence> sentences = new ArrayList<>(); List<Integer> paragraphs = new ArrayList<>(); paragraphs.add(0); for (WebParagraph webParagraph : JCasUtil.select(jCas, WebParagraph.class)) { for (Sentence s : JCasUtil.selectCovered(Sentence.class, webParagraph)) { String sentenceBegin = String.valueOf(s.getBegin()); generators.Sentence sentence = new generators.Sentence(s.getCoveredText(), sentenceBegin); sentences.add(sentence); countSentence++; } int SentenceID = paragraphs.get(paragraphs.size() - 1); if (sentences.size() > 120) while (SentenceID < sentences.size()) { if (!paragraphs.contains(SentenceID)) paragraphs.add(SentenceID); SentenceID = SentenceID + 120; } paragraphs.add(sentences.size()); } System.err.println("Output dir: " + outputDir); int startID = 0; int endID; for (int j = 0; j < paragraphs.size(); j++) { endID = paragraphs.get(j); int sentLength = endID - startID; if (sentLength > 120 || j == paragraphs.size() - 1) { if (sentLength > 120) { endID = paragraphs.get(j - 1); j--; } sentLength = endID - startID; if (sentLength <= 40) groupId = 40; else if (sentLength <= 80 && sentLength > 40) groupId = 80; else if (sentLength > 80) groupId = 120; File folder = new File(outputDir + "/" + groupId); if (!folder.exists()) { System.err.println("creating directory: " + outputDir + "/" + groupId); boolean result = false; try { folder.mkdir(); result = true; } catch (SecurityException se) { //handle it } if (result) { System.out.println("DIR created"); } } String newHtmlFile = folder.getAbsolutePath() + "/" + f.getName() + "_" + rankedResult.clueWebID + "_" + sentLength + ".html"; System.err.println("Printing a file: " + newHtmlFile); File newHTML = new File(newHtmlFile); int t = 0; while (newHTML.exists()) { newHTML = new File(folder.getAbsolutePath() + "/" + f.getName() + "_" + rankedResult.clueWebID + "_" + sentLength + "." + t + ".html"); t++; } mustache.execute(new PrintWriter(new FileWriter(newHTML)), new generators(query, relevantInformationExamples, irrelevantInformationExamples, sentences.subList(startID, endID), queryId, rank)) .flush(); startID = endID; } } } } } } System.out.println("Printed " + countClueWeb + " documents with " + countSentence + " sentences"); }
From source file:org.yardstickframework.report.jfreechart.JFreeChartGraphPlotter.java
/** * @param cmdArgs Arguments./*from w w w . ja v a 2 s . c o m*/ */ public static void main(String[] cmdArgs) { try { JFreeChartGraphPlotterArguments args = new JFreeChartGraphPlotterArguments(); JCommander jCommander = jcommander(cmdArgs, args, "<graph-plotter>"); if (args.help()) { jCommander.usage(); return; } if (args.inputFolders().isEmpty()) { errorHelp("Input folders are not defined."); return; } List<String> inFoldersAsString = args.inputFolders(); List<File> inFolders = new ArrayList<>(inFoldersAsString.size()); for (String folderAsString : inFoldersAsString) inFolders.add(new File(folderAsString).getAbsoluteFile()); for (File inFolder : inFolders) { if (!inFolder.exists()) { errorHelp("Folder does not exist: " + inFolder.getAbsolutePath()); return; } } List<List<List<File>>> benchFolders = new ArrayList<>(); for (File inFolder : inFolders) { File[] dirs0 = inFolder.listFiles(); if (dirs0 == null || dirs0.length == 0) continue; List<File> dirs = new ArrayList<>(Arrays.asList(dirs0)); Collections.sort(dirs, FILE_NAME_COMP); boolean multipleDrivers = false; for (File f : dirs) { if (f.isFile() && MULTIPLE_DRIVERS_MARKER_FILE.equals(f.getName())) { multipleDrivers = true; break; } } List<List<File>> mulDrvFiles = new ArrayList<>(); if (multipleDrivers) { for (File f : dirs) { List<File> files = getFiles(f); if (files != null) mulDrvFiles.add(files); } } else { List<File> files = getFiles(inFolder); if (files != null) mulDrvFiles.add(files); } benchFolders.add(mergeMultipleDriverLists(mulDrvFiles)); } if (benchFolders.isEmpty()) { errorHelp("Input folders are empty or have invalid structure: " + inFoldersAsString); return; } String outputFolder = outputFolder(inFolders); JFreeChartGenerationMode mode = args.generationMode(); if (mode == COMPOUND) processCompoundMode(outputFolder, benchFolders, args); else if (mode == COMPARISON) processComparisonMode(outputFolder, benchFolders, args); else if (mode == STANDARD) processStandardMode(benchFolders, args); else errorHelp("Unknown generation mode: " + args.generationMode()); } catch (ParameterException e) { errorHelp("Invalid parameter.", e); } catch (Exception e) { errorHelp("Failed to execute graph generator.", e); } }
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 w ww.j a v a2 s . co 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.github.christofluyten.experiment.MeasureGendreau.java
/** * @param args/*from www . j av a 2 s. c o m*/ * @throws IOException */ public static void main(String[] args) throws IOException { final List<Gendreau06Scenario> scns = new ArrayList<>( Gendreau06Parser.parser().addDirectory("files/gendreau2006/requests").parse()); Collections.sort(scns, new Comparator<Gendreau06Scenario>() { @Override public int compare(Gendreau06Scenario o1, Gendreau06Scenario o2) { final int compare = o1.getProblemClass().getId().compareTo(o2.getProblemClass().getId()); if (compare == 0) { return o1.getProblemInstanceId().compareTo(o2.getProblemInstanceId()); } return compare; } }); final List<Map<Property, Object>> propsList = new ArrayList<>(); for (final Gendreau06Scenario scen : scns) { final StatisticalSummary urgency = Metrics.measureUrgency(scen); final Multiset<Class<?>> counts = Metrics.getEventTypeCounts(scen); final long scenarioLength = scen.getProblemClass().duration * 60000; final double dyn = Metrics.measureDynamism(scen, scenarioLength); final ImmutableMap<Property, Object> prop = ImmutableMap.<Property, Object>builder() .put(Property.PROBLEM_CLASS, scen.getProblemClass().getId()) .put(Property.INSTANCE_ID, scen.getProblemInstanceId()).put(Property.DYNAMISM, dyn) .put(Property.URGENCY_MEAN, urgency.getMean() / 60000d) .put(Property.URGENCY_SD, urgency.getStandardDeviation() / 60000d) .put(Property.NUM_ORDERS, counts.count(AddParcelEvent.class)) .put(Property.NUM_VEHICLES, counts.count(AddVehicleEvent.class)) .putAll(MAP.get(scen.getProblemInstanceId() + scen.getProblemClass().getId())).build(); propsList.add(prop); } final File targetFile = new File(PROPS_FILE); write(propsList, targetFile, asList(Property.values())); System.out.println("Results written to " + targetFile.getAbsolutePath()); }
From source file:com.twentyn.patentScorer.ScoreMerger.java
public static void main(String[] args) throws Exception { System.out.println("Starting up..."); System.out.flush();/*from ww w . j ava 2 s. c o m*/ Options opts = new Options(); opts.addOption(Option.builder("h").longOpt("help").desc("Print this help message and exit").build()); opts.addOption(Option.builder("r").longOpt("results").required().hasArg() .desc("A directory of search results to read").build()); opts.addOption(Option.builder("s").longOpt("scores").required().hasArg() .desc("A directory of patent classification scores to read").build()); opts.addOption(Option.builder("o").longOpt("output").required().hasArg() .desc("The output file where results will be written.").build()); HelpFormatter helpFormatter = new HelpFormatter(); CommandLineParser cmdLineParser = new DefaultParser(); CommandLine cmdLine = null; try { cmdLine = cmdLineParser.parse(opts, args); } catch (ParseException e) { System.out.println("Caught exception when parsing command line: " + e.getMessage()); helpFormatter.printHelp("DocumentIndexer", opts); System.exit(1); } if (cmdLine.hasOption("help")) { helpFormatter.printHelp("DocumentIndexer", opts); System.exit(0); } File scoresDirectory = new File(cmdLine.getOptionValue("scores")); if (cmdLine.getOptionValue("scores") == null || !scoresDirectory.isDirectory()) { LOGGER.error("Not a directory of score files: " + cmdLine.getOptionValue("scores")); } File resultsDirectory = new File(cmdLine.getOptionValue("results")); if (cmdLine.getOptionValue("results") == null || !resultsDirectory.isDirectory()) { LOGGER.error("Not a directory of results files: " + cmdLine.getOptionValue("results")); } FileWriter outputWriter = new FileWriter(cmdLine.getOptionValue("output")); ObjectMapper objectMapper = new ObjectMapper(); objectMapper.enable(SerializationFeature.INDENT_OUTPUT); objectMapper.setVisibility(PropertyAccessor.ALL, JsonAutoDetect.Visibility.ANY); FilenameFilter jsonFilter = new FilenameFilter() { public final Pattern JSON_PATTERN = Pattern.compile("\\.json$"); public boolean accept(File dir, String name) { return JSON_PATTERN.matcher(name).find(); } }; Map<String, PatentScorer.ClassificationResult> scores = new HashMap<>(); LOGGER.info("Reading scores from directory at " + scoresDirectory.getAbsolutePath()); for (File scoreFile : scoresDirectory.listFiles(jsonFilter)) { BufferedReader reader = new BufferedReader(new FileReader(scoreFile)); int count = 0; String line; while ((line = reader.readLine()) != null) { PatentScorer.ClassificationResult res = objectMapper.readValue(line, PatentScorer.ClassificationResult.class); scores.put(res.docId, res); count++; } LOGGER.info("Read " + count + " scores from " + scoreFile.getAbsolutePath()); } Map<String, List<DocumentSearch.SearchResult>> synonymsToResults = new HashMap<>(); Map<String, List<DocumentSearch.SearchResult>> inchisToResults = new HashMap<>(); LOGGER.info("Reading results from directory at " + resultsDirectory); // With help from http://stackoverflow.com/questions/6846244/jackson-and-generic-type-reference. JavaType resultsType = objectMapper.getTypeFactory().constructCollectionType(List.class, DocumentSearch.SearchResult.class); List<File> resultsFiles = Arrays.asList(resultsDirectory.listFiles(jsonFilter)); Collections.sort(resultsFiles, new Comparator<File>() { @Override public int compare(File o1, File o2) { return o1.getName().compareTo(o2.getName()); } }); for (File resultsFile : resultsFiles) { BufferedReader reader = new BufferedReader(new FileReader(resultsFile)); CharBuffer buffer = CharBuffer.allocate(Long.valueOf(resultsFile.length()).intValue()); int bytesRead = reader.read(buffer); LOGGER.info("Read " + bytesRead + " bytes from " + resultsFile.getName() + " (length is " + resultsFile.length() + ")"); List<DocumentSearch.SearchResult> results = objectMapper.readValue(new CharArrayReader(buffer.array()), resultsType); LOGGER.info("Read " + results.size() + " results from " + resultsFile.getAbsolutePath()); int count = 0; for (DocumentSearch.SearchResult sres : results) { for (DocumentSearch.ResultDocument resDoc : sres.getResults()) { String docId = resDoc.getDocId(); PatentScorer.ClassificationResult classificationResult = scores.get(docId); if (classificationResult == null) { LOGGER.warn("No classification result found for " + docId); } else { resDoc.setClassifierScore(classificationResult.getScore()); } } if (!synonymsToResults.containsKey(sres.getSynonym())) { synonymsToResults.put(sres.getSynonym(), new ArrayList<DocumentSearch.SearchResult>()); } synonymsToResults.get(sres.getSynonym()).add(sres); count++; if (count % 1000 == 0) { LOGGER.info("Processed " + count + " search result documents"); } } } Comparator<DocumentSearch.ResultDocument> resultDocumentComparator = new Comparator<DocumentSearch.ResultDocument>() { @Override public int compare(DocumentSearch.ResultDocument o1, DocumentSearch.ResultDocument o2) { int cmp = o2.getClassifierScore().compareTo(o1.getClassifierScore()); if (cmp != 0) { return cmp; } cmp = o2.getScore().compareTo(o1.getScore()); return cmp; } }; for (Map.Entry<String, List<DocumentSearch.SearchResult>> entry : synonymsToResults.entrySet()) { DocumentSearch.SearchResult newSearchRes = null; // Merge all result documents into a single search result. for (DocumentSearch.SearchResult sr : entry.getValue()) { if (newSearchRes == null) { newSearchRes = sr; } else { newSearchRes.getResults().addAll(sr.getResults()); } } if (newSearchRes == null || newSearchRes.getResults() == null) { LOGGER.error("Search results for " + entry.getKey() + " are null."); continue; } Collections.sort(newSearchRes.getResults(), resultDocumentComparator); if (!inchisToResults.containsKey(newSearchRes.getInchi())) { inchisToResults.put(newSearchRes.getInchi(), new ArrayList<DocumentSearch.SearchResult>()); } inchisToResults.get(newSearchRes.getInchi()).add(newSearchRes); } List<String> sortedKeys = new ArrayList<String>(inchisToResults.keySet()); Collections.sort(sortedKeys); List<GroupedInchiResults> orderedResults = new ArrayList<>(sortedKeys.size()); Comparator<DocumentSearch.SearchResult> synonymSorter = new Comparator<DocumentSearch.SearchResult>() { @Override public int compare(DocumentSearch.SearchResult o1, DocumentSearch.SearchResult o2) { return o1.getSynonym().compareTo(o2.getSynonym()); } }; for (String inchi : sortedKeys) { List<DocumentSearch.SearchResult> res = inchisToResults.get(inchi); Collections.sort(res, synonymSorter); orderedResults.add(new GroupedInchiResults(inchi, res)); } objectMapper.writerWithView(Object.class).writeValue(outputWriter, orderedResults); outputWriter.close(); }
From source file:com.jslsolucoes.tagria.doc.generator.DocGenerator.java
public static void main(String[] args) throws IOException { String workspace = args[0];// ww w.j a v a2 s. c o m Map<String, List<Tag>> groupments = new HashMap<>(); String html = FileUtils.readFileToString( new File(workspace + "/tagria-lib/src/main/resources/META-INF/html.tld"), CHARSET); String ajax = FileUtils.readFileToString( new File(workspace + "/tagria-lib/src/main/resources/META-INF/ajax.tld"), CHARSET); XStream xStream = new XStream(); xStream.processAnnotations(Taglib.class); Taglib taglibForHtml = (Taglib) xStream.fromXML(html); Taglib taglibForAjax = (Taglib) xStream.fromXML(ajax); List<Tag> tags = new ArrayList<Tag>(); tags.addAll(taglibForHtml.getTags()); tags.addAll(taglibForAjax.getTags()); for (Tag tag : tags) { List<Tag> groups = groupments.get(tag.getGroup()); if (groups == null) { groupments.put(tag.getGroup(), new ArrayList<>()); } groupments.get(tag.getGroup()).add(tag); StringBuilder template = new StringBuilder( "<%@include file=\"../app/taglibs.jsp\"%> " + "<html:view title=\"{title}\"> " + " <html:panel> " + " <html:panelHead label=\"" + tag.getName() + "\"></html:panelHead> " + " <html:panelBody> " + " <html:tabPanel> " + " <html:tab label=\"{about}\" active=\"true\"> " + " <html:alert state=\"warning\"> " + " " + tag.getDescription() + " " + " </html:alert> " + " </html:tab> " + " <html:tab label=\"{attributes}\"> "); if (CollectionUtils.isEmpty(tag.getAttributes())) { template.append("<html:alert state=\"info\" label=\"{tag.empty.attributes}\"></html:alert>"); } else { template.append("<html:table><html:tableLine>" + "<html:tableColumn header=\"true\"><fmt:message key=\"tag.attribute\"/></html:tableColumn>" + "<html:tableColumn header=\"true\"><fmt:message key=\"tag.required\"/></html:tableColumn>" + "<html:tableColumn header=\"true\"><fmt:message key=\"tag.type\"/></html:tableColumn>" + "<html:tableColumn header=\"true\"><fmt:message key=\"tag.description\"/></html:tableColumn>" + "</html:tableLine>"); for (Attribute attribute : tag.getAttributes()) { template.append("<html:tableLine>" + "<html:tableColumn>" + attribute.getName() + "</html:tableColumn>" + "<html:tableColumn>" + (attribute.getRequired() == null ? false : true) + "</html:tableColumn>" + "<html:tableColumn>" + attribute.getType() + "</html:tableColumn>" + "<html:tableColumn>" + attribute.getDescription() + "</html:tableColumn>" + "</html:tableLine>"); } template.append("</html:table>"); } template.append(" " + " </html:tab> " + " <html:tab label=\"{demo}\"> " + " " + tag.getExample() + " " + " </html:tab> " + " <html:tab label=\"{source}\"> " + " <html:code> " + " <html:view>" + tag.getExampleEscaped() + "</html:view> " + " </html:code> " + " </html:tab> " + " </html:tabPanel> " + " </html:panelBody> " + " </html:panel> " + " </html:view> "); FileUtils.writeStringToFile(new File( workspace + "/tagria-doc/src/main/webapp/WEB-INF/jsp/component/" + tag.getName() + ".jsp"), template.toString(), CHARSET); } for (List<Tag> values : groupments.values()) { Collections.sort(values, new Comparator<Tag>() { @Override public int compare(Tag o1, Tag o2) { return o1.getName().compareTo(o2.getName()); } }); } StringBuilder menu = new StringBuilder("<html:div cssClass=\"menu\"><html:listGroup>"); for (String key : new TreeSet<String>(groupments.keySet())) { menu.append("<html:listGroupItem><html:collapsable label=\"" + key + "\"><html:listGroup>"); for (Tag tag : groupments.get(key)) { menu.append("<html:listGroupItem><html:link label=\"" + StringUtils.capitalize(tag.getName()) + "\" target=\"conteudo\" url=\"/component/" + tag.getName() + "\"></html:link></html:listGroupItem>"); } menu.append("</html:listGroup></html:collapsable></html:listGroupItem>"); } menu.append("</html:listGroup></html:div>"); File home = new File(workspace + "/tagria-doc/src/main/webapp/WEB-INF/jsp/app/index.jsp"); FileUtils.writeStringToFile(home, FileUtils.readFileToString(home, CHARSET) .replaceAll("<html:div cssClass=\"menu\">[\\s\\S]*?</html:div>", menu.toString()), CHARSET); }
From source file:amie.keys.CSAKey.java
public static void main(String[] args) throws IOException, InterruptedException { final Triple<MiningAssistant, Float, String> parsedArgs = parseArguments(args); final Set<Rule> output = new LinkedHashSet<>(); // Helper object that contains the implementation for the calculation // of confidence and support // The file with the non-keys, one per line long timea = System.currentTimeMillis(); List<List<String>> inputNonKeys = Utilities.parseNonKeysFile(parsedArgs.third); System.out.println(inputNonKeys.size() + " input non-keys"); final List<List<String>> nonKeys = pruneBySupport(inputNonKeys, parsedArgs.second, parsedArgs.first.getKb());/* www . ja v a 2s .com*/ Collections.sort(nonKeys, new Comparator<List<String>>() { @Override public int compare(List<String> o1, List<String> o2) { int r = Integer.compare(o2.size(), o1.size()); if (r == 0) { return Integer.compare(o2.hashCode(), o1.hashCode()); } return r; } }); System.out.println(nonKeys.size() + " non-keys after pruning"); int totalLoad = computeLoad(nonKeys); System.out.println(totalLoad + " is the total load"); int nThreads = Runtime.getRuntime().availableProcessors(); //int batchSize = Math.max(Math.min(maxBatchSize, totalLoad / nThreads), minBatchSize); int batchSize = Math.max(Math.min(maxLoad, totalLoad / nThreads), minLoad); final Queue<int[]> chunks = new PriorityQueue(50, new Comparator<int[]>() { @Override public int compare(int[] o1, int[] o2) { return Integer.compare(o2[2], o1[2]); } }); final HashSet<HashSet<Integer>> nonKeysInt = new HashSet<>(); final HashMap<String, Integer> property2Id = new HashMap<>(); final HashMap<Integer, String> id2Property = new HashMap<>(); final List<Integer> propertiesList = new ArrayList<>(); int support = (int) parsedArgs.second.floatValue(); KB kb = parsedArgs.first.getKb(); buildDictionaries(nonKeys, nonKeysInt, property2Id, id2Property, propertiesList, support, kb); final List<HashSet<Integer>> nonKeysIntList = new ArrayList<>(nonKeysInt); int start = 0; int[] nextIdx = nextIndex(nonKeysIntList, 0, batchSize); int end = nextIdx[0]; int load = nextIdx[1]; while (start < nonKeysIntList.size()) { int[] chunk = new int[] { start, end, load }; chunks.add(chunk); start = end; nextIdx = nextIndex(nonKeysIntList, end, batchSize); end = nextIdx[0]; load = nextIdx[1]; } Thread[] threads = new Thread[Math.min(Runtime.getRuntime().availableProcessors(), chunks.size())]; for (int i = 0; i < threads.length; ++i) { threads[i] = new Thread(new Runnable() { @Override public void run() { while (true) { int[] chunk = null; synchronized (chunks) { if (!chunks.isEmpty()) { chunk = chunks.poll(); } else { break; } } System.out.println("Processing chunk " + Arrays.toString(chunk)); mine(parsedArgs, nonKeysIntList, property2Id, id2Property, propertiesList, chunk[0], chunk[1], output); } } }); threads[i].start(); } for (int i = 0; i < threads.length; ++i) { threads[i].join(); } long timeb = System.currentTimeMillis(); System.out.println("==== Unique C-keys ====="); for (Rule r : output) { System.out.println(Utilities.formatKey(r)); } System.out.println( "VICKEY found " + output.size() + " unique conditional keys in " + (timeb - timea) + " ms"); }
From source file:FaceRatios.java
@SuppressWarnings("serial") public static void main(String[] args) { int r = FSDK.ActivateLibrary(FACE_SDK_LICENSE); if (r == FSDK.FSDKE_OK) { FSDK.Initialize();//from w w w. j ava2s . com FSDK.SetFaceDetectionParameters(true, true, 384); Map<String, Map<String, ArrayList<Double>>> faceProperties = new HashMap<>(); for (String directory : new File(FACE_DIRECTORY).list()) { if (new File(FACE_DIRECTORY + directory).isDirectory()) { Map<String, ArrayList<Double>> properties = new HashMap<String, ArrayList<Double>>() { { for (String property : propertyNames) put(property, new ArrayList<Double>()); } }; File[] files = new File(FACE_DIRECTORY + directory).listFiles(); System.out.println("Analyzing " + directory + " with " + files.length + " files\n"); for (File file : files) { if (file.isFile()) { HImage imageHandle = new HImage(); FSDK.LoadImageFromFileW(imageHandle, file.getAbsolutePath()); FSDK.TFacePosition.ByReference facePosition = new FSDK.TFacePosition.ByReference(); if (FSDK.DetectFace(imageHandle, facePosition) == FSDK.FSDKE_OK) { FSDK_Features.ByReference facialFeatures = new FSDK_Features.ByReference(); FSDK.DetectFacialFeaturesInRegion(imageHandle, (FSDK.TFacePosition) facePosition, facialFeatures); Point[] featurePoints = new Point[FSDK.FSDK_FACIAL_FEATURE_COUNT]; for (int i = 0; i < FSDK.FSDK_FACIAL_FEATURE_COUNT; i++) { featurePoints[i] = new Point(0, 0); featurePoints[i].x = facialFeatures.features[i].x; featurePoints[i].y = facialFeatures.features[i].y; } double eyeDistance = featureDistance(featurePoints, FeatureID.LEFT_EYE, FeatureID.RIGHT_EYE); double rightEyeSize = featureDistance(featurePoints, FeatureID.RIGHT_EYE_INNER_CORNER, FeatureID.RIGHT_EYE_OUTER_CORNER); double leftEyeSize = featureDistance(featurePoints, FeatureID.LEFT_EYE_INNER_CORNER, FeatureID.LEFT_EYE_OUTER_CORNER); double averageEyeSize = (rightEyeSize + leftEyeSize) / 2; double mouthLength = featureDistance(featurePoints, FeatureID.MOUTH_RIGHT_CORNER, FeatureID.MOUTH_LEFT_CORNER); double mouthHeight = featureDistance(featurePoints, FeatureID.MOUTH_BOTTOM, FeatureID.MOUTH_TOP); double noseHeight = featureDistance(featurePoints, FeatureID.NOSE_BOTTOM, FeatureID.NOSE_BRIDGE); double chinHeight = featureDistance(featurePoints, FeatureID.CHIN_BOTTOM, FeatureID.MOUTH_BOTTOM); double chinToBridgeHeight = featureDistance(featurePoints, FeatureID.CHIN_BOTTOM, FeatureID.NOSE_BRIDGE); double faceContourLeft = (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getY() - featurePoints[FeatureID.FACE_CONTOUR2.getIndex()].getY()) / (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getX() - featurePoints[FeatureID.FACE_CONTOUR2.getIndex()].getX()); double faceContourRight = (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getY() - featurePoints[FeatureID.FACE_CONTOUR12.getIndex()].getY()) / (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getX() - featurePoints[FeatureID.FACE_CONTOUR12.getIndex()].getX()); double bridgeLeftEyeDistance = featureDistance(featurePoints, FeatureID.LEFT_EYE_INNER_CORNER, FeatureID.NOSE_BRIDGE); double bridgeRightEyeDistance = featureDistance(featurePoints, FeatureID.RIGHT_EYE_INNER_CORNER, FeatureID.NOSE_BRIDGE); properties.get("eyeSize/eyeDistance").add(averageEyeSize / eyeDistance); properties.get("eyeSizeDisparity") .add(Math.abs(leftEyeSize - rightEyeSize) / averageEyeSize); properties.get("bridgeToEyeDisparity") .add(Math.abs(bridgeLeftEyeDistance - bridgeRightEyeDistance) / ((bridgeLeftEyeDistance + bridgeRightEyeDistance) / 2)); properties.get("eyeDistance/mouthLength").add(eyeDistance / mouthLength); properties.get("eyeDistance/noseHeight").add(eyeDistance / noseHeight); properties.get("eyeSize/mouthLength").add(eyeDistance / mouthLength); properties.get("eyeSize/noseHeight").add(eyeDistance / noseHeight); properties.get("mouthLength/mouthHeight").add(mouthLength / mouthHeight); properties.get("chinHeight/noseHeight").add(chinHeight / noseHeight); properties.get("chinHeight/chinToBridgeHeight") .add(chinHeight / chinToBridgeHeight); properties.get("noseHeight/chinToBridgeHeight") .add(noseHeight / chinToBridgeHeight); properties.get("mouthHeight/chinToBridgeHeight") .add(mouthHeight / chinToBridgeHeight); properties.get("faceCountourAngle") .add(Math.toDegrees(Math.atan((faceContourLeft - faceContourRight) / (1 + faceContourLeft * faceContourRight)))); } FSDK.FreeImage(imageHandle); } } System.out.format("%32s\t%8s\t%8s\t%3s%n", "Property", "", "", "c"); System.out.println(new String(new char[76]).replace("\0", "-")); ArrayList<Entry<String, ArrayList<Double>>> propertyList = new ArrayList<>( properties.entrySet()); Collections.sort(propertyList, new Comparator<Entry<String, ArrayList<Double>>>() { @Override public int compare(Entry<String, ArrayList<Double>> arg0, Entry<String, ArrayList<Double>> arg1) { DescriptiveStatistics dStats0 = new DescriptiveStatistics(listToArray(arg0.getValue())); DescriptiveStatistics dStats1 = new DescriptiveStatistics(listToArray(arg1.getValue())); return new Double(dStats0.getStandardDeviation() / dStats0.getMean()) .compareTo(dStats1.getStandardDeviation() / dStats1.getMean()); } }); for (Entry<String, ArrayList<Double>> property : propertyList) { DescriptiveStatistics dStats = new DescriptiveStatistics(listToArray(property.getValue())); System.out.format("%32s\t%4f\t%4f\t%3s%n", property.getKey(), dStats.getMean(), dStats.getStandardDeviation(), Math.round(dStats.getStandardDeviation() / dStats.getMean() * 100) + "%"); } System.out.println("\n"); faceProperties.put(directory, properties); } } for (String propertyName : propertyNames) { DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset(); for (Entry<String, Map<String, ArrayList<Double>>> face : faceProperties.entrySet()) { dataset.add(face.getValue().get(propertyName), "Default Series", face.getKey()); } PropertyBoxWhisker plot = new PropertyBoxWhisker(propertyName, dataset); plot.pack(); plot.setVisible(true); } } }
From source file:mzmatch.ipeak.normalisation.VanDeSompele.java
public static void main(String args[]) { try {//www . j a v a2 s.c o m Tool.init(); // parse the commandline options Options options = new Options(); CmdLineParser cmdline = new CmdLineParser(options); // check whether we need to show the help cmdline.parse(args); if (options.help) { Tool.printHeader(System.out, application, version); cmdline.printUsage(System.out, ""); return; } if (options.verbose) { Tool.printHeader(System.out, application, version); cmdline.printOptions(); } // check the command-line parameters { // if the output directories do not exist, create them if (options.output != null) Tool.createFilePath(options.output, true); } // load the data if (options.verbose) System.out.println("Loading data"); ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true); Header header = result.header; IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement; int nrmeasurements = header.getNrMeasurementInfos(); // remove the stability factor annotation for (IPeak peak : peaksets) peak.removeAnnotation("stability factor"); // load the database if (options.verbose) System.out.println("Loading the molecule database"); HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database)); // filter the set to include only identifiable metabolites if (options.verbose) System.out.println("Creating selection"); Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>(); for (Molecule molecule : database.values()) { double mass = molecule.getMass(Mass.MONOISOTOPIC); double delta = PeriodicTable.PPM(mass, options.ppm); // get the most intense peak containing all the measurements Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta, mass + delta); Collections.sort(neighbourhoud, IPeak.sort_intensity_descending); for (IPeakSet<? extends IPeak> neighbour : neighbourhoud) if (count(neighbour) == nrmeasurements) { selection.add(neighbour); break; } } // calculate the stability factor for each peak in the selection if (options.verbose) System.out.println("Calculating stability factors"); for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) { double stddeviations[] = new double[selection.size()]; IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1); for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) { IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2); double values[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { int measurementid1 = peakset1.get(measurementid).getMeasurementID(); int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1)); int measurementid2 = peakset2.get(measurementid).getMeasurementID(); int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2)); if (setid1 != setid2 || measurementid1 != measurementid2) System.err.println("[WARNING]: differing setid or spectrumid for comparison"); values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity() / peakset2.get(measurementid).getIntensity()) / Math.log(2); } stddeviations[peakid2] = Statistical.stddev(values); } peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations)); } // sort on the stability factor Collections.sort(selection, new IPeak.AnnotationAscending("stability factor")); // take the top 10% and calculate the geometric mean if (options.verbose) System.out.println("Calculating normalisation factors"); int nrselected = (int) (0.1 * selection.size()); if (nrselected < 10) nrselected = (10 < selection.size() ? 10 : selection.size()); double normalization_factors[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { double values[] = new double[nrselected]; for (int i = 0; i < nrselected; ++i) { IPeak peak = selection.get(i).get(measurementid); values[i] = peak.getIntensity(); } normalization_factors[measurementid] = Statistical.geomean(values); } // scale the found normalization factors double maxnf = Statistical.max(normalization_factors); for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid) normalization_factors[sampleid] /= maxnf; // write the selection if needed if (options.selection != null) { if (options.verbose) System.out.println("Writing original selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection)), null); } // normalize all the peaks if (options.verbose) System.out.println("Normalizing all the entries"); for (IPeakSet<? extends IPeak> peakset : peaksets) { for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { // TODO why did I do this again ? int id = 0; int setid = 0; int spectrumid = 0; for (int i = 0; i < header.getNrSetInfos(); ++i) { SetInfo set = header.getSetInfos().get(i); if (id + set.getNrMeasurementIDs() > measurementid) { setid = i; spectrumid = measurementid - id; break; } else id += set.getNrMeasurementIDs(); } MassChromatogram<Peak> masschromatogram = null; for (IPeak p : peakset) { int mymeasurementid = p.getMeasurementID(); int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid)); if (mysetid == setid && mymeasurementid == spectrumid) { masschromatogram = (MassChromatogram<Peak>) p; break; } } if (masschromatogram == null) continue; for (IPeak peak : masschromatogram.getPeaks()) peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]); } } // write the selection if needed if (options.selection_normalized != null) { if (options.verbose) System.out.println("Writing the normalized selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null); } // write the factors if needed if (options.factors != null) { if (options.verbose) System.out.println("Writing the normalization factors"); PrintStream out = new PrintStream(options.factors); for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t" + normalization_factors[measurementid]); } // write the plot if needed if (options.img != null) { if (options.verbose) System.out.println("Writing the graph"); DefaultCategoryDataset dataset = new DefaultCategoryDataset(); JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor", dataset, PlotOrientation.VERTICAL, false, // legend false, // tooltips false // urls ); CategoryPlot plot = (CategoryPlot) linechart.getPlot(); CategoryAxis axis = (CategoryAxis) plot.getDomainAxis(); axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesShapesFilled(0, true); renderer.setSeriesShapesVisible(0, true); linechart.setBackgroundPaint(Color.WHITE); linechart.setBorderVisible(false); linechart.setAntiAlias(true); plot.setBackgroundPaint(Color.WHITE); plot.setDomainGridlinesVisible(true); plot.setRangeGridlinesVisible(true); // create the datasets for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) dataset.addValue(normalization_factors[measurementid], "", header.getMeasurementInfo(measurementid).getLabel()); JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500); } // write the normalized values if (options.verbose) System.out.println("Writing the normalized data"); PeakMLWriter.write(result.header, peaksets.getPeaks(), null, new GZIPOutputStream(new FileOutputStream(options.output)), null); } catch (Exception e) { Tool.unexpectedError(e, application); } }