Example usage for java.lang System currentTimeMillis

List of usage examples for java.lang System currentTimeMillis

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Introduction

In this page you can find the example usage for java.lang System currentTimeMillis.

Prototype

@HotSpotIntrinsicCandidate
public static native long currentTimeMillis();

Source Link

Document

Returns the current time in milliseconds.

Usage

From source file:com.foudroyantfactotum.mod.fousarchive.midi.generation.MidiImageGeneration.java

public static void main(String[] args)
        throws IOException, InvalidMidiDataException, InterruptedException, ExecutionException {
    try (InputStream is = new FileInputStream("")) {
        final long startTime = System.currentTimeMillis();
        final ImmutablePair<String, BufferedImage> res = new MidiImageGeneration(is, 119, 5000).buildImage();
        final long endTime = System.currentTimeMillis();

        Logger.info(UserLogger.GENERAL, String.format("startTime: %s endTime: %s totalTime: %s file: %s",
                startTime, endTime, endTime - startTime, res.getLeft()));
        ImageIO.write(res.getRight(), "png", new File(String.format("/tmp/%s.png", res.getLeft())));
    }//w  w  w  .  j av a2  s . c o m
}

From source file:gov.lanl.adore.djatoka.DjatokaExtract.java

/**
 * Uses apache commons cli to parse input args. Passes parsed
 * parameters to IExtract implementation.
 * @param args command line parameters to defined input,output,etc.
 *///from  w ww. j  a va2 s  . c o m
public static void main(String[] args) {
    // create the command line parser
    CommandLineParser parser = new PosixParser();

    // create the Options
    Options options = new Options();
    options.addOption("i", "input", true, "Filepath of the input file.");
    options.addOption("o", "output", true, "Filepath of the output file.");
    options.addOption("l", "level", true, "Resolution level to extract.");
    options.addOption("d", "reduce", true, "Resolution levels to subtract from max resolution.");
    options.addOption("r", "region", true, "Format: Y,X,H,W. ");
    options.addOption("c", "cLayer", true, "Compositing Layer Index.");
    options.addOption("s", "scale", true,
            "Format: Option 1. Define a long-side dimension (e.g. 96); Option 2. Define absolute w,h values (e.g. 1024,768); Option 3. Define a single dimension (e.g. 1024,0) with or without Level Parameter; Option 4. Use a single decimal scaling factor (e.g. 0.854)");
    options.addOption("t", "rotate", true, "Number of degrees to rotate image (i.e. 90, 180, 270).");
    options.addOption("f", "format", true,
            "Mimetype of the image format to be provided as response. Default: image/jpeg");
    options.addOption("a", "AltImpl", true, "Alternate IExtract Implemenation");

    try {
        if (args.length == 0) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("gov.lanl.adore.djatoka.DjatokaExtract", options);
            System.exit(0);
        }

        // parse the command line arguments
        CommandLine line = parser.parse(options, args);
        String input = line.getOptionValue("i");
        String output = line.getOptionValue("o");

        DjatokaDecodeParam p = new DjatokaDecodeParam();
        String level = line.getOptionValue("l");
        if (level != null)
            p.setLevel(Integer.parseInt(level));
        String reduce = line.getOptionValue("d");
        if (level == null && reduce != null)
            p.setLevelReductionFactor(Integer.parseInt(reduce));
        String region = line.getOptionValue("r");
        if (region != null)
            p.setRegion(region);
        String cl = line.getOptionValue("c");
        if (cl != null) {
            int clayer = Integer.parseInt(cl);
            if (clayer > 0)
                p.setCompositingLayer(clayer);
        }
        String scale = line.getOptionValue("s");
        if (scale != null) {
            String[] v = scale.split(",");
            if (v.length == 1) {
                if (v[0].contains("."))
                    p.setScalingFactor(Double.parseDouble(v[0]));
                else {
                    int[] dims = new int[] { -1, Integer.parseInt(v[0]) };
                    p.setScalingDimensions(dims);
                }
            } else if (v.length == 2) {
                int[] dims = new int[] { Integer.parseInt(v[0]), Integer.parseInt(v[1]) };
                p.setScalingDimensions(dims);
            }
        }
        String rotate = line.getOptionValue("t");
        if (rotate != null)
            p.setRotationDegree(Integer.parseInt(rotate));
        String format = line.getOptionValue("f");
        if (format == null)
            format = "image/jpeg";
        String alt = line.getOptionValue("a");
        if (output == null)
            output = input + ".jpg";

        long x = System.currentTimeMillis();
        IExtract ex = new KduExtractExe();
        if (alt != null)
            ex = (IExtract) Class.forName(alt).newInstance();
        DjatokaExtractProcessor e = new DjatokaExtractProcessor(ex);
        e.extractImage(input, output, p, format);
        logger.info("Extraction Time: " + ((double) (System.currentTimeMillis() - x) / 1000) + " seconds");

    } catch (ParseException e) {
        logger.error("Parse exception:" + e.getMessage(), e);
    } catch (DjatokaException e) {
        logger.error("djatoka Extraction exception:" + e.getMessage(), e);
    } catch (InstantiationException e) {
        logger.error("Unable to initialize alternate implemenation:" + e.getMessage(), e);
    } catch (Exception e) {
        logger.error("Unexpected exception:" + e.getMessage(), e);
    }
}

From source file:DruidResponseTime.java

public static void main(String[] args) throws Exception {
    try (CloseableHttpClient client = HttpClients.createDefault()) {
        HttpPost post = new HttpPost("http://localhost:8082/druid/v2/?pretty");
        post.addHeader("content-type", "application/json");
        CloseableHttpResponse res;//  ww  w .  ja v a2s .c  o m

        if (STORE_RESULT) {
            File dir = new File(RESULT_DIR);
            if (!dir.exists()) {
                dir.mkdirs();
            }
        }

        int length;

        // Make sure all segments online
        System.out.println("Test if number of records is " + RECORD_NUMBER);
        post.setEntity(new StringEntity("{" + "\"queryType\":\"timeseries\","
                + "\"dataSource\":\"tpch_lineitem\"," + "\"intervals\":[\"1992-01-01/1999-01-01\"],"
                + "\"granularity\":\"all\"," + "\"aggregations\":[{\"type\":\"count\",\"name\":\"count\"}]}"));
        while (true) {
            System.out.print('*');
            res = client.execute(post);
            boolean valid;
            try (BufferedInputStream in = new BufferedInputStream(res.getEntity().getContent())) {
                length = in.read(BYTE_BUFFER);
                valid = new String(BYTE_BUFFER, 0, length, "UTF-8").contains("\"count\" : 6001215");
            }
            res.close();
            if (valid) {
                break;
            } else {
                Thread.sleep(5000);
            }
        }
        System.out.println("Number of Records Test Passed");

        for (int i = 0; i < QUERIES.length; i++) {
            System.out.println(
                    "--------------------------------------------------------------------------------");
            System.out.println("Start running query: " + QUERIES[i]);
            try (BufferedReader reader = new BufferedReader(
                    new FileReader(QUERY_FILE_DIR + File.separator + i + ".json"))) {
                length = reader.read(CHAR_BUFFER);
                post.setEntity(new StringEntity(new String(CHAR_BUFFER, 0, length)));
            }

            // Warm-up Rounds
            System.out.println("Run " + WARMUP_ROUND + " times to warm up cache...");
            for (int j = 0; j < WARMUP_ROUND; j++) {
                res = client.execute(post);
                res.close();
                System.out.print('*');
            }
            System.out.println();

            // Test Rounds
            int[] time = new int[TEST_ROUND];
            int totalTime = 0;
            System.out.println("Run " + TEST_ROUND + " times to get average time...");
            for (int j = 0; j < TEST_ROUND; j++) {
                long startTime = System.currentTimeMillis();
                res = client.execute(post);
                long endTime = System.currentTimeMillis();
                if (STORE_RESULT && j == 0) {
                    try (BufferedInputStream in = new BufferedInputStream(res.getEntity().getContent());
                            BufferedWriter writer = new BufferedWriter(
                                    new FileWriter(RESULT_DIR + File.separator + i + ".json", false))) {
                        while ((length = in.read(BYTE_BUFFER)) > 0) {
                            writer.write(new String(BYTE_BUFFER, 0, length, "UTF-8"));
                        }
                    }
                }
                res.close();
                time[j] = (int) (endTime - startTime);
                totalTime += time[j];
                System.out.print(time[j] + "ms ");
            }
            System.out.println();

            // Process Results
            double avgTime = (double) totalTime / TEST_ROUND;
            double stdDev = 0;
            for (int temp : time) {
                stdDev += (temp - avgTime) * (temp - avgTime) / TEST_ROUND;
            }
            stdDev = Math.sqrt(stdDev);
            System.out.println("The average response time for the query is: " + avgTime + "ms");
            System.out.println("The standard deviation is: " + stdDev);
        }
    }
}

From source file:com.asakusafw.yaess.bootstrap.Yaess.java

/**
 * Program entry./*from   w w w .j a v a  2  s . c om*/
 * @param args program arguments
 */
public static void main(String... args) {
    CommandLineUtil.prepareLogContext();
    YSLOG.info("I00000");
    long start = System.currentTimeMillis();
    int status = execute(args);
    long end = System.currentTimeMillis();
    YSLOG.info("I00999", status, end - start);
    System.exit(status);
}

From source file:com.vangent.hieos.empi.pixpdq.loader.PIDFeedRandomLoader.java

/**
 *
 * @param args//  ww  w.j  a v a2  s. c o m
 */
public static void main(String[] args) {
    PIDFeedRandomLoader pfl = new PIDFeedRandomLoader();
    long start = System.currentTimeMillis();
    Thread[] threads = new Thread[MAX_THREADS];
    for (int i = 0; i < MAX_THREADS; i++) {
        PIDFeedRunnable pidFeedRunnable = pfl.getPIDFeedRunnable(TEMPLATE, ENTERPRISE_ASSIGNING_AUTHORITY,
                LOCAL_ASSIGNING_AUTHORITY, RUN_COUNT_PER_THREAD, ENDPOINT);
        threads[i] = new Thread(pidFeedRunnable);
        threads[i].start();
    }
    for (int i = 0; i < threads.length; i++) {
        try {
            threads[i].join();
        } catch (InterruptedException ignore) {
        }
    }
    long elapsedTime = System.currentTimeMillis() - start;
    double txnSec = ((double) MAX_THREADS * (double) RUN_COUNT_PER_THREAD) / ((double) elapsedTime / 1000.0);
    System.out.println(" done ... TOTAL TIME = " + elapsedTime + "ms" + ", txn/sec = " + txnSec);
}

From source file:mvm.rya.indexing.external.ExternalIndexMain.java

public static void main(String[] args) throws Exception {
    Preconditions.checkArgument(args.length == 6, "java " + ExternalIndexMain.class.getCanonicalName()
            + " sparqlFile cbinstance cbzk cbuser cbpassword rdfTablePrefix.");

    final String sparqlFile = args[0];

    instStr = args[1];//from   ww  w  . ja v  a2 s  . co  m
    zooStr = args[2];
    userStr = args[3];
    passStr = args[4];
    tablePrefix = args[5];

    String queryString = FileUtils.readFileToString(new File(sparqlFile));

    // Look for Extra Indexes
    Instance inst = new ZooKeeperInstance(instStr, zooStr);
    Connector c = inst.getConnector(userStr, passStr.getBytes());

    System.out.println("Searching for Indexes");
    Map<String, String> indexTables = Maps.newLinkedHashMap();
    for (String table : c.tableOperations().list()) {
        if (table.startsWith(tablePrefix + "INDEX_")) {
            Scanner s = c.createScanner(table, new Authorizations());
            s.setRange(Range.exact(new Text("~SPARQL")));
            for (Entry<Key, Value> e : s) {
                indexTables.put(table, e.getValue().toString());
            }
        }
    }

    List<ExternalTupleSet> index = Lists.newArrayList();

    if (indexTables.isEmpty()) {
        System.out.println("No Index found");
    } else {
        for (String table : indexTables.keySet()) {
            String indexSparqlString = indexTables.get(table);
            System.out.println("====================== INDEX FOUND ======================");
            System.out.println(" table : " + table);
            System.out.println(" sparql : ");
            System.out.println(indexSparqlString);

            index.add(new AccumuloIndexSet(indexSparqlString, c, table));
        }
    }

    // Connect to Rya
    Sail s = getRyaSail();
    SailRepository repo = new SailRepository(s);
    repo.initialize();

    // Perform Query

    CountingTupleQueryResultHandler count = new CountingTupleQueryResultHandler();

    SailRepositoryConnection conn;
    if (index.isEmpty()) {
        conn = repo.getConnection();

    } else {
        ExternalProcessor processor = new ExternalProcessor(index);

        Sail processingSail = new ExternalSail(s, processor);
        SailRepository smartSailRepo = new SailRepository(processingSail);
        smartSailRepo.initialize();

        conn = smartSailRepo.getConnection();
    }

    startTime = System.currentTimeMillis();
    lastTime = startTime;
    System.out.println("Query Started");
    conn.prepareTupleQuery(QueryLanguage.SPARQL, queryString).evaluate(count);

    System.out.println("Count of Results found : " + count.i);
    System.out.println("Total query time (s) : " + (System.currentTimeMillis() - startTime) / 1000.);
}

From source file:com.johnson.grab.browser.HttpClientUtil.java

public static void main(String[] args) throws IOException, CrawlException {
    //        final String url = "http://192.168.24.248:8080/HbaseDb/youku/";
    //        String url = "http://business.sohu.com/20131021/n388557348.shtml?pvid=tc_business&a=&b=%E6%A5%BC%E5%B8%82%E6%B3%A1%E6%B2%AB%E7%A0%B4%E7%81%AD%E5%B0%86%E5%9C%A82015%E5%B9%B4%E5%BA%95%E4%B9%8B%E5%89%8D";
    final String url = "http://www.sohu.com";
    final int threadNum = 20;
    final int loop = 100;
    Thread[] threads = new Thread[threadNum];
    final List<Integer> times = new ArrayList<Integer>();
    final long s = System.currentTimeMillis();
    for (int i = 0; i < threads.length; i++) {
        threads[i] = new Thread() {
            public void run() {
                for (int i = 0; i < loop; i++) {
                    try {
                        getContent(url);
                    } catch (CrawlException e) {
                        e.printStackTrace();
                    } catch (IOException e) {
                        e.printStackTrace();
                    } catch (Throwable t) {
                        t.printStackTrace();
                    }/*from  w w  w. j a  va2  s .  co  m*/
                    long e = System.currentTimeMillis();
                    times.add((int) (e - s));
                }
            }
        };
        threads[i].start();
    }
    while (times.size() < threadNum * loop) {
        int current = times.size();
        System.out.println("total: " + threadNum * loop + ", current: " + current + ", left: "
                + (threadNum * loop - current));
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
    long e = System.currentTimeMillis();
    int totalTime = 0;
    for (Integer time : times) {
        totalTime += time;
    }
    System.out.println("------------------------------------------------------");
    System.out.println("thread num: " + threadNum + ", loop: " + loop);
    System.out.println("totalTime: " + totalTime + ", averTime: " + totalTime / (threadNum * loop));
    System.out.println("finalTime: " + (e - s) + ", throughput: " + (e - s) / (threadNum * loop));
}

From source file:cn.jumper.study.http.ClientFormLogin.java

public static void main(String[] args) throws Exception {
    BasicCookieStore cookieStore = new BasicCookieStore();
    CloseableHttpClient httpclient = HttpClients.custom().setDefaultCookieStore(cookieStore).build();

    HttpHost proxy = new HttpHost("192.168.10.3", 8080, "http");

    RequestConfig config = RequestConfig.custom().setProxy(proxy).build();

    try {/*w w w.  j  a  v a 2  s.  c om*/
        HttpGet httpget = new HttpGet("http://www.ksf-food.com/admin/Login.asp");
        httpget.setConfig(config);
        CloseableHttpResponse response1 = httpclient.execute(httpget);
        try {
            HttpEntity entity = response1.getEntity();

            System.out.println("Login form get: " + response1.getStatusLine());
            EntityUtils.consume(entity);

            System.out.println("Initial set of cookies:");
            List<Cookie> cookies = cookieStore.getCookies();
            if (cookies.isEmpty()) {
                System.out.println("None");
            } else {
                for (int i = 0; i < cookies.size(); i++) {
                    System.out.println("- " + cookies.get(i).toString());
                }
            }
        } finally {
            response1.close();
        }

        String code = "";
        try {
            HttpUriRequest httpgetCode = RequestBuilder.get()
                    .setUri("http://www.ksf-food.com/admin/inc/checkcode.asp").setConfig(config).build();

            /*
             * HttpGet httpgetCode = new HttpGet(
             * "http://www.qufuev.com/admin/inc/checkcode.asp");
             * httpgetCode.setConfig(config);
             */

            System.out.println("Executing request " + httpgetCode.getRequestLine());
            System.out.println("========================================================");
            System.out.println("==httpget header ==");
            for (Header header : httpgetCode.getAllHeaders()) {
                System.out.println(header.getName() + ":" + header.getValue());
            }
            System.out.println("==httpget header ==");

            ResponseHandler<String> responseHandler = new ResponseHandler<String>() {
                public String handleResponse(final HttpResponse response)
                        throws ClientProtocolException, IOException {
                    int status = response.getStatusLine().getStatusCode();
                    if (status >= 200 && status < 300) {
                        HttpEntity entity = response.getEntity();
                        System.out.println("==respons header ==");
                        for (Header header : response.getAllHeaders()) {
                            System.out.println(header.getName() + ":" + header.getValue());
                        }
                        System.out.println("==respons header ==");
                        String fileName = System.currentTimeMillis() + "";
                        DataOutputStream dataOutputStream = new DataOutputStream(
                                new FileOutputStream("d://test//e3//" + fileName + ".jpg"));
                        dataOutputStream.write(EntityUtils.toByteArray(entity));
                        dataOutputStream.close();
                        return ImageTest.getAllOcr("d://test//e3//" + fileName + ".jpg");
                    } else {
                        throw new ClientProtocolException("Unexpected response status: " + status);
                    }
                }

            };
            code = httpclient.execute(httpgetCode, responseHandler);
            System.out.println("ClientFormLogin.main()-CheckCode:" + code);
            System.out.println("----------------------------------------");
        } catch (IOException e) {
            e.printStackTrace();
        }

        HttpUriRequest login = RequestBuilder.post()
                .setUri(new URI("http://www.ksf-food.com/admin/Admin_ChkLogin.asp"))
                .addParameter("UserName", "username").addParameter("Password", "password")
                .addParameter("CheckCode", code).setConfig(config).build();

        System.out.println("========================================================");
        System.out.println("==httpget header ==");
        for (Header header : login.getAllHeaders()) {
            System.out.println(header.getName() + ":" + header.getValue());
        }

        CloseableHttpResponse response2 = httpclient.execute(login);
        try {
            HttpEntity entity = response2.getEntity();

            System.out.println("Login form post: " + response2.getStatusLine());
            // EntityUtils.consume(entity);
            System.out.println("ClientFormLogin.main():\\n" + EntityUtils.toString(entity, "GBK"));

            System.out.println("Post logon cookies:");
            List<Cookie> cookies = cookieStore.getCookies();
            if (cookies.isEmpty()) {
                System.out.println("None");
            } else {
                for (int i = 0; i < cookies.size(); i++) {
                    System.out.println("- " + cookies.get(i).toString());
                }
            }
        } finally {
            response2.close();
        }
    } finally {
        httpclient.close();
    }
}

From source file:eu.scape_project.pc.hadoop.TikaIdentifyHadoopJob.java

/**
 * The main entry point.//ww  w .  j a v a2  s .c  om
 */
public static void main(String[] args) throws ParseException {
    Configuration conf = new Configuration();
    GenericOptionsParser gop = new GenericOptionsParser(conf, args);
    HadoopJobCliConfig pc = new HadoopJobCliConfig();
    CommandLineParser cmdParser = new PosixParser();
    CommandLine cmd = cmdParser.parse(HadoopJobOptions.OPTIONS, gop.getRemainingArgs());
    if ((args.length == 0) || (cmd.hasOption(HadoopJobOptions.HELP_OPT))) {
        HadoopJobOptions.exit("Usage", 0);
    } else {
        HadoopJobOptions.initOptions(cmd, pc);
    }
    String dir = pc.getDirStr();

    String name = pc.getHadoopJobName();
    if (name == null || name.equals("")) {
        name = "tika_identification";
    }

    try {
        Job job = new Job(conf, name);

        // local debugging
        //            job.getConfiguration().set("mapred.job.tracker", "local");
        //            job.getConfiguration().set("fs.default.name", "file:///");

        job.setJarByClass(TikaIdentifyHadoopJob.class);

        job.setMapperClass(TikaIdentifyMapper.class);
        //job.setCombinerClass(TikaIdentifyReducer.class);
        job.setReducerClass(TikaIdentifyReducer.class);

        job.setInputFormatClass(TextInputFormat.class);

        job.setOutputFormatClass(TextOutputFormat.class);
        //SequenceFileOutputFormat.setOutputCompressionType(job, SequenceFile.CompressionType.NONE);

        //conf.setMapOutputKeyClass(Text.class);
        job.setMapOutputKeyClass(Text.class);
        job.setMapOutputValueClass(LongWritable.class);

        job.setOutputKeyClass(Text.class);
        job.setOutputValueClass(LongWritable.class);

        SequenceFileInputFormat.addInputPath(job, new Path(dir));
        String outpath = "output/" + System.currentTimeMillis() + "tid";
        FileOutputFormat.setOutputPath(job, new Path(outpath));
        job.waitForCompletion(true);
        System.out.print(outpath);
        System.exit(0);
    } catch (Exception e) {
        logger.error("I/O error", e);
    }
}

From source file:edu.msu.cme.rdp.readseq.utils.QualityTrimmer.java

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file");
    options.addOption("l", "less-than", false, "Trim at <= instead of strictly =");
    options.addOption("i", "illumina", false, "Illumina trimming mode");

    FastqWriter fastqOut = null;//from w  w  w .ja v  a2 s .  c o m
    FastaWriter fastaOut = null;

    byte qualTrim = -1;

    boolean writeFasta = true;
    boolean trimle = false;
    boolean illumina = false;

    List<SeqReader> readers = new ArrayList();
    List<File> seqFiles = new ArrayList();

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("fastq-out")) {
            writeFasta = false;
        }

        if (line.hasOption("less-than")) {
            trimle = true;
        }
        if (line.hasOption("illumina")) {
            illumina = true;
        }

        args = line.getArgs();

        if (args.length < 2) {
            throw new Exception("Unexpected number of arguments");
        }

        if (args[0].length() != 1) {
            throw new Exception("Expected single character quality score");
        }

        qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0));

        for (int index = 1; index < args.length; index++) {
            File seqFile = new File(args[index]);
            SeqReader reader;
            if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) {
                if (index + 1 == args.length) {
                    throw new Exception("Fasta files must be immediately followed by their quality file");
                }

                File qualFile = new File(args[index + 1]);
                if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) {
                    throw new Exception(seqFile + " was not followed by a fasta quality file");
                }

                reader = new QSeqReader(seqFile, qualFile);
                index++;
            } else {
                if (seqFile.getName().endsWith(".gz")) {
                    reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile)));
                } else {
                    reader = new SequenceReader(seqFile);
                }
            }

            readers.add(reader);
            seqFiles.add(seqFile);
        }
    } catch (Exception e) {
        new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] <ascii_score> <seq_file> [qual_file]",
                options, true);
        System.err.println("Error: " + e.getMessage());
        System.exit(1);
    }

    for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) {
        File seqFile = seqFiles.get(readerIndex);
        String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf("."));
        if (writeFasta) {
            fastaOut = new FastaWriter(outStem + ".fasta");
        } else {
            fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction);
        }

        int[] lengthHisto = new int[200];

        SeqReader reader = readers.get(readerIndex);

        QSequence qseq;

        long totalLength = 0;
        int totalSeqs = 0;
        long trimmedLength = 0;
        int trimmedSeqs = 0;

        int zeroLengthAfterTrimming = 0;

        long startTime = System.currentTimeMillis();

        while ((qseq = (QSequence) reader.readNextSequence()) != null) {
            char[] bases = qseq.getSeqString().toCharArray();
            byte[] qual = qseq.getQuality();

            if (bases.length != qual.length) {
                System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq");
                continue;
            }

            totalSeqs++;
            totalLength += bases.length;

            int trimIndex = -1;
            if (illumina && qual[bases.length - 1] == qualTrim) {
                trimIndex = bases.length - 1;
                while (trimIndex >= 0 && qual[trimIndex] == qualTrim) {
                    trimIndex--;
                }

                trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base
            } else if (!illumina) {
                for (int index = 0; index < bases.length; index++) {
                    if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) {
                        trimIndex = index;
                        break;
                    }
                }
            }

            String outSeq;
            byte[] outQual;
            if (trimIndex == -1) {
                outSeq = qseq.getSeqString();
                outQual = qseq.getQuality();
            } else {
                outSeq = new String(bases, 0, trimIndex);
                outQual = Arrays.copyOfRange(qual, 0, trimIndex);
                trimmedSeqs++;
            }
            int len = outSeq.length();
            trimmedLength += len;

            if (len >= lengthHisto.length) {
                lengthHisto = Arrays.copyOf(lengthHisto, len + 1);
            }
            lengthHisto[len]++;

            if (outSeq.length() == 0) {
                //System.err.println(qseq.getSeqName() + ": length 0 after trimming");
                zeroLengthAfterTrimming++;
                continue;
            }

            if (writeFasta) {
                fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq);
            } else {
                fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual);
            }
        }

        reader.close();

        if (writeFasta) {
            fastaOut.close();
        } else {
            fastqOut.close();
        }

        System.out.println(
                "Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s");
        System.out.println("Before trimming:");
        System.out.println("Total Sequences:           " + totalSeqs);
        System.out.println("Total Sequence Data:       " + totalLength);
        System.out.println("Average sequence length:   " + ((float) totalLength / totalSeqs));
        System.out.println();
        System.out.println("After trimming:");
        System.out.println("Total Sequences:           " + (totalSeqs - zeroLengthAfterTrimming));
        System.out.println("Sequences Trimmed:         " + trimmedSeqs);
        System.out.println("Total Sequence Data:       " + trimmedLength);
        System.out.println("Average sequence length:   "
                + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming)));
        System.out.println();

        System.out.println("Length\tCount");
        for (int index = 0; index < lengthHisto.length; index++) {
            if (lengthHisto[index] == 0) {
                continue;
            }

            System.out.println(index + "\t" + lengthHisto[index]);
        }

        System.out.println();
        System.out.println();
        System.out.println();
    }
}