Example usage for java.util Set size

List of usage examples for java.util Set size

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Introduction

In this page you can find the example usage for java.util Set size.

Prototype

int size();

Source Link

Document

Returns the number of elements in this set (its cardinality).

Usage

From source file:com.act.lcms.db.analysis.IonDetectionAnalysis.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  va2  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", 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_LCMS_FILE_DIRECTORY));
    if (!lcmsDir.isDirectory()) {
        System.err.format("File at %s is not a directory", lcmsDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR);

    // Get include and excluse ions from command line
    Set<String> includeIons;
    if (cl.hasOption(OPTION_INCLUDE_IONS)) {
        includeIons = new HashSet<>(Arrays.asList(cl.getOptionValues(OPTION_INCLUDE_IONS)));
        LOGGER.info("Including ions in search: %s", StringUtils.join(includeIons, ", "));
    } else {
        includeIons = new HashSet<>();
        includeIons.add(DEFAULT_ION);
    }

    try (DB db = DB.openDBFromCLI(cl)) {
        ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir);

        File inputPredictionCorpus = new File(cl.getOptionValue(OPTION_INPUT_PREDICTION_CORPUS));

        Map<Double, Set<Pair<String, String>>> massChargeToChemicalAndIon = constructMassChargeToChemicalIonsFromInputFile(
                inputPredictionCorpus, includeIons, cl.hasOption(OPTION_LIST_OF_INCHIS_INPUT_FILE));

        Pair<Set<Pair<String, Double>>, Map<String, Double>> values = constructFakeNameToMassChargeAndSetOfMassChargePairs(
                massChargeToChemicalAndIon.keySet());
        Set<Pair<String, Double>> searchMZs = values.getLeft();
        Map<String, Double> chemIDToMassCharge = values.getRight();

        LOGGER.info("The number of mass charges are: %d", searchMZs.size());

        Map<ScanData.KIND, List<LCMSWell>> wellTypeToLCMSWells = readInputExperimentalSetup(db,
                new File(cl.getOptionValue(OPTION_INPUT_POSITIVE_AND_NEGATIVE_CONTROL_WELLS_FILE)));

        // Get experimental setup ie. positive and negative wells from config file
        List<LCMSWell> positiveWells = wellTypeToLCMSWells.get(ScanData.KIND.POS_SAMPLE);
        List<LCMSWell> negativeWells = wellTypeToLCMSWells.get(ScanData.KIND.NEG_CONTROL);

        LOGGER.info("Number of positive wells is: %d", positiveWells.size());
        LOGGER.info("Number of negative wells is: %d", negativeWells.size());

        HashMap<Integer, Plate> plateCache = new HashMap<>();
        String outputPrefix = cl.getOptionValue(OPTION_OUTPUT_PREFIX);

        IonDetectionAnalysis<LCMSWell> ionDetectionAnalysis = new IonDetectionAnalysis<LCMSWell>(lcmsDir,
                positiveWells, negativeWells, plottingDirectory, plateCache, searchMZs, db);

        ionDetectionAnalysis.runLCMSMiningAnalysisAndPlotResults(chemIDToMassCharge, massChargeToChemicalAndIon,
                outputPrefix, cl.hasOption(OPTION_NON_REPLICATE_ANALYSIS));
    }
}

From source file:de.unisb.cs.st.javaslicer.slicing.Slicer.java

public static void main(String[] args) throws InterruptedException {
    Options options = createOptions();//www  .j ava2 s.c  om
    CommandLineParser parser = new GnuParser();
    CommandLine cmdLine;

    try {
        cmdLine = parser.parse(options, args, true);
    } catch (ParseException e) {
        System.err.println("Error parsing the command line arguments: " + e.getMessage());
        return;
    }

    if (cmdLine.hasOption('h')) {
        printHelp(options, System.out);
        System.exit(0);
    }

    String[] additionalArgs = cmdLine.getArgs();
    if (additionalArgs.length != 2) {
        printHelp(options, System.err);
        System.exit(-1);
    }
    // ?? 1. ? 2.?
    File traceFile = new File(additionalArgs[0]);
    String slicingCriterionString = additionalArgs[1];

    Long threadId = null;
    if (cmdLine.hasOption('t')) { // the interesting thread id for slicing 
        try {
            threadId = Long.parseLong(cmdLine.getOptionValue('t'));
        } catch (NumberFormatException e) {
            System.err.println("Illegal thread id: " + cmdLine.getOptionValue('t'));
            System.exit(-1);
        }
    }

    TraceResult trace;
    try {
        trace = TraceResult.readFrom(traceFile);
    } catch (IOException e) {
        System.err.format("Could not read the trace file \"%s\": %s%n", traceFile, e);
        System.exit(-1);
        return;
    }

    List<SlicingCriterion> sc = null; // a list contains the instruction's info corresponds to the slicing criterion
    //slicingCriterionString get from additionalArgs[1]
    try {
        sc = StaticSlicingCriterion.parseAll(slicingCriterionString, trace.getReadClasses());
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing slicing criterion: " + e.getMessage());
        System.exit(-1);
        return;
    }

    List<ThreadId> threads = trace.getThreads(); // the threads that generate the traces
    if (threads.size() == 0) {
        System.err.println("The trace file contains no tracing information.");
        System.exit(-1);
    }

    // threadID is used to mark the interesting thread
    ThreadId tracing = null;
    for (ThreadId t : threads) {
        if (threadId == null) {
            if ("main".equals(t.getThreadName())
                    && (tracing == null || t.getJavaThreadId() < tracing.getJavaThreadId()))
                tracing = t;
        } else if (t.getJavaThreadId() == threadId.longValue()) {
            tracing = t;
        }
    }

    if (tracing == null) {
        System.err.println(threadId == null ? "Couldn't find the main thread."
                : "The thread you specified was not found.");
        System.exit(-1);
        return;
    }

    long startTime = System.nanoTime();
    Slicer slicer = new Slicer(trace);
    if (cmdLine.hasOption("progress")) // the parameter process indicates that we need to monitor the process of slicing
        slicer.addProgressMonitor(new ConsoleProgressMonitor());
    boolean multithreaded;
    if (cmdLine.hasOption("multithreaded")) {
        String multithreadedStr = cmdLine.getOptionValue("multithreaded");
        multithreaded = ("1".equals(multithreadedStr) || "true".equals(multithreadedStr));
    } else {
        multithreaded = Runtime.getRuntime().availableProcessors() > 1;
    }

    boolean warnUntracedMethods = cmdLine.hasOption("warn-untraced"); // give some warns when encounters untraced functions

    //sliceInstructionCollector implements the interface slice visitor, which travel the dependence graph
    SliceInstructionsCollector collector = new SliceInstructionsCollector(); // the collector is used to collect the instructions in the dependence graph according to the slice criterion. 
    slicer.addSliceVisitor(collector);
    // zhushi by yhb

    if (warnUntracedMethods)
        slicer.addUntracedCallVisitor(new PrintUniqueUntracedMethods()); // the user need the untraced function info, so add untraced call visitor

    slicer.process(tracing, sc, multithreaded); //----------------------the key process of slicing!!!
    Set<InstructionInstance> slice = collector.getDynamicSlice(); // return the slice result from the collector
    long endTime = System.nanoTime();

    Instruction[] sliceArray = slice.toArray(new Instruction[slice.size()]); // convert the set to array
    Arrays.sort(sliceArray); // in order to ensure the sequence of dynamic execution

    // show the slicing result
    System.out.println("The dynamic slice for criterion " + sc + ":");
    for (Instruction insn : sliceArray) {
        System.out.format((Locale) null, "%s.%s:%d %s%n", insn.getMethod().getReadClass().getName(),
                insn.getMethod().getName(), insn.getLineNumber(), insn.toString());
    }
    System.out.format((Locale) null, "%nSlice consists of %d bytecode instructions.%n", sliceArray.length);
    System.out.format((Locale) null, "Computation took %.2f seconds.%n", 1e-9 * (endTime - startTime));
}

From source file:org.ptm.translater.App.java

public static void main(String... args) {
    GenericXmlApplicationContext ctx = new GenericXmlApplicationContext();
    ctx.load("file:src/main/resources/spring/datasource.xml");
    ctx.refresh();//from   w  w w  . j av a 2  s .  c  om

    GenericXmlApplicationContext ctx2 = new GenericXmlApplicationContext();
    ctx2.load("file:src/main/resources/spring/datasource2.xml");
    ctx2.refresh();

    ArchiveDao archiveDao = ctx.getBean("archiveDao", ArchiveDao.class);
    List<Archive> archives = archiveDao.findAll();

    UserDao userDao = ctx2.getBean("userDao", UserDao.class);
    TagDao tagDao = ctx2.getBean("tagDao", TagDao.class);
    PhotoDao photoDao = ctx2.getBean("photoDao", PhotoDao.class);

    List<Tag> tagz = tagDao.findAll();
    Map<String, Long> hashTags = new HashMap<String, Long>();
    for (Tag tag : tagz)
        hashTags.put(tag.getName(), tag.getId());

    MongoCache cache = new MongoCache();
    Calendar calendar = Calendar.getInstance();

    Map<String, String> associates = new HashMap<String, String>();

    for (Archive archive : archives) {
        AppUser appUser = new AppUser();
        appUser.setName(archive.getName());
        appUser.setEmail(archive.getUid() + "@mail.th");
        appUser.setPassword("123456");

        Role role = new Role();
        role.setRoleId("ROLE_USER");
        appUser.setRole(role);

        userDao.save(appUser);
        System.out.println("\tCreate user " + appUser);

        for (Photo photo : archive.getPhotos()) {
            // ?  ??? 
            if (cache.contains(photo.getUid()))
                continue;

            System.out.println("\tNew photo");
            org.ptm.translater.ch2.domain.Photo photo2 = new org.ptm.translater.ch2.domain.Photo();
            photo2.setAppUser(appUser);
            photo2.setName(photo.getTitle());
            photo2.setLicense((byte) 7);
            photo2.setDescription(photo.getDescription());

            SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
            try {
                calendar.setTime(sdf.parse(photo.getTaken()));

                if (calendar.get(Calendar.YEAR) != 0 && calendar.get(Calendar.YEAR) > 1998)
                    continue;
                photo2.setYear(calendar.get(Calendar.YEAR));
                photo2.setMonth(calendar.get(Calendar.MONTH) + 1);
                photo2.setDay(calendar.get(Calendar.DAY_OF_MONTH));
            } catch (Exception ex) {
                ex.printStackTrace();
            }

            if (photo.getLongitude() != null && photo.getLongitude().length() > 0) {
                //                    String key = photo.getLongitude()+"#"+photo.getLatitude();
                photo2.setLatitude(photo.getLatitude());
                photo2.setLongitude(photo.getLongitude());
                //                    if (associates.containsKey(key)) {
                //                        photo2.setAddress(associates.get(key));
                //                    } else {
                //                        Geocoder geocoder = new Geocoder();
                //                        GeocoderRequestBuilder geocoderRequest = new GeocoderRequestBuilder();
                //                        GeocoderRequest request =
                //                            geocoderRequest.setLocation(new LatLng(photo.getLongitude(), photo.getLatitude())).getGeocoderRequest();
                //
                //                        GeocodeResponse response = geocoder.geocode(request);
                //                        if (response.getResults().size() > 0) {
                //                            photo2.setAddress(response.getResults().get(0).getFormattedAddress());
                //                        }
                //                        try { Thread.sleep(2000); } catch (InterruptedException ex) { ex.printStackTrace(); }
                //                    }
            }

            System.out.println("\tFind tags");
            Set<Tag> tags = new HashSet<Tag>();
            for (org.ptm.translater.ch1.domain.Tag tag : photo.getTags()) {
                Tag item = new Tag();
                item.setName(tag.getName());
                if (hashTags.containsKey(tag.getName())) {
                    item.setId(hashTags.get(tag.getName()));
                } else {
                    tagDao.save(item);
                    hashTags.put(item.getName(), item.getId());
                }
                System.out.println("\t\tinit tag " + tag.getName());
                tags.add(item);
            }
            photo2.setTags(tags);
            System.out.println("\tFind " + tags.size() + " tags");
            photoDao.save(photo2);
            System.out.println("\tSave photo");

            Imaginator img = new Imaginator();
            img.setFolder(photo2.getId().toString());
            img.setPath();

            for (PhotoSize ps : photo.getSizes()) {
                if (ps.getLabel().equals("Original")) {
                    img.setImage(ps.getSource());
                    break;
                }
            }
            img.generate();
            System.out.println("\tGenerate image of photo");
            img = null;
            cache.create(photo.getUid());
            cache.create(photo2);

            System.out.println("Generate: " + photo2);
        }
    }
}

From source file:gr.iti.mklab.bubing.parser.ITIHTMLParser.java

public static void main(String arg[]) throws IllegalArgumentException, IOException, URISyntaxException,
        JSAPException, NoSuchAlgorithmException {

    final SimpleJSAP jsap = new SimpleJSAP(ITIHTMLParser.class.getName(),
            "Produce the digest of a page: the page is downloaded or passed as argument by specifying a file",
            new Parameter[] {
                    new UnflaggedOption("url", JSAP.STRING_PARSER, JSAP.REQUIRED, "The url of the page."),
                    new Switch("crossAuthorityDuplicates", 'c', "cross-authority-duplicates"),
                    new FlaggedOption("charBufferSize", JSAP.INTSIZE_PARSER, Integer.toString(CHAR_BUFFER_SIZE),
                            JSAP.NOT_REQUIRED, 'b', "buffer",
                            "The size of the parser character buffer (0 for dynamic sizing)."),
                    new FlaggedOption("file", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'f',
                            "file", "The page to be processed."),
                    new FlaggedOption("digester", JSAP.STRING_PARSER, "MD5", JSAP.NOT_REQUIRED, 'd', "digester",
                            "The digester to be used.") });

    JSAPResult jsapResult = jsap.parse(arg);
    if (jsap.messagePrinted())
        System.exit(1);// www .  j  ava  2  s .  c  o m

    final String url = jsapResult.getString("url");
    final String digester = jsapResult.getString("digester");
    final boolean crossAuthorityDuplicates = jsapResult.userSpecified("crossAuthorityDuplicates");
    final int charBufferSize = jsapResult.getInt("charBufferSize");

    final ITIHTMLParser<Void> htmlParser = new ITIHTMLParser<Void>(BinaryParser.forName(digester),
            (TextProcessor<Void>) null, crossAuthorityDuplicates, charBufferSize);
    final SetLinkReceiver linkReceiver = new SetLinkReceiver();
    final byte[] digest;

    if (!jsapResult.userSpecified("file")) {
        final URI uri = new URI(url);
        final HttpGet request = new HttpGet(uri);
        request.setConfig(RequestConfig.custom().setRedirectsEnabled(false).build());
        digest = htmlParser.parse(uri, HttpClients.createDefault().execute(request), linkReceiver);
    } else {
        final String file = jsapResult.getString("file");
        String content = IOUtils.toString(new InputStreamReader(new FileInputStream(file)));
        digest = htmlParser.parse(BURL.parse(url), new StringHttpMessages.HttpResponse(content), linkReceiver);
    }

    System.out.println("DigestHexString: " + Hex.encodeHexString(digest));
    System.out.println("Links: " + linkReceiver.urls);

    Set<String> urlStrings = new ObjectOpenHashSet<String>();
    for (URI link : linkReceiver.urls)
        urlStrings.add(link.toString());
    if (urlStrings.size() != linkReceiver.urls.size())
        System.out.println(
                "There are " + linkReceiver.urls.size() + " URIs but " + urlStrings.size() + " strings");

}

From source file:edu.umass.cs.reconfiguration.ReconfigurableNode.java

/**
 * {@code args} contains a list of app arguments followed by a list of
 * active or reconfigurator node IDs at the end. The string "start all" is
 * accepted as a proxy for the list of all nodes if the socket addresses of
 * all nodes are on the local machine./*w ww  .  j a  v  a  2s  . c om*/
 * 
 * @param args
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    Config.register(args);
    PaxosConfig.sanityCheck();
    ReconfigurationConfig.setConsoleHandler();
    if (Config.getGlobalBoolean(PC.EMULATE_DELAYS))
        AbstractPacketDemultiplexer.emulateDelays();

    if (args.length == 0)
        throw new RuntimeException(
                "At least one node ID must be specified as a command-line argument for starting "
                        + ReconfigurableNode.class);
    ReconfigurableNodeConfig<String> nodeConfig = new DefaultNodeConfig<String>(PaxosConfig.getActives(),
            ReconfigurationConfig.getReconfigurators());
    PaxosConfig.sanityCheck(nodeConfig);
    Set<String> servers = getAllNodes(args);

    if (clear) {
        for (String id : servers)
            try {
                SQLReconfiguratorDB.dropState(id,
                        new ConsistentReconfigurableNodeConfig<String>(new DefaultNodeConfig<String>(
                                PaxosConfig.getActives(), ReconfigurationConfig.getReconfigurators())));
            } catch (Exception e) {
                /* ignore all exceptions as they correspond to non-local
                 * nodes */
                e.printStackTrace();
            }
        return;
    }

    String sysPropAppArgsAsString = System.getProperty(ReconfigurationConfig.CommandArgs.appArgs.toString());
    // append cmdline args to system property based args
    String cmdlineAppArgs = getAppArgs(args);
    String[] appArgs = ((sysPropAppArgsAsString != null ? sysPropAppArgsAsString : "") + " " + cmdlineAppArgs)
            .split("\\s");
    int numServers = servers.size();
    if (numServers == 0)
        throw new RuntimeException("No valid server names supplied");
    System.out.print("Initializing gigapaxos server" + (numServers > 1 ? "s" : "") + " [ ");
    for (String node : servers) {
        System.out
                .print(node + ":" + nodeConfig.getNodeAddress(node) + ":" + nodeConfig.getNodePort(node) + " ");
        new DefaultReconfigurableNode(node,
                // must use a different nodeConfig for each
                new DefaultNodeConfig<String>(PaxosConfig.getActives(),
                        ReconfigurationConfig.getReconfigurators()),
                appArgs, false);
    }
    System.out.println("]; server" + (numServers > 1 ? "s" : "") + servers + " ready");
}

From source file:de.clusteval.serverclient.BackendClient.java

/**
 * @param args//from  www  .  j  av  a2 s .  c  o  m
 *            Command line parameters for the backend client (see
 *            {@link #params}).
 * @throws IOException
 */
@SuppressWarnings("unused")
public static void main(String[] args) throws IOException {
    try {
        CommandLine params = parseParams(args, false);

        if (params.hasOption("help")) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("clustevalClient", clientCLIOptions);
            System.exit(0);
        }

        if (params.hasOption("version")) {
            System.out.println(VERSION);
            System.exit(0);
        }

        initLogging(params);

        Logger log = LoggerFactory.getLogger(BackendClient.class);

        System.out.println("Starting clusteval client");
        System.out.println(VERSION);
        System.out.println("=========================");

        // if command line arguments (except connection parameters) are
        // passed, we do not start a console
        Set<String> paramKeys = new HashSet<String>();
        @SuppressWarnings("unchecked")
        Iterator<Option> it = params.iterator();
        while (it.hasNext()) {
            paramKeys.add(it.next().getOpt());
        }

        paramKeys.remove("ip");
        paramKeys.remove("port");
        paramKeys.remove("clientId");
        if (paramKeys.size() > 0) {
            try {
                new BackendClient(args);
            } catch (Exception e) {
            }
        } else {
            String clientId;
            if (params.hasOption("clientId"))
                clientId = params.getOptionValue("clientId");
            else
                // parse args because of possible connection parameters
                clientId = new BackendClient(args).clientId;

            reader = new ConsoleReader();

            List<Completer> completers = new LinkedList<Completer>();
            completers.add(new BackendClientCompleter(clientId, args));

            String ip = params.hasOption("ip") ? params.getOptionValue("ip") : "localhost";
            String port = params.hasOption("port") ? params.getOptionValue("port") : "1099";

            setDefaultPromptAndCompleter(ip, port, completers);

            String line;

            while ((line = reader.readLine()) != null) {

                if (line.equalsIgnoreCase("quit") || line.equalsIgnoreCase("exit")) {
                    break;
                }

                boolean connectException = false;
                do {
                    try {
                        new BackendClient(
                                ArraysExt.merge(args, ("-clientId " + clientId + " -" + line).split(" ")));
                        connectException = false;
                    } catch (ConnectException e) {
                        e.printStackTrace();
                        connectException = true;
                    } catch (Exception e) {
                        log.warn(e.getMessage());
                    }
                    Thread.sleep(1000);
                } while (connectException);
                // }
            }
        }
    } catch (ParseException e) {
        System.err.println("Parsing failed.  Reason: " + e.getMessage());

        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("clustevalClient",
                "Invoking this client without any parameters will open a shell with tab-completion.",
                clientCLIOptions, "", true);
    } catch (Throwable t) {
        // t.printStackTrace();
    }
}

From source file:com.act.biointerpretation.ProductExtractor.java

public static void main(String[] args) throws Exception {
    CLIUtil cliUtil = new CLIUtil(ProductExtractor.class, HELP_MESSAGE, OPTION_BUILDERS);
    CommandLine cl = cliUtil.parseCommandLine(args);

    String orgPrefix = cl.getOptionValue(OPTION_ORGANISM_PREFIX);
    LOGGER.info("Using organism prefix %s", orgPrefix);

    MongoDB db = new MongoDB(DEFAULT_DB_HOST, DEFAULT_DB_PORT, cl.getOptionValue(OPTION_DB_NAME));

    Map<Long, String> validOrganisms = new TreeMap<>();
    DBIterator orgIter = db.getDbIteratorOverOrgs();
    Organism o = null;/*from  w  w w.j a va 2s.co m*/
    while ((o = db.getNextOrganism(orgIter)) != null) {
        if (!o.getName().isEmpty() && o.getName().startsWith(orgPrefix)) {
            validOrganisms.put(o.getUUID(), o.getName());
        }
    }

    LOGGER.info("Found %d valid organisms", validOrganisms.size());

    Set<Long> productIds = new TreeSet<>(); // Use something with implicit ordering we can traverse in order.
    DBIterator reactionIterator = db.getIteratorOverReactions();
    Reaction r;
    while ((r = db.getNextReaction(reactionIterator)) != null) {
        Set<JSONObject> proteins = r.getProteinData();
        boolean valid = false;
        for (JSONObject j : proteins) {
            if (j.has("organism") && validOrganisms.containsKey(j.getLong("organism"))) {
                valid = true;
                break;
            } else if (j.has("organisms")) {
                JSONArray organisms = j.getJSONArray("organisms");
                for (int i = 0; i < organisms.length(); i++) {
                    if (validOrganisms.containsKey(organisms.getLong(i))) {
                        valid = true;
                        break;
                    }
                }
            }
        }

        if (valid) {
            for (Long id : r.getProducts()) {
                productIds.add(id);
            }
            for (Long id : r.getProductCofactors()) {
                productIds.add(id);
            }
        }
    }

    LOGGER.info("Found %d valid product ids for '%s'", productIds.size(), orgPrefix);
    PrintWriter writer = cl.hasOption(OPTION_OUTPUT_FILE)
            ? new PrintWriter(new FileWriter(cl.getOptionValue(OPTION_OUTPUT_FILE)))
            : new PrintWriter(System.out);

    for (Long id : productIds) {
        Chemical c = db.getChemicalFromChemicalUUID(id);
        String inchi = c.getInChI();
        if (inchi.startsWith("InChI=") && !inchi.startsWith("InChI=/FAKE")) {
            writer.println(inchi);
        }
    }

    if (cl.hasOption(OPTION_OUTPUT_FILE)) {
        writer.close();
    }
    LOGGER.info("Done.");
}

From source file:com.music.tools.ScaleTester.java

public static void main(String[] args) {
    System.out.println(//from  ww  w  .j  a v a 2s  .  c o  m
            "Usage: java ScaleTester <fundamental frequency> <chromatic scale size> <scale size> <use ET>");
    final AudioFormat af = new AudioFormat(sampleRate, 16, 1, true, true);
    try {
        fundamentalFreq = getArgument(args, 0, FUNDAMENTAL_FREQUENCY, Double.class);
        int pitchesInChromaticScale = getArgument(args, 1, CHROMATIC_SCALE_SILZE, Integer.class);

        List<Double> harmonicFrequencies = new ArrayList<>();
        List<String> ratios = new ArrayList<>();
        Set<Double> frequencies = new HashSet<Double>();
        frequencies.add(fundamentalFreq);
        int octaveMultiplier = 2;
        for (int i = 2; i < 100; i++) {
            // Exclude the 7th harmonic TODO exclude the 11th as well?
            // http://www.phy.mtu.edu/~suits/badnote.html
            if (i % 7 == 0) {
                continue;
            }
            double actualFreq = fundamentalFreq * i;
            double closestTonicRatio = actualFreq / (fundamentalFreq * octaveMultiplier);
            if (closestTonicRatio < 1 || closestTonicRatio > 2) {
                octaveMultiplier *= 2;
            }
            double closestTonic = actualFreq - actualFreq % (fundamentalFreq * octaveMultiplier);
            double normalizedFreq = fundamentalFreq * (actualFreq / closestTonic);

            harmonicFrequencies.add(actualFreq);
            frequencies.add(normalizedFreq);
            if (frequencies.size() == pitchesInChromaticScale) {
                break;
            }
        }

        System.out.println("Harmonic (overtone) frequencies: " + harmonicFrequencies);
        System.out.println("Transposed harmonic frequencies: " + frequencies);

        List<Double> chromaticScale = new ArrayList<>(frequencies);
        Collections.sort(chromaticScale);

        // find the "perfect" interval (e.g. perfect fifth)
        int perfectIntervalIndex = 0;
        int idx = 0;
        for (Iterator<Double> it = chromaticScale.iterator(); it.hasNext();) {
            Double noteFreq = it.next();
            long[] fraction = findCommonFraction(noteFreq / fundamentalFreq);
            fractionCache.put(noteFreq, fraction);
            if (fraction[0] == 3 && fraction[1] == 2) {
                perfectIntervalIndex = idx;
                System.out.println("Perfect interval (3/2) idx: " + perfectIntervalIndex);
            }
            idx++;
            ratios.add(Arrays.toString(fraction));
        }
        System.out.println("Ratios to fundemental frequency: " + ratios);

        if (getBooleanArgument(args, 4, USE_ET)) {
            chromaticScale = temper(chromaticScale);
        }

        System.out.println();
        System.out.println("Chromatic scale: " + chromaticScale);

        Set<Double> scaleSet = new HashSet<Double>();
        scaleSet.add(chromaticScale.get(0));
        idx = 0;
        List<Double> orderedInCircle = new ArrayList<>();
        // now go around the circle of perfect intervals and put the notes
        // in order
        while (orderedInCircle.size() < chromaticScale.size()) {
            orderedInCircle.add(chromaticScale.get(idx));
            idx += perfectIntervalIndex;
            idx = idx % chromaticScale.size();
        }
        System.out.println("Pitches Ordered in circle of perfect intervals: " + orderedInCircle);

        List<Double> scale = new ArrayList<Double>(scaleSet);
        int currentIdxInCircle = orderedInCircle.size() - 1; // start with
                                                             // the last
                                                             // note in the
                                                             // circle
        int scaleSize = getArgument(args, 3, SCALE_SIZE, Integer.class);
        while (scale.size() < scaleSize) {
            double pitch = orderedInCircle.get(currentIdxInCircle % orderedInCircle.size());
            if (!scale.contains(pitch)) {
                scale.add(pitch);
            }
            currentIdxInCircle++;
        }
        Collections.sort(scale);

        System.out.println("Scale: " + scale);

        SourceDataLine line = AudioSystem.getSourceDataLine(af);
        line.open(af);
        line.start();

        Double[] scaleFrequencies = scale.toArray(new Double[scale.size()]);

        // first play the whole scale
        WaveMelodyGenerator.playScale(line, scaleFrequencies);
        // then generate a random melody in the scale
        WaveMelodyGenerator.playMelody(line, scaleFrequencies);

        line.drain();
        line.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:com.glaf.core.util.StringTools.java

public static void main(String[] args) {
    String text = "123,234,345,567,789";
    List<String> rows = StringTools.split(text, ",");
    System.out.println(rows.get(2));
    System.out.println(rows);//from   www  .  j  ava  2  s .c  o m
    for (int i = 0, len = rows.size(); i < len; i++) {
        System.out.println(rows.get(i));
    }

    Set<String> x = new HashSet<String>();
    for (int i = 0; i < 9999; i++) {
        String str = StringTools.random();
        x.add(str);
        System.out.println(str);
    }
    System.out.println("size=" + x.size());

    Random random = new Random();

    for (int i = 1; i < 100; i++) {
        int k = Math.abs(random.nextInt(9999));
        int a = String.valueOf(k).length();
        int b = String.valueOf(9999).length();
        System.out.println("a=" + a);
        System.out.println("b=" + b);
        String xx = "";
        if (a != b) {
            for (int j = 0; j < (b - a); j++) {
                xx = "0" + xx;
            }
        }
        xx = xx + k;
        System.out.println(xx);
    }

    System.out.println(toUnderLineName("ISOCertifiedStaff"));
    System.out.println(toUnderLineName("CertifiedStaff"));
    System.out.println(toUnderLineName("UserID"));
    System.out.println(toCamelCase("iso_certified_staff"));
    System.out.println(toCamelCase("certified_staff"));
    System.out.println(toCamelCase("user_id"));
}

From source file:edu.cuhk.hccl.evaluation.EvaluationApp.java

public static void main(String[] args) throws IOException, TasteException {
    File realFile = new File(args[0]);
    File estimateFile = new File(args[1]);

    // Build real-rating map
    Map<String, long[]> realMap = buildRatingMap(realFile);

    // Build estimate-rating map
    Map<String, long[]> estimateMap = buildRatingMap(estimateFile);

    // Compare realMap with estimateMap
    Map<Integer, List<Double>> realList = new HashMap<Integer, List<Double>>();
    Map<Integer, List<Double>> estimateList = new HashMap<Integer, List<Double>>();

    // Use set to store non-duplicate pairs only
    Set<String> noRatingList = new HashSet<String>();

    for (String pair : realMap.keySet()) {
        long[] realRatings = realMap.get(pair);
        long[] estimateRatings = estimateMap.get(pair);

        if (realRatings == null || estimateRatings == null)
            continue;

        for (int i = 0; i < realRatings.length; i++) {
            long real = realRatings[i];
            long estimate = estimateRatings[i];

            // continue if the aspect rating can not be estimated due to incomplete reviews
            if (estimate <= 0) {
                noRatingList.add(pair.replace("@", "\t"));
                continue;
            }//from   w w  w . ja va  2 s.c o  m

            if (real > 0 && estimate > 0) {
                if (!realList.containsKey(i))
                    realList.put(i, new ArrayList<Double>());

                realList.get(i).add((double) real);

                if (!estimateList.containsKey(i))
                    estimateList.put(i, new ArrayList<Double>());

                estimateList.get(i).add((double) estimate);
            }
        }
    }

    System.out.println("[INFO] RMSE, MAE for estimate ratings: ");
    System.out.println("------------------------------");
    System.out.println("Index \t RMSE \t MAE");
    for (int i = 1; i < 6; i++) {
        double rmse = Metric.computeRMSE(realList.get(i), estimateList.get(i));
        double mae = Metric.computeMAE(realList.get(i), estimateList.get(i));

        System.out.printf("%d \t %.3f \t %.3f \n", i, rmse, mae);
    }

    System.out.println("------------------------------");

    if (noRatingList.size() > 0) {
        String noRatingFileName = "evaluation-no-ratings.txt";
        FileUtils.writeLines(new File(noRatingFileName), noRatingList, false);

        System.out.println("[INFO] User-item pairs with no ratings are saved in file: " + noRatingFileName);
    } else {
        System.out.println("[INFO] All user-item pairs have ratings.");
    }
}