Example usage for java.lang Math round

List of usage examples for java.lang Math round

Introduction

In this page you can find the example usage for java.lang Math round.

Prototype

public static long round(double a) 

Source Link

Document

Returns the closest long to the argument, with ties rounding to positive infinity.

Usage

From source file:com.cloudera.oryx.app.traffic.TrafficUtil.java

public static void main(String[] args) throws Exception {
    if (args.length < 3) {
        System.err.println("usage: TrafficUtil [hosts] [requestIntervalMS] [threads] [... other args]");
        return;//from w ww  . j  a va  2s .  c o  m
    }

    String[] hostStrings = COMMA.split(args[0]);
    Preconditions.checkArgument(hostStrings.length >= 1);
    int requestIntervalMS = Integer.parseInt(args[1]);
    Preconditions.checkArgument(requestIntervalMS >= 0);
    int numThreads = Integer.parseInt(args[2]);
    Preconditions.checkArgument(numThreads >= 1);

    String[] otherArgs = new String[args.length - 3];
    System.arraycopy(args, 3, otherArgs, 0, otherArgs.length);

    List<URI> hosts = Arrays.stream(hostStrings).map(URI::create).collect(Collectors.toList());

    int perClientRequestIntervalMS = numThreads * requestIntervalMS;

    Endpoints alsEndpoints = new Endpoints(ALSEndpoint.buildALSEndpoints());
    AtomicLong requestCount = new AtomicLong();
    AtomicLong serverErrorCount = new AtomicLong();
    AtomicLong clientErrorCount = new AtomicLong();
    AtomicLong exceptionCount = new AtomicLong();

    long start = System.currentTimeMillis();
    ExecUtils.doInParallel(numThreads, numThreads, true, i -> {
        RandomGenerator random = RandomManager.getRandom(Integer.toString(i).hashCode() ^ System.nanoTime());
        ExponentialDistribution msBetweenRequests;
        if (perClientRequestIntervalMS > 0) {
            msBetweenRequests = new ExponentialDistribution(random, perClientRequestIntervalMS);
        } else {
            msBetweenRequests = null;
        }

        ClientConfig clientConfig = new ClientConfig();
        PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager();
        connectionManager.setMaxTotal(numThreads);
        connectionManager.setDefaultMaxPerRoute(numThreads);
        clientConfig.property(ApacheClientProperties.CONNECTION_MANAGER, connectionManager);
        clientConfig.connectorProvider(new ApacheConnectorProvider());
        Client client = ClientBuilder.newClient(clientConfig);

        try {
            while (true) {
                try {
                    WebTarget target = client.target("http://" + hosts.get(random.nextInt(hosts.size())));
                    Endpoint endpoint = alsEndpoints.chooseEndpoint(random);
                    Invocation invocation = endpoint.makeInvocation(target, otherArgs, random);

                    long startTime = System.currentTimeMillis();
                    Response response = invocation.invoke();
                    try {
                        response.readEntity(String.class);
                    } finally {
                        response.close();
                    }
                    long elapsedMS = System.currentTimeMillis() - startTime;

                    int statusCode = response.getStatusInfo().getStatusCode();
                    if (statusCode >= 400) {
                        if (statusCode >= 500) {
                            serverErrorCount.incrementAndGet();
                        } else {
                            clientErrorCount.incrementAndGet();
                        }
                    }

                    endpoint.recordTiming(elapsedMS);

                    if (requestCount.incrementAndGet() % 10000 == 0) {
                        long elapsed = System.currentTimeMillis() - start;
                        log.info("{}ms:\t{} requests\t({} client errors\t{} server errors\t{} exceptions)",
                                elapsed, requestCount.get(), clientErrorCount.get(), serverErrorCount.get(),
                                exceptionCount.get());
                        for (Endpoint e : alsEndpoints.getEndpoints()) {
                            log.info("{}", e);
                        }
                    }

                    if (msBetweenRequests != null) {
                        int desiredElapsedMS = (int) Math.round(msBetweenRequests.sample());
                        if (elapsedMS < desiredElapsedMS) {
                            Thread.sleep(desiredElapsedMS - elapsedMS);
                        }
                    }
                } catch (Exception e) {
                    exceptionCount.incrementAndGet();
                    log.warn("{}", e.getMessage());
                }
            }
        } finally {
            client.close();
        }
    });
}

From source file:Text2ColumntStorageMR.java

@SuppressWarnings("deprecation")
public static void main(String[] args) throws Exception {

    if (args.length != 3) {
        System.out.println("Text2ColumnStorageMR <input> <output> <columnStorageMode>");
        System.exit(-1);//from   w ww. j  a  v a  2 s  .c  om
    }

    JobConf conf = new JobConf(Text2ColumntStorageMR.class);

    conf.setJobName("Text2ColumnStorageMR");

    conf.setNumMapTasks(1);
    conf.setNumReduceTasks(4);

    conf.setOutputKeyClass(LongWritable.class);
    conf.setOutputValueClass(Unit.Record.class);

    conf.setMapperClass(TextFileMapper.class);
    conf.setReducerClass(ColumnStorageReducer.class);

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat((Class<? extends OutputFormat>) ColumnStorageHiveOutputFormat.class);
    conf.set("mapred.output.compress", "flase");

    Head head = new Head();
    initHead(head);

    head.toJobConf(conf);

    int bt = Integer.valueOf(args[2]);

    FileInputFormat.setInputPaths(conf, args[0]);
    Path outputPath = new Path(args[1]);
    FileOutputFormat.setOutputPath(conf, outputPath);

    FileSystem fs = outputPath.getFileSystem(conf);
    fs.delete(outputPath, true);

    JobClient jc = new JobClient(conf);
    RunningJob rj = null;
    rj = jc.submitJob(conf);

    String lastReport = "";
    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss,SSS");
    long reportTime = System.currentTimeMillis();
    long maxReportInterval = 3 * 1000;
    while (!rj.isComplete()) {
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
        }

        int mapProgress = Math.round(rj.mapProgress() * 100);
        int reduceProgress = Math.round(rj.reduceProgress() * 100);

        String report = " map = " + mapProgress + "%,  reduce = " + reduceProgress + "%";

        if (!report.equals(lastReport) || System.currentTimeMillis() >= reportTime + maxReportInterval) {

            String output = dateFormat.format(Calendar.getInstance().getTime()) + report;
            System.out.println(output);
            lastReport = report;
            reportTime = System.currentTimeMillis();
        }
    }

    System.exit(0);

}

From source file:de.codesourcery.geoip.Main.java

public static void main(String[] args) throws Exception {
    final IGeoLocator<StringSubject> locator = createGeoLocator();

    final JFrame frame = new JFrame("GeoIP");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

    frame.addWindowListener(new WindowAdapter() {
        public void windowClosing(java.awt.event.WindowEvent e) {
            try {
                locator.dispose();//from  w w w .  jav  a2 s.c o m
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        };
    });

    final MapImage image = MapImage.getRobinsonWorldMap(); // MapImage.getMillerWorldMap();      
    final MapCanvas canvas = new MapCanvas(image);

    for (GeoLocation<StringSubject> loc : locator.locate(getSpammers())) {
        if (loc.hasValidCoordinates()) {
            canvas.addCoordinate(PointRenderer.createPoint(loc, Color.YELLOW));
        }
    }

    //      canvas.addCoordinate( PointRenderer.createPoint( ZERO , Color.YELLOW ) );
    //      canvas.addCoordinate( PointRenderer.createPoint( WELLINGTON , Color.RED ) );
    //      canvas.addCoordinate( PointRenderer.createPoint( MELBOURNE , Color.RED ) );
    //      canvas.addCoordinate( PointRenderer.createPoint( HAMBURG , Color.RED ) );

    final double heightToWidth = image.height() / (double) image.width(); // preserve aspect ratio of map
    canvas.setPreferredSize(new Dimension(640, (int) Math.round(640 * heightToWidth)));

    JPanel panel = new JPanel();
    panel.setLayout(new FlowLayout());

    panel.add(new JLabel("Scale-X"));
    final JTextField scaleX = new JTextField(Double.toString(image.getScaleX()));
    scaleX.setColumns(5);

    final JTextField scaleY = new JTextField(Double.toString(image.getScaleY()));
    scaleY.setColumns(5);

    final ActionListener listener = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {

            double x = Double.parseDouble(scaleX.getText());
            double y = Double.parseDouble(scaleY.getText());
            image.setScale(x, y);
            canvas.repaint();
        }
    };
    scaleX.addActionListener(listener);
    scaleY.addActionListener(listener);

    panel.add(new JLabel("Scale-X"));
    panel.add(scaleX);

    panel.add(new JLabel("Scale-Y"));
    panel.add(scaleY);

    final JTextField ipAddress = new JTextField("www.kickstarter.com");
    ipAddress.setColumns(20);

    final ActionListener ipListener = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            final String destinationIP = ipAddress.getText();
            if (StringUtils.isBlank(destinationIP)) {
                return;
            }

            /*
             * Perform traceroute.
             */
            final List<String> hops;
            try {
                if (TracePath.isPathTracingAvailable()) {
                    hops = TracePath.trace(destinationIP);
                } else {
                    System.err.println("tracepath not available.");
                    if (TracePath.isValidAddress(destinationIP)) {
                        hops = new ArrayList<>();
                        hops.add(destinationIP);
                    } else {
                        System.err.println(destinationIP + " is no valid IP");
                        return;
                    }
                }
            } catch (Exception ex) {
                System.err.println("Failed to trace " + destinationIP);
                ex.printStackTrace();
                return;
            }

            System.out.println("Trace contains " + hops.size() + " IPs");

            /*
             * Gather locations.
             */
            final List<StringSubject> subjects = new ArrayList<>();
            for (String ip : hops) {
                subjects.add(new StringSubject(ip));
            }

            final List<GeoLocation<StringSubject>> locations;
            try {
                long time = -System.currentTimeMillis();
                locations = locator.locate(subjects);
                time += System.currentTimeMillis();

                System.out.println("Locating hops for " + destinationIP + " returned " + locations.size()
                        + " valid locations ( time: " + time + " ms)");
                System.out.flush();

            } catch (Exception e2) {
                e2.printStackTrace();
                return;
            }

            /*
             * Weed-out invalid/unknown locations.
             */
            {
                GeoLocation<StringSubject> previous = null;
                for (Iterator<GeoLocation<StringSubject>> it = locations.iterator(); it.hasNext();) {
                    final GeoLocation<StringSubject> location = it.next();
                    if (!location.hasValidCoordinates()
                            || (previous != null && previous.coordinate().equals(location.coordinate()))) {
                        it.remove();
                        System.err.println("Ignoring invalid/duplicate location for " + location);
                    } else {
                        previous = location;
                    }
                }
            }

            /*
             * Populate chart.
             */

            System.out.println("Adding " + locations.size() + " hops to chart");
            System.out.flush();

            canvas.removeAllCoordinates();

            if (locations.size() == 1) {
                canvas.addCoordinate(
                        PointRenderer.createPoint(locations.get(0), getLabel(locations.get(0)), Color.BLACK));
            } else if (locations.size() > 1) {
                GeoLocation<StringSubject> previous = locations.get(0);
                MapPoint previousPoint = PointRenderer.createPoint(previous, getLabel(previous), Color.BLACK);
                final int len = locations.size();
                for (int i = 1; i < len; i++) {
                    final GeoLocation<StringSubject> current = locations.get(i);
                    //                  final MapPoint currentPoint = PointRenderer.createPoint( current , getLabel( current ) , Color.BLACK );
                    final MapPoint currentPoint = PointRenderer.createPoint(current, Color.BLACK);

                    //                  canvas.addCoordinate( LineRenderer.createLine( previousPoint , currentPoint , Color.RED ) );
                    canvas.addCoordinate(CurvedLineRenderer.createLine(previousPoint, currentPoint, Color.RED));

                    previous = locations.get(i);
                    previousPoint = currentPoint;
                }
            }
            System.out.println("Finished adding");
            System.out.flush();
            canvas.repaint();
        }
    };
    ipAddress.addActionListener(ipListener);

    panel.add(new JLabel("IP"));
    panel.add(ipAddress);

    frame.getContentPane().setLayout(new BorderLayout());
    frame.getContentPane().add(panel, BorderLayout.NORTH);
    frame.getContentPane().add(canvas, BorderLayout.CENTER);
    frame.pack();
    frame.setVisible(true);
}

From source file:fr.inria.atlanmod.instantiator.neoEMF.Launcher.java

public static void main(String[] args) throws GenerationException, IOException {

    ResourceSetImpl resourceSet = new ResourceSetImpl();
    { // initializing the registry

        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(EcorePackage.eNS_PREFIX,
                new EcoreResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap()
                .put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoEMFURI.NEOEMF_HBASE_SCHEME,
                NeoEMFResourceFactory.eINSTANCE);

    }/*from   w w w .j a v  a2  s . c  om*/

    Options options = new Options();

    configureOptions(options);

    CommandLineParser parser = new GnuParser();

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

        String epackage_class = commandLine.getOptionValue(E_PACKAGE_CLASS);

        LOGGER.info("Start loading the package");
        Class<?> inClazz = Launcher.class.getClassLoader().loadClass(epackage_class);
        EPackage _package = (EPackage) inClazz.getMethod("init").invoke(null);

        Resource metamodelResource = new XMIResourceImpl(URI.createFileURI("dummy"));
        metamodelResource.getContents().add(_package);
        LOGGER.info("Finish loading the package");

        int size = Launcher.DEFAULT_AVERAGE_MODEL_SIZE;
        if (commandLine.hasOption(SIZE)) {
            Number number = (Number) commandLine.getParsedOptionValue(SIZE);
            size = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        float variation = Launcher.DEFAULT_DEVIATION;
        if (commandLine.hasOption(VARIATION)) {
            Number number = (Number) commandLine.getParsedOptionValue(VARIATION);
            if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) {
                throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", VARIATION,
                        number.floatValue()));
            }
            variation = number.floatValue();
        }

        float propVariation = Launcher.DEFAULT_DEVIATION;
        if (commandLine.hasOption(PROP_VARIATION)) {
            Number number = (Number) commandLine.getParsedOptionValue(PROP_VARIATION);
            if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) {
                throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}",
                        PROP_VARIATION, number.floatValue()));
            }
            propVariation = number.floatValue();
        }

        long seed = System.currentTimeMillis();
        if (commandLine.hasOption(SEED)) {
            seed = ((Number) commandLine.getParsedOptionValue(SEED)).longValue();
        }

        Range<Integer> range = Range.between(Math.round(size * (1 - variation)),
                Math.round(size * (1 + variation)));

        GenericMetamodelConfig config = new GenericMetamodelConfig(metamodelResource, range, seed);
        GenericMetamodelGenerator modelGen = new GenericMetamodelGenerator(config);

        if (commandLine.hasOption(OUTPUT_PATH)) {
            String outDir = commandLine.getOptionValue(OUTPUT_PATH);
            //java.net.URI intermediateURI = java.net.URI.create(outDir);
            modelGen.setSamplesPath(outDir);
        }

        int numberOfModels = 1;
        if (commandLine.hasOption(N_MODELS)) {
            numberOfModels = ((Number) commandLine.getParsedOptionValue(N_MODELS)).intValue();
        }

        int valuesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_VALUES_LENGTH;
        if (commandLine.hasOption(VALUES_SIZE)) {
            Number number = (Number) commandLine.getParsedOptionValue(VALUES_SIZE);
            valuesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        int referencesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_REFERENCES_SIZE;
        if (commandLine.hasOption(VALUES_SIZE)) {
            Number number = (Number) commandLine.getParsedOptionValue(DEGREE);
            referencesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        config.setValuesRange(Math.round(valuesSize * (1 - propVariation)),
                Math.round(valuesSize * (1 + propVariation)));

        config.setReferencesRange(Math.round(referencesSize * (1 - propVariation)),
                Math.round(referencesSize * (1 + propVariation)));

        config.setPropertiesRange(Math.round(referencesSize * (1 - propVariation)),
                Math.round(referencesSize * (1 + propVariation)));

        long start = System.currentTimeMillis();
        modelGen.runGeneration(resourceSet, numberOfModels, size, variation);
        long end = System.currentTimeMillis();
        LOGGER.info(
                MessageFormat.format("Generation finished after {0} s", Long.toString((end - start) / 1000)));

        if (commandLine.hasOption(DIAGNOSE)) {
            for (Resource resource : resourceSet.getResources()) {
                LOGGER.info(
                        MessageFormat.format("Requested validation for resource ''{0}''", resource.getURI()));
                BasicDiagnostic diagnosticChain = diagnoseResource(resource);
                if (!isFailed(diagnosticChain)) {
                    LOGGER.info(MessageFormat.format("Result of the diagnosis of resurce ''{0}'' is ''OK''",
                            resource.getURI()));
                } else {
                    LOGGER.severe(MessageFormat.format("Found ''{0}'' error(s) in the resource ''{1}''",
                            diagnosticChain.getChildren().size(), resource.getURI()));
                    for (Diagnostic diagnostic : diagnosticChain.getChildren()) {
                        LOGGER.fine(diagnostic.getMessage());
                    }
                }
            }
            LOGGER.info("Validation finished");
        }

    } catch (ParseException e) {
        System.err.println(e.getLocalizedMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.setOptionComparator(new OptionComarator<Option>());
        try {
            formatter.setWidth(Math.max(Terminal.getTerminal().getTerminalWidth(), 80));
        } catch (Throwable t) {
            LOGGER.warning("Unable to get console information");
        }
        ;
        formatter.printHelp("java -jar <this-file.jar>", options, true);
        System.exit(ERROR);
    } catch (ClassNotFoundException t) {
        System.err.println("ERROR: Unable to load class" + t.getLocalizedMessage());
        StringWriter stringWriter = new StringWriter();
        t.printStackTrace(new PrintWriter(stringWriter));
        System.err.println(stringWriter.toString());
    } catch (Throwable t) {
        System.err.println("ERROR: " + t.getLocalizedMessage());
        StringWriter stringWriter = new StringWriter();
        t.printStackTrace(new PrintWriter(stringWriter));
        System.err.println(t);
        LOGGER.severe(stringWriter.toString());
        System.exit(ERROR);
    }
}

From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java

public static void main(String[] args) {

    if (args.length != 4) {
        System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n"
                + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n"
                + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n");
    } else {/* ww  w . j av a 2s. c  o m*/

        BufferedWriter outBuff = null;

        try {

            File inFile = new File(args[0]);
            File fastaFile = new File(args[1]);
            File outFile = new File(args[2]);
            File blastFile = new File(args[3]);

            //Primero cargo todos los datos del archivo xml del blast
            BufferedReader buffReader = new BufferedReader(new FileReader(blastFile));
            StringBuilder stBuilder = new StringBuilder();
            String line = null;

            while ((line = buffReader.readLine()) != null) {
                stBuilder.append(line);
            }

            buffReader.close();
            System.out.println("Creating blastoutput...");
            BlastOutput blastOutput = new BlastOutput(stBuilder.toString());
            System.out.println("BlastOutput created! :)");
            stBuilder.delete(0, stBuilder.length());

            HashMap<String, String> blastProteinsMap = new HashMap<String, String>();
            ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations();
            for (Iteration iteration : iterations) {
                blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString());
            }
            //freeing some memory
            blastOutput = null;
            //------------------------------------------------------------------------

            //Initializing writer for output file
            outBuff = new BufferedWriter(new FileWriter(outFile));

            //reading gene annotation xml file.....
            buffReader = new BufferedReader(new FileReader(inFile));
            stBuilder = new StringBuilder();
            line = null;
            while ((line = buffReader.readLine()) != null) {
                stBuilder.append(line);
            }
            buffReader.close();

            XMLElement genesXML = new XMLElement(stBuilder.toString());
            //freeing some memory I don't need anymore
            stBuilder.delete(0, stBuilder.length());

            //reading file with the reference proteins set
            ArrayList<String> proteinsReferenceSet = new ArrayList<String>();
            buffReader = new BufferedReader(new FileReader(fastaFile));
            while ((line = buffReader.readLine()) != null) {
                if (line.charAt(0) == '>') {
                    proteinsReferenceSet.add(line.split("\\|")[1]);
                }
            }
            buffReader.close();

            Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME);

            List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME);

            System.out.println("There are " + contigs.size() + " contigs to be checked... ");

            outBuff.write("There are " + contigs.size() + " contigs to be checked... \n");
            outBuff.write("Proteins reference set: \n");
            for (String st : proteinsReferenceSet) {
                outBuff.write(st + ",");
            }
            outBuff.write("\n");

            for (Element elem : contigs) {
                ContigXML contig = new ContigXML(elem);

                //escribo el id del contig en el que estoy
                outBuff.write("Checking contig: " + contig.getId() + "\n");
                outBuff.flush();

                List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME);
                System.out.println("geneList.size() = " + geneList.size());

                int numeroDeGenesParaAnalizar = geneList.size() / FACTOR;
                if (numeroDeGenesParaAnalizar == 0) {
                    numeroDeGenesParaAnalizar++;
                }

                ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>();

                outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: "
                        + numeroDeGenesParaAnalizar + "\n");

                for (int j = 0; j < numeroDeGenesParaAnalizar; j++) {
                    int geneIndex;

                    boolean geneIsDismissed = false;
                    do {
                        geneIsDismissed = false;
                        geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size()));
                        PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement());
                        if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) {
                            geneIsDismissed = true;
                        }
                    } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed);

                    indicesUtilizados.add(geneIndex);
                    System.out.println("geneIndex = " + geneIndex);

                    //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad
                    PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement());

                    outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: "
                            + gene.getAnnotationUniprotId() + "\n");
                    outBuff.write("eValue: " + gene.getEvalue() + "\n");

                    //--------------PETICION POST HTTP BLAST----------------------
                    PostMethod post = new PostMethod(BLAST_URL);
                    post.addParameter("program", "blastx");
                    post.addParameter("sequence", gene.getSequence());
                    post.addParameter("database", "uniprotkb");
                    post.addParameter("email", "ppareja@era7.com");
                    post.addParameter("exp", "1e-10");
                    post.addParameter("stype", "dna");

                    // execute the POST
                    HttpClient client = new HttpClient();
                    int status = client.executeMethod(post);
                    System.out.println("status post = " + status);
                    InputStream inStream = post.getResponseBodyAsStream();

                    String fileName = "jobid.txt";
                    FileOutputStream outStream = new FileOutputStream(new File(fileName));
                    byte[] buffer = new byte[1024];
                    int len;

                    while ((len = inStream.read(buffer)) != -1) {
                        outStream.write(buffer, 0, len);
                    }
                    outStream.close();

                    //Once the file is created I just have to read one line in order to extract the job id
                    buffReader = new BufferedReader(new FileReader(new File(fileName)));
                    String jobId = buffReader.readLine();
                    buffReader.close();

                    System.out.println("jobId = " + jobId);

                    //--------------HTTP CHECK JOB STATUS REQUEST----------------------
                    GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId);
                    String jobStatus = "";
                    do {

                        try {
                            Thread.sleep(1000);//sleep for 1000 ms                                
                        } catch (InterruptedException ie) {
                            //If this thread was intrrupted by nother thread
                        }

                        status = client.executeMethod(get);
                        //System.out.println("status get = " + status);

                        inStream = get.getResponseBodyAsStream();

                        fileName = "jobStatus.txt";
                        outStream = new FileOutputStream(new File(fileName));

                        while ((len = inStream.read(buffer)) != -1) {
                            outStream.write(buffer, 0, len);
                        }
                        outStream.close();

                        //Once the file is created I just have to read one line in order to extract the job id
                        buffReader = new BufferedReader(new FileReader(new File(fileName)));
                        jobStatus = buffReader.readLine();
                        //System.out.println("jobStatus = " + jobStatus);
                        buffReader.close();

                    } while (!jobStatus.equals(FINISHED_JOB_STATUS));

                    //Once I'm here the blast should've already finished

                    //--------------JOB RESULTS HTTP REQUEST----------------------
                    get = new GetMethod(JOB_RESULT_URL + jobId + "/out");

                    status = client.executeMethod(get);
                    System.out.println("status get = " + status);

                    inStream = get.getResponseBodyAsStream();

                    fileName = "jobResults.txt";
                    outStream = new FileOutputStream(new File(fileName));

                    while ((len = inStream.read(buffer)) != -1) {
                        outStream.write(buffer, 0, len);
                    }
                    outStream.close();

                    //--------parsing the blast results file-----

                    TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>();

                    buffReader = new BufferedReader(new FileReader(new File(fileName)));
                    while ((line = buffReader.readLine()) != null) {
                        if (line.length() > 3) {
                            String prefix = line.substring(0, 3);
                            if (prefix.equals("TR:") || prefix.equals("SP:")) {
                                String[] columns = line.split(" ");
                                String id = columns[1];
                                //System.out.println("id = " + id);

                                String e = "";

                                String[] arraySt = line.split("\\.\\.\\.");
                                if (arraySt.length > 1) {
                                    arraySt = arraySt[1].trim().split(" ");
                                    int contador = 0;
                                    for (int k = 0; k < arraySt.length && contador <= 2; k++) {
                                        String string = arraySt[k];
                                        if (!string.equals("")) {
                                            contador++;
                                            if (contador == 2) {
                                                e = string;
                                            }
                                        }

                                    }
                                } else {
                                    //Number before e-
                                    String[] arr = arraySt[0].split("e-")[0].split(" ");
                                    String numeroAntesE = arr[arr.length - 1];
                                    String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0];
                                    e = numeroAntesE + "e-" + numeroDespuesE;
                                }

                                double eValue = Double.parseDouble(e);
                                //System.out.println("eValue = " + eValue);
                                GeneEValuePair g = new GeneEValuePair(id, eValue);
                                featuresBlast.add(g);
                            }
                        }
                    }

                    GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(),
                            gene.getEvalue());

                    System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id);
                    System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue);
                    boolean blastContainsGene = false;
                    for (GeneEValuePair geneEValuePair : featuresBlast) {
                        if (geneEValuePair.id.equals(currentGeneEValuePair.id)) {
                            blastContainsGene = true;
                            //le pongo la e que tiene en el wu-blast para poder comparar
                            currentGeneEValuePair.eValue = geneEValuePair.eValue;
                            break;
                        }
                    }

                    if (blastContainsGene) {
                        outBuff.write("The protein was found in the WU-BLAST result.. \n");
                        //Una vez que se que esta en el blast tengo que ver que sea la mejor
                        GeneEValuePair first = featuresBlast.first();
                        outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id
                                + " , " + first.eValue + "\n");
                        if (first.id.equals(currentGeneEValuePair.id)) {
                            outBuff.write("Proteins with best eValue match up \n");
                        } else {
                            if (first.eValue == currentGeneEValuePair.eValue) {
                                outBuff.write(
                                        "The one with best eValue is not the same protein but has the same eValue \n");
                            } else if (first.eValue > currentGeneEValuePair.eValue) {
                                outBuff.write(
                                        "The one with best eValue is not the same protein but has a worse eValue :) \n");
                            } else {
                                outBuff.write(
                                        "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n");
                                //System.exit(-1);
                                if (proteinsReferenceSet.contains(first.id)) {
                                    //The protein is in the reference set and that shouldn't happen
                                    outBuff.write(
                                            "The protein was found on the reference set, checking if it belongs to the same contig...\n");
                                    String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId());
                                    if (iterationSt != null) {
                                        outBuff.write(
                                                "The protein was found in the BLAST used at the beginning of the annotation process.\n");
                                        Iteration iteration = new Iteration(iterationSt);
                                        ArrayList<Hit> hits = iteration.getIterationHits();
                                        boolean contigFound = false;
                                        Hit errorHit = null;
                                        for (Hit hit : hits) {
                                            if (hit.getHitDef().indexOf(contig.getId()) >= 0) {
                                                contigFound = true;
                                                errorHit = hit;
                                                break;
                                            }
                                        }
                                        if (contigFound) {
                                            outBuff.write(
                                                    "ERROR: A hit from the same contig was find in the Blast file: \n"
                                                            + errorHit.toString() + "\n");
                                        } else {
                                            outBuff.write("There is no hit with the same contig! :)\n");
                                        }
                                    } else {
                                        outBuff.write(
                                                "The protein is NOT in the BLAST used at the beginning of the annotation process.\n");
                                    }

                                } else {
                                    //The protein was not found on the reference set so everything's ok
                                    outBuff.write(
                                            "The protein was not found on the reference, everything's ok :)\n");
                                }
                            }
                        }

                    } else {
                        outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n");

                        //System.exit(-1);
                    }

                }

            }

        } catch (Exception ex) {
            ex.printStackTrace();
        } finally {
            try {
                //closing outputfile
                outBuff.close();
            } catch (IOException ex) {
                Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex);
            }
        }

    }
}

From source file:fr.inria.atlanmod.dag.instantiator.Launcher.java

public static void main(String[] args) throws GenerationException, IOException {

    ResourceSetImpl resourceSet = new ResourceSetImpl();
    { // initializing the registry

        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(EcorePackage.eNS_PREFIX,
                new EcoreResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap()
                .put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoEMFURI.NEOEMF_HBASE_SCHEME,
                NeoEMFResourceFactory.eINSTANCE);

    }/*from   ww w . ja v a  2 s  .c o m*/

    Options options = new Options();

    configureOptions(options);

    CommandLineParser parser = new GnuParser();

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

        //         String epackage_class = commandLine.getOptionValue(E_PACKAGE_CLASS);
        //         
        //         LOGGER.info("Start loading the package");
        //         Class<?> inClazz = Launcher.class.getClassLoader().loadClass(epackage_class);
        //         EPackage _package = (EPackage) inClazz.getMethod("init").invoke(null);
        //         
        //         Resource metamodelResource = new XMIResourceImpl(URI.createFileURI("dummy"));
        //          metamodelResource.getContents().add(_package);
        //          LOGGER.info("Finish loading the package");

        int size = Launcher.DEFAULT_AVERAGE_MODEL_SIZE;
        if (commandLine.hasOption(SIZE)) {
            Number number = (Number) commandLine.getParsedOptionValue(SIZE);
            size = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        float variation = Launcher.DEFAULT_DEVIATION;
        if (commandLine.hasOption(VARIATION)) {
            Number number = (Number) commandLine.getParsedOptionValue(VARIATION);
            if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) {
                throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", VARIATION,
                        number.floatValue()));
            }
            variation = number.floatValue();
        }

        float propVariation = Launcher.DEFAULT_DEVIATION;
        if (commandLine.hasOption(PROP_VARIATION)) {
            Number number = (Number) commandLine.getParsedOptionValue(PROP_VARIATION);
            if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) {
                throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}",
                        PROP_VARIATION, number.floatValue()));
            }
            propVariation = number.floatValue();
        }

        long seed = System.currentTimeMillis();
        if (commandLine.hasOption(SEED)) {
            seed = ((Number) commandLine.getParsedOptionValue(SEED)).longValue();
        }

        Range<Integer> range = Range.between(Math.round(size * (1 - variation)),
                Math.round(size * (1 + variation)));

        ISpecimenConfiguration config = new DagMetamodelConfig(range, seed);
        IGenerator generator = new DagGenerator(config, config.getSeed());

        GenericMetamodelGenerator modelGen = new GenericMetamodelGenerator(generator);

        if (commandLine.hasOption(OUTPUT_PATH)) {
            String outDir = commandLine.getOptionValue(OUTPUT_PATH);
            //java.net.URI intermediateURI = java.net.URI.create(outDir);
            modelGen.setSamplesPath(outDir);
        }

        int numberOfModels = 1;
        if (commandLine.hasOption(N_MODELS)) {
            numberOfModels = ((Number) commandLine.getParsedOptionValue(N_MODELS)).intValue();
        }

        int valuesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_VALUES_LENGTH;
        if (commandLine.hasOption(VALUES_SIZE)) {
            Number number = (Number) commandLine.getParsedOptionValue(VALUES_SIZE);
            valuesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        int referencesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_REFERENCES_SIZE;
        if (commandLine.hasOption(DEGREE)) {
            Number number = (Number) commandLine.getParsedOptionValue(DEGREE);
            referencesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue());
        }

        config.setValuesRange(Math.round(valuesSize * (1 - propVariation)),
                Math.round(valuesSize * (1 + propVariation)));

        config.setReferencesRange(Math.round(referencesSize * (1 - propVariation)),
                Math.round(referencesSize * (1 + propVariation)));

        config.setPropertiesRange(Math.round(referencesSize * (1 - propVariation)),
                Math.round(referencesSize * (1 + propVariation)));

        long start = System.currentTimeMillis();
        modelGen.runGeneration(resourceSet, numberOfModels, size, variation);
        long end = System.currentTimeMillis();
        LOGGER.info(
                MessageFormat.format("Generation finished after {0} s", Long.toString((end - start) / 1000)));

        //         for (Resource rsc : resourceSet.getResources()) {
        //            if (rsc.getContents().get(0) instanceof DAG) {
        //               
        //            }
        //               
        //         }

        if (commandLine.hasOption(DIAGNOSE)) {
            for (Resource resource : resourceSet.getResources()) {
                LOGGER.info(
                        MessageFormat.format("Requested validation for resource ''{0}''", resource.getURI()));
                BasicDiagnostic diagnosticChain = diagnoseResource(resource);
                if (!isFailed(diagnosticChain)) {
                    LOGGER.info(MessageFormat.format("Result of the diagnosis of resurce ''{0}'' is ''OK''",
                            resource.getURI()));
                } else {
                    LOGGER.severe(MessageFormat.format("Found ''{0}'' error(s) in the resource ''{1}''",
                            diagnosticChain.getChildren().size(), resource.getURI()));
                    for (Diagnostic diagnostic : diagnosticChain.getChildren()) {
                        LOGGER.fine(diagnostic.getMessage());
                    }
                }
            }
            LOGGER.info("Validation finished");
        }

    } catch (ParseException e) {
        System.err.println(e.getLocalizedMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.setOptionComparator(new OptionComarator<Option>());
        try {
            formatter.setWidth(Math.max(Terminal.getTerminal().getTerminalWidth(), 80));
        } catch (Throwable t) {
            LOGGER.warning("Unable to get console information");
        }
        ;
        formatter.printHelp("java -jar <this-file.jar>", options, true);
        System.exit(ERROR);
    } catch (Throwable t) {
        System.err.println("ERROR: " + t.getLocalizedMessage());
        StringWriter stringWriter = new StringWriter();
        t.printStackTrace(new PrintWriter(stringWriter));
        System.err.println(t);
        LOGGER.severe(stringWriter.toString());
        System.exit(ERROR);
    }
}

From source file:Text2FormatStorageMR.java

@SuppressWarnings("deprecation")
public static void main(String[] args) throws Exception {

    if (args.length != 2) {
        System.out.println("FormatFileMR <input> <output>");
        System.exit(-1);//from   w  w w  .  java 2 s .c  om
    }

    JobConf conf = new JobConf(FormatStorageMR.class);

    conf.setJobName("Text2FormatMR");

    conf.setNumMapTasks(1);
    conf.setNumReduceTasks(4);

    conf.setOutputKeyClass(LongWritable.class);
    conf.setOutputValueClass(Unit.Record.class);

    conf.setMapperClass(TextFileTestMapper.class);
    conf.setReducerClass(FormatFileTestReducer.class);

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(FormatStorageOutputFormat.class);
    conf.set("mapred.output.compress", "flase");

    Head head = new Head();
    initHead(head);

    head.toJobConf(conf);

    FileInputFormat.setInputPaths(conf, args[0]);
    Path outputPath = new Path(args[1]);
    FileOutputFormat.setOutputPath(conf, outputPath);

    FileSystem fs = outputPath.getFileSystem(conf);
    fs.delete(outputPath, true);

    JobClient jc = new JobClient(conf);
    RunningJob rj = null;
    rj = jc.submitJob(conf);

    String lastReport = "";
    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss,SSS");
    long reportTime = System.currentTimeMillis();
    long maxReportInterval = 3 * 1000;
    while (!rj.isComplete()) {
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
        }

        int mapProgress = Math.round(rj.mapProgress() * 100);
        int reduceProgress = Math.round(rj.reduceProgress() * 100);

        String report = " map = " + mapProgress + "%,  reduce = " + reduceProgress + "%";

        if (!report.equals(lastReport) || System.currentTimeMillis() >= reportTime + maxReportInterval) {

            String output = dateFormat.format(Calendar.getInstance().getTime()) + report;
            System.out.println(output);
            lastReport = report;
            reportTime = System.currentTimeMillis();
        }
    }

    System.exit(0);

}

From source file:it.units.malelab.ege.MappingPropertiesExperimenter.java

public static void main(String[] args) throws IOException, InterruptedException, ExecutionException {
    final int n = 10000;
    final int nDist = 10000;
    //prepare problems and methods
    List<String> problems = Lists.newArrayList("bool-parity5", "bool-mopm3", "sr-keijzer6", "sr-nguyen7",
            "sr-pagie1", "sr-vladislavleva4", "other-klandscapes3", "other-klandscapes7", "other-text");
    List<String> mappers = new ArrayList<>();
    for (int gs : new int[] { 64, 128, 256, 512, 1024 }) {
        mappers.add("ge-" + gs + "-2");
        mappers.add("ge-" + gs + "-4");
        mappers.add("ge-" + gs + "-8");
        mappers.add("ge-" + gs + "-12");
        mappers.add("pige-" + gs + "-4");
        mappers.add("pige-" + gs + "-8");
        mappers.add("pige-" + gs + "-16");
        mappers.add("pige-" + gs + "-24");
        mappers.add("hge-" + gs + "-0");
        mappers.add("whge-" + gs + "-2");
        mappers.add("whge-" + gs + "-3");
        mappers.add("whge-" + gs + "-5");
    }//w  w  w.  j  a v a2  s  .  c  o  m
    mappers.add("sge-0-5");
    mappers.add("sge-0-6");
    mappers.add("sge-0-7");
    mappers.add("sge-0-8");
    mappers.clear();
    mappers.addAll(Lists.newArrayList("ge-1024-8", "pige-1024-16", "hge-1024-0", "whge-1024-3", "sge-0-6"));
    PrintStream filePrintStream = null;
    if (args.length > 0) {
        filePrintStream = new PrintStream(args[0]);
    } else {
        filePrintStream = System.out;
    }
    filePrintStream.printf("problem;mapper;genotypeSize;param;property;value%n");
    //prepare distances
    Distance<Node<String>> phenotypeDistance = new CachedDistance<>(new LeavesEdit<String>());
    Distance<Sequence> genotypeDistance = new CachedDistance<>(new Hamming());
    //iterate
    for (String problemName : problems) {
        for (String mapperName : mappers) {
            System.out.printf("%20.20s, %20.20s", problemName, mapperName);
            //build problem
            Problem<String, NumericFitness> problem = null;
            if (problemName.equals("bool-parity5")) {
                problem = new Parity(5);
            } else if (problemName.equals("bool-mopm3")) {
                problem = new MultipleOutputParallelMultiplier(3);
            } else if (problemName.equals("sr-keijzer6")) {
                problem = new HarmonicCurve();
            } else if (problemName.equals("sr-nguyen7")) {
                problem = new Nguyen7(1);
            } else if (problemName.equals("sr-pagie1")) {
                problem = new Pagie1();
            } else if (problemName.equals("sr-vladislavleva4")) {
                problem = new Vladislavleva4(1);
            } else if (problemName.equals("other-klandscapes3")) {
                problem = new KLandscapes(3);
            } else if (problemName.equals("other-klandscapes7")) {
                problem = new KLandscapes(7);
            } else if (problemName.equals("other-text")) {
                problem = new Text();
            }
            //build configuration and evolver
            Mapper mapper = null;
            int genotypeSize = Integer.parseInt(mapperName.split("-")[1]);
            int mapperMainParam = Integer.parseInt(mapperName.split("-")[2]);
            if (mapperName.split("-")[0].equals("ge")) {
                mapper = new StandardGEMapper<>(mapperMainParam, 1, problem.getGrammar());
            } else if (mapperName.split("-")[0].equals("pige")) {
                mapper = new PiGEMapper<>(mapperMainParam, 1, problem.getGrammar());
            } else if (mapperName.split("-")[0].equals("sge")) {
                mapper = new SGEMapper<>(mapperMainParam, problem.getGrammar());
            } else if (mapperName.split("-")[0].equals("hge")) {
                mapper = new HierarchicalMapper<>(problem.getGrammar());
            } else if (mapperName.split("-")[0].equals("whge")) {
                mapper = new WeightedHierarchicalMapper<>(mapperMainParam, false, true, problem.getGrammar());
            }
            //prepare things
            Random random = new Random(1);
            Set<Sequence> genotypes = new LinkedHashSet<>(n);
            //build genotypes
            if (mapperName.split("-")[0].equals("sge")) {
                SGEGenotypeFactory<String> factory = new SGEGenotypeFactory<>((SGEMapper) mapper);
                while (genotypes.size() < n) {
                    genotypes.add(factory.build(random));
                }
                genotypeSize = factory.getBitSize();
            } else {
                BitsGenotypeFactory factory = new BitsGenotypeFactory(genotypeSize);
                while (genotypes.size() < n) {
                    genotypes.add(factory.build(random));
                }
            }
            //build and fill map
            Multimap<Node<String>, Sequence> multimap = HashMultimap.create();
            int progress = 0;
            for (Sequence genotype : genotypes) {
                Node<String> phenotype;
                try {
                    if (mapperName.split("-")[0].equals("sge")) {
                        phenotype = mapper.map((SGEGenotype<String>) genotype, new HashMap<>());
                    } else {
                        phenotype = mapper.map((BitsGenotype) genotype, new HashMap<>());
                    }
                } catch (MappingException e) {
                    phenotype = Node.EMPTY_TREE;
                }
                multimap.put(phenotype, genotype);
                progress = progress + 1;
                if (progress % Math.round(n / 10) == 0) {
                    System.out.print(".");
                }
            }
            System.out.println();
            //compute distances
            List<Pair<Double, Double>> allDistances = new ArrayList<>();
            List<Pair<Double, Double>> allValidDistances = new ArrayList<>();
            Multimap<Node<String>, Double> genotypeDistances = ArrayListMultimap.create();
            for (Node<String> phenotype : multimap.keySet()) {
                for (Sequence genotype1 : multimap.get(phenotype)) {
                    for (Sequence genotype2 : multimap.get(phenotype)) {
                        double gDistance = genotypeDistance.d(genotype1, genotype2);
                        genotypeDistances.put(phenotype, gDistance);
                        if (genotypeDistances.get(phenotype).size() > nDist) {
                            break;
                        }
                    }
                    if (genotypeDistances.get(phenotype).size() > nDist) {
                        break;
                    }
                }
            }
            List<Map.Entry<Node<String>, Sequence>> entries = new ArrayList<>(multimap.entries());
            Collections.shuffle(entries, random);
            for (Map.Entry<Node<String>, Sequence> entry1 : entries) {
                for (Map.Entry<Node<String>, Sequence> entry2 : entries) {
                    double gDistance = genotypeDistance.d(entry1.getValue(), entry2.getValue());
                    double pDistance = phenotypeDistance.d(entry1.getKey(), entry2.getKey());
                    allDistances.add(new Pair<>(gDistance, pDistance));
                    if (!Node.EMPTY_TREE.equals(entry1.getKey()) && !Node.EMPTY_TREE.equals(entry2.getKey())) {
                        allValidDistances.add(new Pair<>(gDistance, pDistance));
                    }
                    if (allDistances.size() > nDist) {
                        break;
                    }
                }
                if (allDistances.size() > nDist) {
                    break;
                }
            }
            //compute properties
            double invalidity = (double) multimap.get(Node.EMPTY_TREE).size() / (double) genotypes.size();
            double redundancy = 1 - (double) multimap.keySet().size() / (double) genotypes.size();
            double validRedundancy = redundancy;
            if (multimap.keySet().contains(Node.EMPTY_TREE)) {
                validRedundancy = 1 - ((double) multimap.keySet().size() - 1d)
                        / (double) (genotypes.size() - multimap.get(Node.EMPTY_TREE).size());
            }
            double locality = Utils.pearsonCorrelation(allDistances);
            double validLocality = Utils.pearsonCorrelation(allValidDistances);
            double[] sizes = new double[multimap.keySet().size()];
            double[] meanGenotypeDistances = new double[multimap.keySet().size()];
            int invalidIndex = -1;
            int c = 0;
            for (Node<String> phenotype : multimap.keySet()) {
                if (Node.EMPTY_TREE.equals(phenotype)) {
                    invalidIndex = c;
                }
                sizes[c] = multimap.get(phenotype).size();
                double[] distances = new double[genotypeDistances.get(phenotype).size()];
                int k = 0;
                for (Double distance : genotypeDistances.get(phenotype)) {
                    distances[k] = distance;
                    k = k + 1;
                }
                meanGenotypeDistances[c] = StatUtils.mean(distances);
                c = c + 1;
            }
            double nonUniformity = Math.sqrt(StatUtils.variance(sizes)) / StatUtils.mean(sizes);
            double nonSynonymousity = StatUtils.mean(meanGenotypeDistances)
                    / StatUtils.mean(firsts(allDistances));
            double validNonUniformity = nonUniformity;
            double validNonSynonymousity = nonSynonymousity;
            if (invalidIndex != -1) {
                double[] validSizes = new double[multimap.keySet().size() - 1];
                double[] validMeanGenotypeDistances = new double[multimap.keySet().size() - 1];
                if (invalidIndex > 0) {
                    System.arraycopy(sizes, 0, validSizes, 0, invalidIndex);
                    System.arraycopy(meanGenotypeDistances, 0, validMeanGenotypeDistances, 0, invalidIndex);
                }
                System.arraycopy(sizes, invalidIndex + 1, validSizes, invalidIndex,
                        sizes.length - invalidIndex - 1);
                System.arraycopy(meanGenotypeDistances, invalidIndex + 1, validMeanGenotypeDistances,
                        invalidIndex, meanGenotypeDistances.length - invalidIndex - 1);
                validNonUniformity = Math.sqrt(StatUtils.variance(validSizes)) / StatUtils.mean(validSizes);
                validNonSynonymousity = StatUtils.mean(validMeanGenotypeDistances)
                        / StatUtils.mean(firsts(allValidDistances));
            }
            //compute locality
            filePrintStream.printf("%s;%s;%d;%d;invalidity;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, invalidity);
            filePrintStream.printf("%s;%s;%d;%d;redundancy;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, redundancy);
            filePrintStream.printf("%s;%s;%d;%d;validRedundancy;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, validRedundancy);
            filePrintStream.printf("%s;%s;%d;%d;locality;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, locality);
            filePrintStream.printf("%s;%s;%d;%d;validLLocality;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, validLocality);
            filePrintStream.printf("%s;%s;%d;%d;nonUniformity;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, nonUniformity);
            filePrintStream.printf("%s;%s;%d;%d;validNonUniformity;%f %n", problemName,
                    mapperName.split("-")[0], genotypeSize, mapperMainParam, validNonUniformity);
            filePrintStream.printf("%s;%s;%d;%d;nonSynonymousity;%f %n", problemName, mapperName.split("-")[0],
                    genotypeSize, mapperMainParam, nonSynonymousity);
            filePrintStream.printf("%s;%s;%d;%d;validNonSynonymousity;%f %n", problemName,
                    mapperName.split("-")[0], genotypeSize, mapperMainParam, validNonSynonymousity);
        }
    }
    if (filePrintStream != null) {
        filePrintStream.close();
    }
}

From source file:Main.java

public static double round(float num) {
    return Math.round(num * 100.0) / 100.0;
}

From source file:Main.java

public static long getCurrentUnixTime() {
    return Math.round(System.currentTimeMillis() / 1000d);
}