Example usage for java.util Arrays toString

Introduction

In this page you can find the example usage for java.util Arrays toString.

Prototype

public static String toString(Object[] a)

Source Link

Document

Returns a string representation of the contents of the specified array.

Usage

From source file:microbiosima.SelectiveMicrobiosima.java

/**
 * @param args/*from  w w  w .  j  a  v a 2 s  .co  m*/
 *            the command line arguments
 * @throws java.io.FileNotFoundException
 * @throws java.io.UnsupportedEncodingException
 */

public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException {
    int populationSize = 500;//Integer.parseInt(parameters[1]);
    int microSize = 1000;//Integer.parseInt(parameters[2]);
    int numberOfSpecies = 150;//Integer.parseInt(parameters[3]);
    int numberOfGeneration = 10000;
    int Ngene = 10;
    int numberOfObservation = 100;
    int numberOfReplication = 10;
    double Ngenepm = 5;
    double pctEnv = 0;
    double pctPool = 0;
    double msCoeff = 1;
    double hsCoeff = 1;
    boolean HMS_or_TMS = true;

    Options options = new Options();

    Option help = new Option("h", "help", false, "print this message");
    Option version = new Option("v", "version", false, "print the version information and exit");
    options.addOption(help);
    options.addOption(version);

    options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS")
            .desc("Number generation for observation [default: 100]").build());
    options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP")
            .desc("Number of replication [default: 1]").build());

    Builder C = Option.builder("c").longOpt("config").numberOfArgs(6).argName("Pop Micro Spec Gen")
            .desc("Four Parameters in the following orders: "
                    + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation, (5) number of total traits, (6)number of traits per microbe"
                    + " [default: 500 1000 150 10000 10 5]");
    options.addOption(C.build());

    HelpFormatter formatter = new HelpFormatter();
    String syntax = "microbiosima pctEnv pctPool";
    String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n"
            + "required arguments:\n" + "  pctEnv             Percentage of environmental acquisition\n"
            + "  pctPool            Percentage of pooled environmental component\n"
            + "  msCoeff            Parameter related to microbe selection strength\n"
            + "  hsCoeff            Parameter related to host selection strength\n"
            + "  HMS_or_TMS         String HMS or TMS to specify host-mediated or trait-mediated microbe selection\n"
            + "\noptional arguments:\n";
    String footer = "\n";

    formatter.setWidth(80);

    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = null;

    try {
        cmd = parser.parse(options, args);
        String[] pct_config = cmd.getArgs();

        if (cmd.hasOption("h") || args.length == 0) {
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(0);
        }
        if (cmd.hasOption("v")) {
            System.out.println("Microbiosima " + VERSION);
            System.exit(0);
        }
        if (pct_config.length != 5) {
            System.out.println(
                    "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. It got "
                            + pct_config.length + ": " + Arrays.toString(pct_config));
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(3);
        } else {
            pctEnv = Double.parseDouble(pct_config[0]);
            pctPool = Double.parseDouble(pct_config[1]);
            msCoeff = Double.parseDouble(pct_config[2]);
            hsCoeff = Double.parseDouble(pct_config[3]);
            if (pct_config[4].equals("HMS"))
                HMS_or_TMS = true;
            if (pct_config[4].equals("TMS"))
                HMS_or_TMS = false;
            if (pctEnv < 0 || pctEnv > 1) {
                System.out.println(
                        "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv="
                                + pctEnv + ")! EXIT");
                System.exit(3);
            }
            if (pctPool < 0 || pctPool > 1) {
                System.out.println(
                        "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool="
                                + pctPool + ")! EXIT");
                System.exit(3);
            }
            if (msCoeff < 1) {
                System.out.println(
                        "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff="
                                + msCoeff + ")! EXIT");
                System.exit(3);
            }
            if (hsCoeff < 1) {
                System.out.println(
                        "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff="
                                + hsCoeff + ")! EXIT");
                System.exit(3);
            }
            if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) {
                System.out.println(
                        "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS="
                                + pct_config[4] + ")! EXIT");
                System.exit(3);
            }

        }
        if (cmd.hasOption("config")) {
            String[] configs = cmd.getOptionValues("config");
            populationSize = Integer.parseInt(configs[0]);
            microSize = Integer.parseInt(configs[1]);
            numberOfSpecies = Integer.parseInt(configs[2]);
            numberOfGeneration = Integer.parseInt(configs[3]);
            Ngene = Integer.parseInt(configs[4]);
            Ngenepm = Double.parseDouble(configs[5]);
            if (Ngenepm > Ngene) {
                System.out.println(
                        "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT");
                System.exit(3);
            }
        }
        if (cmd.hasOption("obs")) {
            numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs"));
        }
        if (cmd.hasOption("rep")) {
            numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep"));
        }

    } catch (ParseException e) {
        e.printStackTrace();
        System.exit(3);
    }

    StringBuilder sb = new StringBuilder();
    sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize)
            .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ")
            .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration)
            .append("\n\tNumber generation for observation: ").append(numberOfObservation)
            .append("\n\tNumber of replication: ").append(numberOfReplication)
            .append("\n\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ")
            .append(Ngenepm).append("\n");
    System.out.println(sb.toString());

    double[] environment = new double[numberOfSpecies];
    for (int i = 0; i < numberOfSpecies; i++) {
        environment[i] = 1 / (double) numberOfSpecies;
    }
    int[] fitnessToHost = new int[Ngene];
    int[] fitnessToMicrobe = new int[Ngene];

    for (int rep = 0; rep < numberOfReplication; rep++) {
        String prefix = "" + (rep + 1) + "_";
        String sufix;
        if (HMS_or_TMS)
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt";
        else
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".txt";
        System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix);
        try {
            PrintWriter file1 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix)));
            PrintWriter file2 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix)));
            PrintWriter file3 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix)));
            PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix)));
            PrintWriter file5 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix)));
            PrintWriter file6 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix)));
            PrintWriter file7 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix)));
            PrintWriter file8 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix)));
            PrintWriter file9 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix)));
            PrintWriter file10 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix)));
            PrintWriter file11 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix)));
            PrintWriter file12 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix)));
            for (int i = 0; i < Ngene; i++) {
                fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1;
                fitnessToHost[i] = MathUtil.getNextInt(2) - 1;
            }
            MathUtil.setSeed(rep % numberOfReplication);
            SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm,
                    msCoeff, fitnessToHost, fitnessToMicrobe);
            MathUtil.setSeed();
            SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize,
                    pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS);

            while (population.getNumberOfGeneration() < numberOfGeneration) {
                population.sumSpecies();
                if (population.getNumberOfGeneration() % numberOfObservation == 0) {
                    //file1.print(population.gammaDiversity(false));
                    //file2.print(population.alphaDiversity(false));
                    //file1.print("\t");
                    //file2.print("\t");
                    file1.println(population.gammaDiversity(true));
                    file2.println(population.alphaDiversity(true));
                    //file3.print(population.betaDiversity(true));
                    //file3.print("\t");
                    file3.println(population.BrayCurtis(true));
                    file4.println(population.printOut());
                    file5.println(population.interGenerationDistance());
                    file6.println(population.environmentPopulationDistance());
                    file7.print(population.averageHostFitness());
                    file7.print("\t");
                    file7.println(population.varianceHostFitness());
                    file8.println(population.cosOfMH());
                    file9.println(population.printOutHFitness());
                    file10.println(population.printOutMFitness());
                    file11.println(population.printBacteriaContents());
                }
                population.getNextGen();
            }
            for (SelectiveIndividual host : population.getIndividuals()) {
                file12.println(host.printBacteriaContents());
            }
            file1.close();
            file2.close();
            file3.close();
            file4.close();
            file5.close();
            file6.close();
            file7.close();
            file8.close();
            file9.close();
            file10.close();
            file11.close();
            file12.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryClassDeclarationAttributes.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);//from   w  w w  . jav  a 2  s . co  m
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapQueryClassDeclarationAttributes.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            HashMap<String, EList<NamedElement>> list = JavaQueries.getClassDeclarationAttributes(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO,
                    MessageFormat.format("Query result contains {0} elements", list.entrySet().size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapTraverser.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/* w w  w  .  ja  v  a  2  s . c  o  m*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapTraverser.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);
        resource.getContents().get(0);

        LOG.log(Level.INFO, "Start counting");
        int count = 0;
        long begin = System.currentTimeMillis();
        for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator
                .next(), count++)
            ;
        long end = System.currentTimeMillis();
        LOG.log(Level.INFO, "End counting");
        LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", uri, count));
        LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:eu.amidst.core.inference.MPEInferenceExperiments.java

/**
 * The class constructor./*from  ww  w  .j av a2  s.c o  m*/
 * @param args Array of options: "filename variable a b N useVMP" if variable is continuous or "filename variable w N useVMP" for discrete
 */
public static void main(String[] args) throws Exception {

    int seedNetwork = 61236719 + 123;

    int numberOfGaussians = 20;

    int numberOfMultinomials = numberOfGaussians;
    BayesianNetworkGenerator.setSeed(seedNetwork);
    BayesianNetworkGenerator.setNumberOfGaussianVars(numberOfGaussians);
    BayesianNetworkGenerator.setNumberOfMultinomialVars(numberOfMultinomials, 2);
    BayesianNetworkGenerator.setNumberOfLinks((int) 1.3 * (numberOfGaussians + numberOfMultinomials));

    BayesianNetwork bn = BayesianNetworkGenerator.generateBayesianNetwork();

    int seed = seedNetwork + 231591;

    //if (Main.VERBOSE) System.out.println(bn.getDAG());
    if (Main.VERBOSE)
        System.out.println(bn.toString());

    MPEInference mpeInference = new MPEInference();
    mpeInference.setModel(bn);
    mpeInference.setParallelMode(true);

    if (Main.VERBOSE)
        System.out.println("CausalOrder: "
                + Arrays.toString(Utils.getTopologicalOrder(mpeInference.getOriginalModel().getDAG()).stream()
                        .map(Variable::getName).toArray()));
    List<Variable> modelVariables = Utils.getTopologicalOrder(bn.getDAG());
    if (Main.VERBOSE)
        System.out.println();

    // Including evidence:
    //double observedVariablesRate = 0.00;
    //Assignment evidence = randomEvidence(seed, observedVariablesRate, bn);
    //mpeInference.setEvidence(evidence);

    int parallelSamples = 100;
    int samplingMethodSize = 10000;

    mpeInference.setSampleSize(parallelSamples);

    /***********************************************
     *        SIMULATED ANNEALING
     ************************************************/

    // MPE INFERENCE WITH SIMULATED ANNEALING, ALL VARIABLES
    if (Main.VERBOSE)
        System.out.println();
    long timeStart = System.nanoTime();
    mpeInference.runInference(MPEInference.SearchAlgorithm.SA_GLOBAL);

    Assignment mpeEstimate = mpeInference.getEstimate();
    if (Main.VERBOSE)
        System.out.println("MPE estimate (SA.All): " + mpeEstimate.outputString(modelVariables)); //toString(modelVariables)
    if (Main.VERBOSE)
        System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
    long timeStop = System.nanoTime();
    double execTime = (double) (timeStop - timeStart) / 1000000000.0;
    if (Main.VERBOSE)
        System.out.println("computed in: " + Double.toString(execTime) + " seconds");
    //if (Main.VERBOSE) System.out.println(.toString(mapInference.getOriginalModel().getStaticVariables().iterator().));
    if (Main.VERBOSE)
        System.out.println();

    // MPE INFERENCE WITH SIMULATED ANNEALING, SOME VARIABLES AT EACH TIME
    timeStart = System.nanoTime();
    mpeInference.runInference(MPEInference.SearchAlgorithm.SA_LOCAL);

    mpeEstimate = mpeInference.getEstimate();
    if (Main.VERBOSE)
        System.out.println("MPE estimate  (SA.Some): " + mpeEstimate.outputString(modelVariables)); //toString(modelVariables)
    if (Main.VERBOSE)
        System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
    timeStop = System.nanoTime();
    execTime = (double) (timeStop - timeStart) / 1000000000.0;
    if (Main.VERBOSE)
        System.out.println("computed in: " + Double.toString(execTime) + " seconds");
    //if (Main.VERBOSE) System.out.println(.toString(mapInference.getOriginalModel().getStaticVariables().iterator().));
    if (Main.VERBOSE)
        System.out.println();

    /***********************************************
     *        HILL CLIMBING
     ************************************************/

    // MPE INFERENCE WITH HILL CLIMBING, ALL VARIABLES
    timeStart = System.nanoTime();
    mpeInference.runInference(MPEInference.SearchAlgorithm.HC_GLOBAL);

    mpeEstimate = mpeInference.getEstimate();
    //modelVariables = mpeInference.getOriginalModel().getVariables().getListOfVariables();
    if (Main.VERBOSE)
        System.out.println("MPE estimate (HC.All): " + mpeEstimate.outputString(modelVariables));
    if (Main.VERBOSE)
        System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
    timeStop = System.nanoTime();
    execTime = (double) (timeStop - timeStart) / 1000000000.0;
    if (Main.VERBOSE)
        System.out.println("computed in: " + Double.toString(execTime) + " seconds");
    if (Main.VERBOSE)
        System.out.println();

    //  MPE INFERENCE WITH HILL CLIMBING, ONE VARIABLE AT EACH TIME
    timeStart = System.nanoTime();
    mpeInference.runInference(MPEInference.SearchAlgorithm.HC_LOCAL);

    mpeEstimate = mpeInference.getEstimate();
    if (Main.VERBOSE)
        System.out.println("MPE estimate  (HC.Some): " + mpeEstimate.outputString(modelVariables)); //toString(modelVariables)
    if (Main.VERBOSE)
        System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
    timeStop = System.nanoTime();
    execTime = (double) (timeStop - timeStart) / 1000000000.0;
    if (Main.VERBOSE)
        System.out.println("computed in: " + Double.toString(execTime) + " seconds");
    if (Main.VERBOSE)
        System.out.println();

    /***********************************************
     *        SAMPLING AND DETERMINISTIC
     ************************************************/

    // MPE INFERENCE WITH SIMULATION AND PICKING MAX

    mpeInference.setSampleSize(samplingMethodSize);

    timeStart = System.nanoTime();
    mpeInference.runInference(MPEInference.SearchAlgorithm.SAMPLING);

    mpeEstimate = mpeInference.getEstimate();
    //modelVariables = mpeInference.getOriginalModel().getVariables().getListOfVariables();
    if (Main.VERBOSE)
        System.out.println("MPE estimate (SAMPLING): " + mpeEstimate.outputString(modelVariables));
    if (Main.VERBOSE)
        System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
    timeStop = System.nanoTime();
    execTime = (double) (timeStop - timeStart) / 1000000000.0;
    if (Main.VERBOSE)
        System.out.println("computed in: " + Double.toString(execTime) + " seconds");
    if (Main.VERBOSE)
        System.out.println();

    if (bn.getNumberOfVars() <= 50) {

        // MPE INFERENCE, DETERMINISTIC
        timeStart = System.nanoTime();
        mpeInference.runInference(MPEInference.SearchAlgorithm.EXHAUSTIVE);

        mpeEstimate = mpeInference.getEstimate();
        //modelVariables = mpeInference.getOriginalModel().getVariables().getListOfVariables();
        if (Main.VERBOSE)
            System.out.println("MPE estimate (DETERM.): " + mpeEstimate.outputString(modelVariables));
        if (Main.VERBOSE)
            System.out.println("with probability: " + Math.exp(mpeInference.getLogProbabilityOfEstimate())
                    + ", logProb: " + mpeInference.getLogProbabilityOfEstimate());
        timeStop = System.nanoTime();
        execTime = (double) (timeStop - timeStart) / 1000000000.0;
        if (Main.VERBOSE)
            System.out.println("computed in: " + Double.toString(execTime) + " seconds");
        if (Main.VERBOSE)
            System.out.println();

    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.MorsaTraverser.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);// ww w.ja  v  a 2  s  .c  o m
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        URI uri = URI.createURI("morsa://" + commandLine.getOptionValue(IN));

        Class<?> inClazz = MorsaTraverser.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put("morsa",
                new MorsaResourceFactoryImpl(new MongoDBMorsaBackendFactory()));

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        loadOpts.put(IMorsaResource.OPTION_SERVER_URI, "localhost");
        loadOpts.put(IMorsaResource.OPTION_MAX_SAVE_CACHE_SIZE, 30000);
        loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, false);
        //         loadOpts.put(IMorsaResource.OPTION_CACHE_POLICY, FIFOEObjectCachePolicy.class.getName());
        //         loadOpts.put(IMorsaResource.OPTION_MAX_CACHE_SIZE, 30000);
        //         loadOpts.put(IMorsaResource.OPTION_CACHE_FLUSH_FACTOR, 0.3f);
        //         loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD_STRATEGY, IMorsaResource.OPTION_SINGLE_LOAD_STRATEGY);
        //         loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, true);

        resource.load(loadOpts);

        LOG.log(Level.INFO, "Start counting");
        int count = 0;
        long begin = System.currentTimeMillis();
        for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator
                .next(), count++)
            ;
        long end = System.currentTimeMillis();
        LOG.log(Level.INFO, "End counting");
        LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", uri, count));
        LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

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

public static void main(String[] args) {
    System.out.println(// w ww.  j a  v a  2s  .  co  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:fr.inria.atlanmod.kyanos.benchmarks.Migrator.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);/*from  w  w  w  . j  ava  2s .  c  om*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output file");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(IN_EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of input EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option outClassOpt = OptionBuilder.create(OUT_EPACKAGE_CLASS);
    outClassOpt.setArgName("CLASS");
    outClassOpt.setDescription("FQN of output EPackage implementation class");
    outClassOpt.setArgs(1);
    outClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(outClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);
        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = URI.createFileURI(commandLine.getOptionValue(OUT));
        Class<?> inClazz = Migrator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(IN_EPACKAGE_CLASS));
        Class<?> outClazz = Migrator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(OUT_EPACKAGE_CLASS));

        @SuppressWarnings("unused")
        EPackage inEPackage = (EPackage) inClazz.getMethod("init").invoke(null);
        EPackage outEPackage = (EPackage) outClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());

        Resource sourceResource = resourceSet.getResource(sourceUri, true);
        Resource targetResource = resourceSet.createResource(targetUri);

        targetResource.getContents().clear();
        LOG.log(Level.INFO, "Start migration");
        targetResource.getContents()
                .add(MigratorUtil.migrate(sourceResource.getContents().get(0), outEPackage));
        LOG.log(Level.INFO, "Migration finished");

        Map<String, Object> saveOpts = new HashMap<String, Object>();
        saveOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saving done");
    } catch (ParseException e) {
        showError(e.toString());
        showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.ReferencesCounter.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);/*from  w  w  w .  j av a  2 s.c o m*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output file");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(IN_EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of input EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option labelOpt = OptionBuilder.create(LABEL);
    labelOpt.setArgName("LABEL");
    labelOpt.setDescription("Label for the data set");
    labelOpt.setArgs(1);
    labelOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(labelOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);
        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        Class<?> inClazz = ReferencesCounter.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(IN_EPACKAGE_CLASS));
        @SuppressWarnings("unused")
        EPackage inEPackage = (EPackage) inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());

        Resource sourceResource = resourceSet.getResource(sourceUri, true);

        FileWriter writer = new FileWriter(new File(commandLine.getOptionValue(OUT)));
        try {
            writer.write(commandLine.getOptionValue(LABEL));
            writer.write("\n");

            for (Iterator<EObject> iterator = sourceResource.getAllContents(); iterator.hasNext();) {
                EObject eObject = iterator.next();
                for (EStructuralFeature feature : eObject.eClass().getEAllStructuralFeatures()) {
                    if (feature.isMany() && eObject.eIsSet(feature)) {
                        EList<?> value = (EList<?>) eObject.eGet(feature);
                        //                     if (value.size() > 10) 
                        writer.write(String.format("%d\n", value.size()));
                    }
                }
            }
        } finally {
            IOUtils.closeQuietly(writer);
        }

    } catch (ParseException e) {
        showError(e.toString());
        showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.CdoQuery.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input CDO resource directory");
    inputOpt.setArgs(1);//from   w  w  w  .  j a  v a  2  s .  c o  m
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option repoOpt = OptionBuilder.create(REPO_NAME);
    repoOpt.setArgName("REPO_NAME");
    repoOpt.setDescription("CDO Repository name");
    repoOpt.setArgs(1);
    repoOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);
    options.addOption(repoOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        String repositoryDir = commandLine.getOptionValue(IN);
        String repositoryName = commandLine.getOptionValue(REPO_NAME);

        Class<?> inClazz = CdoQuery.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        EmbeddedCDOServer server = new EmbeddedCDOServer(repositoryDir, repositoryName);
        try {
            server.run();
            CDOSession session = server.openSession();
            CDOTransaction transaction = session.openTransaction();
            Resource resource = transaction.getRootResource();

            {
                LOG.log(Level.INFO, "Start query");
                long begin = System.currentTimeMillis();
                EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource);
                long end = System.currentTimeMillis();
                LOG.log(Level.INFO, "End query");
                LOG.log(Level.INFO,
                        MessageFormat.format("Query result (list) contains {0} elements", list.size()));
                LOG.log(Level.INFO,
                        MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            }

            {
                LOG.log(Level.INFO, "Start query");
                long begin = System.currentTimeMillis();
                EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsLoop(resource);
                long end = System.currentTimeMillis();
                LOG.log(Level.INFO, "End query");
                LOG.log(Level.INFO,
                        MessageFormat.format("Query result (loops) contains {0} elements", list.size()));
                LOG.log(Level.INFO,
                        MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            }

            transaction.close();
            session.close();
        } finally {
            server.stop();
        }
    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.ikanow.aleph2.data_import_manager.harvest.modules.LocalHarvestTestModule.java

/** Entry point
 * @param args - config_file source_key harvest_tech_id
 * @throws Exception //from w ww .  ja v  a  2  s  .  co  m
 */
public static void main(final String[] args) {
    try {
        if (args.length < 3) {
            System.out.println("CLI: config_file source_key harvest_tech_jar_path");
            System.exit(-1);
        }
        System.out.println("Running with command line: " + Arrays.toString(args));
        Config config = ConfigFactory.parseFile(new File(args[0]));

        LocalHarvestTestModule app = ModuleUtils.initializeApplication(Arrays.asList(), Optional.of(config),
                Either.left(LocalHarvestTestModule.class));
        app.start(args[1], args[2], Arrays.copyOfRange(args, 3, args.length));
    } catch (Exception e) {
        try {
            System.out.println("Got all the way to main");
            e.printStackTrace();
        } catch (Exception e2) { // the exception failed!
            System.out.println(ErrorUtils.getLongForm("Got all the way to main: {0}", e));
        }
    }
}