Example usage for java.util List addAll

List of usage examples for java.util List addAll

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Introduction

In this page you can find the example usage for java.util List addAll.

Prototype

boolean addAll(Collection<? extends E> c);

Source Link

Document

Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator (optional operation).

Usage

From source file:AmazonKinesisCreate.java

public static void main(String[] args) throws Exception {
    init();//from   w  ww  .ja  v a 2s . c o  m

    final String myStreamName = "philsteststream";
    final Integer myStreamSize = 1;

    // Create a stream. The number of shards determines the provisioned throughput.

    CreateStreamRequest createStreamRequest = new CreateStreamRequest();
    createStreamRequest.setStreamName(myStreamName);
    createStreamRequest.setShardCount(myStreamSize);

    // pt
    kinesisClient.createStream(createStreamRequest);

    // The stream is now being created.
    LOG.info("Creating Stream : " + myStreamName);
    waitForStreamToBecomeAvailable(myStreamName);

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }
    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
    }

    LOG.info("Putting records in stream : " + myStreamName);
    // Write 10 records to the stream
    for (int j = 0; j < 10; j++) {

        try {
            PutRecordRequest putRecordRequest = new PutRecordRequest();
            putRecordRequest.setStreamName(myStreamName);
            putRecordRequest.setData(ByteBuffer.wrap(String.format("testData-%d", j).getBytes()));
            putRecordRequest.setPartitionKey(String.format("partitionKey-%d", j));
            PutRecordResult putRecordResult = kinesisClient.putRecord(putRecordRequest);
            System.out.println("Successfully putrecord, partition key : " + putRecordRequest.getPartitionKey()
                    + ", ShardID : " + putRecordResult.getShardId());
            Thread.sleep(1000);

        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    // Delete the stream.

    /*
    LOG.info("Deleting stream : " + myStreamName);
    DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
    deleteStreamRequest.setStreamName(myStreamName);
            
    kinesisClient.deleteStream(deleteStreamRequest);
    // The stream is now being deleted.
    LOG.info("Stream is now being deleted : " + myStreamName);
            
    LOG.info("Streaming completed" + myStreamName);
    */

}

From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step3HITCreator.java

@SuppressWarnings("unchecked")
public static void main(String[] args) throws IOException {
    String inputDir = args[0];//from w w  w .j  a  v  a 2s  .c  o m
    File outputDir = new File(args[1]);

    // sandbox or real MTurk?
    final boolean useSandbox = false;

    // required only for pilot
    // final int randomArgumentPairsCount = 50;

    // pseudo-random generator
    final Random random = new Random(1);

    for (Map.Entry<String, SortedSet<String>> entry : BATCHES.entrySet()) {
        Step3HITCreator hitCreator = new Step3HITCreator(useSandbox);
        hitCreator.outputPath = new File(outputDir, entry.getKey());
        hitCreator.initialize();

        // we will process only a subset first
        List<ArgumentPair> allArgumentPairs = new ArrayList<>();

        Collection<File> files = IOHelper.listXmlFiles(new File(inputDir));

        System.out.println(files);

        // read all files for the given batch
        for (File file : files) {
            if (entry.getValue().contains(file.getName())) {
                allArgumentPairs.addAll((List<ArgumentPair>) XStreamTools.getXStream().fromXML(file));
            }
        }

        // we have to shuffle them
        Collections.shuffle(allArgumentPairs, random);

        // only for pilot
        // List<ArgumentPair> selectedArgumentPairs = allArgumentPairs
        //      .subList(0, randomArgumentPairsCount);

        // for (ArgumentPair argumentPair : selectedArgumentPairs) {
        for (ArgumentPair argumentPair : allArgumentPairs) {
            hitCreator.process(argumentPair);
        }

        hitCreator.collectionProcessComplete();
    }
}

From source file:AmazonKinesisDelete.java

public static void main(String[] args) throws Exception {
    init();//w  w w  . jav a 2s .  c om

    //final String myStreamName = "anotestBstream";
    //final Integer myStreamSize = 1;

    // Create a stream. The number of shards determines the provisioned throughput.

    //        CreateStreamRequest createStreamRequest = new CreateStreamRequest();
    //        createStreamRequest.setStreamName(myStreamName);
    //        createStreamRequest.setShardCount(myStreamSize);

    // pt
    //       kinesisClient.createStream(createStreamRequest);

    // The stream is now being created.
    //       LOG.info("Creating Stream : " + myStreamName);
    //       waitForStreamToBecomeAvailable(myStreamName);

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }

    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
        String actStreamName = streamNames.get(i);

        DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
        //deleteStreamRequest.setStreamName(myStreamName);
        deleteStreamRequest.setStreamName(actStreamName);

        kinesisClient.deleteStream(deleteStreamRequest);
        // The stream is now being deleted.
        LOG.info("Stream is now being deleted : " + actStreamName);
    }

    /*      
          LOG.info("Putting records in stream : " + myStreamName);
          // Write 10 records to the stream
          for (int j = 0; j < 10; j++) {
    PutRecordRequest putRecordRequest = new PutRecordRequest();
    putRecordRequest.setStreamName(myStreamName);
    putRecordRequest.setData(ByteBuffer.wrap(String.format("testData-%d", j).getBytes()));
    putRecordRequest.setPartitionKey(String.format("partitionKey-%d", j));
    PutRecordResult putRecordResult = kinesisClient.putRecord(putRecordRequest);
    System.out.println("Successfully putrecord, partition key : " + putRecordRequest.getPartitionKey()
            + ", ShardID : " + putRecordResult.getShardId());
          }
    */

    // Delete the stream.

    /*      LOG.info("Deleting stream : " + myStreamName);
          DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
          deleteStreamRequest.setStreamName(myStreamName);
            
          kinesisClient.deleteStream(deleteStreamRequest);
          // The stream is now being deleted.
          LOG.info("Stream is now being deleted : " + myStreamName);
                  
          LOG.info("Streaming completed" + myStreamName);
    */

}

From source file:TestDumpRecord.java

public static void main(String[] args) throws NITFException {
    List<String> argList = Arrays.asList(args);
    List<File> files = new LinkedList<File>();
    for (String arg : argList) {
        File f = new File(arg);
        if (f.isDirectory()) {
            File[] dirFiles = f.listFiles(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    String ext = FilenameUtils.getExtension(name).toLowerCase();
                    return ext.matches("nitf|nsf|ntf");
                }//from   w  w w  . j a  v a2  s  . c  om
            });
            files.addAll(Arrays.asList(dirFiles));
        } else
            files.add(f);
    }

    Reader reader = new Reader();
    for (File file : files) {
        PrintStream out = System.out;

        out.println("=== " + file.getAbsolutePath() + " ===");
        IOHandle handle = new IOHandle(file.getAbsolutePath());
        Record record = reader.read(handle);
        dumpRecord(record, reader, out);
        handle.close();

        record.destruct(); // tells the memory manager to decrement the ref
        // count
    }
}

From source file:AmazonKinesisGet.java

public static void main(String[] args) throws Exception {
    init();/*w w  w .j  a  v a2  s .c  o m*/

    final String myStreamName = "philsteststream";
    final Integer myStreamSize = 1;

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);

        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }
    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
    }

    //System.out.println(streamNames.get(0));
    String myownstream = streamNames.get(0);

    // Retrieve the Shards from a Stream
    DescribeStreamRequest describeStreamRequest = new DescribeStreamRequest();
    describeStreamRequest.setStreamName(myownstream);
    DescribeStreamResult describeStreamResult;
    List<Shard> shards = new ArrayList<>();
    String lastShardId = null;

    do {
        describeStreamRequest.setExclusiveStartShardId(lastShardId);
        describeStreamResult = kinesisClient.describeStream(describeStreamRequest);
        shards.addAll(describeStreamResult.getStreamDescription().getShards());
        if (shards.size() > 0) {
            lastShardId = shards.get(shards.size() - 1).getShardId();
        }
    } while (describeStreamResult.getStreamDescription().getHasMoreShards());

    // Get Data from the Shards in a Stream
    // Hard-coded to use only 1 shard
    String shardIterator;
    GetShardIteratorRequest getShardIteratorRequest = new GetShardIteratorRequest();
    getShardIteratorRequest.setStreamName(myownstream);
    //get(0) shows hardcoded to 1 stream
    getShardIteratorRequest.setShardId(shards.get(0).getShardId());
    // using TRIM_HORIZON but could use alternatives
    getShardIteratorRequest.setShardIteratorType("TRIM_HORIZON");

    GetShardIteratorResult getShardIteratorResult = kinesisClient.getShardIterator(getShardIteratorRequest);
    shardIterator = getShardIteratorResult.getShardIterator();

    // Continuously read data records from shard.
    List<Record> records;

    while (true) {
        // Create new GetRecordsRequest with existing shardIterator.
        // Set maximum records to return to 1000.

        GetRecordsRequest getRecordsRequest = new GetRecordsRequest();
        getRecordsRequest.setShardIterator(shardIterator);
        getRecordsRequest.setLimit(1000);

        GetRecordsResult result = kinesisClient.getRecords(getRecordsRequest);

        // Put result into record list. Result may be empty.
        records = result.getRecords();

        // Print records
        for (Record record : records) {
            ByteBuffer byteBuffer = record.getData();
            System.out.println(String.format("Seq No: %s - %s", record.getSequenceNumber(),
                    new String(byteBuffer.array())));
        }

        try {
            Thread.sleep(1000);
        } catch (InterruptedException exception) {
            throw new RuntimeException(exception);
        }

        shardIterator = result.getNextShardIterator();
    }

}

From source file:com.act.lcms.MassCalculator2.java

public static void main(String[] args) throws Exception {
    CommandLine cl = CLI_UTIL.parseCommandLine(args);

    if (cl.hasOption(OPTION_LICENSE_FILE)) {
        LOGGER.info("Using license file at %s", cl.getOptionValue(OPTION_LICENSE_FILE));
        LicenseManager.setLicenseFile(cl.getOptionValue(OPTION_LICENSE_FILE));
    }//from   www  .j  a v  a 2s .c  om

    List<String> inchis = new ArrayList<>();

    if (cl.hasOption(OPTION_INPUT_FILE)) {
        try (BufferedReader reader = new BufferedReader(new FileReader(cl.getOptionValue(OPTION_INPUT_FILE)))) {
            String line;
            while ((line = reader.readLine()) != null) {
                inchis.add(line);
            }
        }
    }

    if (cl.getArgList().size() > 0) {
        LOGGER.info("Reading %d InChIs from the command line", cl.getArgList().size());
        inchis.addAll(cl.getArgList());
    }

    try (PrintWriter writer = new PrintWriter(
            cl.hasOption(OPTION_OUTPUT_FILE) ? new FileWriter(cl.getOptionValue(OPTION_OUTPUT_FILE))
                    : new OutputStreamWriter(System.out))) {
        writer.format("InChI\tMass\tCharge\n");

        for (String inchi : inchis) {
            try {
                Pair<Double, Integer> massAndCharge = calculateMassAndCharge(inchi);
                writer.format("%s\t%.6f\t%3d\n", inchi, massAndCharge.getLeft(), massAndCharge.getRight());
            } catch (MolFormatException e) {
                LOGGER.error("Unable to compute mass for %s: %s", inchi, e.getMessage());
            }
        }
    }
}

From source file:ca.on.oicr.pde.deciders.GenomicAlignmentNovoalignDecider.java

public static void main(String args[]) {

    List<String> params = new ArrayList<String>();
    params.add("--plugin");
    params.add(GenomicAlignmentNovoalignDecider.class.getCanonicalName());
    params.add("--");
    params.addAll(Arrays.asList(args));
    System.out.println("Parameters: " + Arrays.deepToString(params.toArray()));
    net.sourceforge.seqware.pipeline.runner.PluginRunner.main(params.toArray(new String[params.size()]));

}

From source file:com.twitter.bazel.checkstyle.CppCheckstyle.java

public static void main(String[] args) throws IOException {
    CommandLineParser parser = new DefaultParser();

    // create the Options
    Options options = new Options();
    options.addOption(Option.builder("f").required(true).hasArg().longOpt("extra_action_file")
            .desc("bazel extra action protobuf file").build());
    options.addOption(Option.builder("c").required(true).hasArg().longOpt("cpplint_file")
            .desc("Executable cpplint file to invoke").build());

    try {/*from  w ww . j av a2 s.c o m*/
        // parse the command line arguments
        CommandLine line = parser.parse(options, args);

        String extraActionFile = line.getOptionValue("f");
        String cpplintFile = line.getOptionValue("c");

        Collection<String> sourceFiles = getSourceFiles(extraActionFile);
        if (sourceFiles.size() == 0) {
            LOG.fine("No cpp files found by checkstyle");
            return;
        }

        LOG.fine(sourceFiles.size() + " cpp files found by checkstyle");

        // Create and run the command
        List<String> commandBuilder = new ArrayList<>();
        commandBuilder.add(cpplintFile);
        commandBuilder.add("--linelength=100");
        // TODO: https://github.com/twitter/heron/issues/466,
        // Remove "runtime/references" when we fix all non-const references in our codebase.
        // TODO: https://github.com/twitter/heron/issues/467,
        // Remove "runtime/threadsafe_fn" when we fix all non-threadsafe libc functions
        commandBuilder.add("--filter=-build/header_guard,-runtime/references,-runtime/threadsafe_fn");
        commandBuilder.addAll(sourceFiles);
        runLinter(commandBuilder);

    } catch (ParseException exp) {
        LOG.severe(String.format("Invalid input to %s: %s", CLASSNAME, exp.getMessage()));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java " + CLASSNAME, options);
    }
}

From source file:diffhunter.DiffHunter.java

/**
 * @param args the command line arguments
 * @throws org.apache.commons.cli.ParseException
 * @throws java.io.IOException//from  ww w .  j  a  v a  2  s. co m
 */
public static void main(String[] args) throws ParseException, IOException {

    //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString();

    // TODO code application logic here
    /*args = new String[]
    {
    "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData"
    };*/

    /*args = new String[]
    {
    "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData"
    };*/
    Options options = new Options();

    // add t option
    options.addOption("i", "index", false, "Indexing BED files.");
    options.addOption("b", "bed", true, "bed file to be indexed");
    options.addOption("o", "output", true, "Folder that the index/comparison file will be created.");
    options.addOption("r", "reference", true, "Reference annotation file to be used for indexing");
    options.addOption("c", "compare", false, "Finding differences between two conditions");
    options.addOption("1", "first", true, "First sample index location");
    options.addOption("2", "second", true, "Second sample index location");
    options.addOption("w", "window", true, "Length of window for identifying differences");
    options.addOption("s", "sliding", true, "Length of sliding");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);

    boolean indexing = false;
    boolean comparing = false;

    //Indexing!
    if (cmd.hasOption("i")) {
        //if(cmd.hasOption("1"))
        //System.err.println("sasan");

        //System.out.println("sasa");
        indexing = true;

    } else if (cmd.hasOption("c")) {
        //System.err.println("");
        comparing = true;

    } else {
        //System.err.println("Option is not deteced.");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("diffhunter", options);
        return;
    }

    //Indexing is selected
    //
    if (indexing == true) {
        //Since indexing is true.
        //User have to provide file for indexing.
        if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String bedfile_ = cmd.getOptionValue("b");
        String reference_file = cmd.getOptionValue("r");
        String folder_loc = cmd.getOptionValue("o");

        String sample_name = FilenameUtils.getBaseName(bedfile_);

        try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(
                Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) {
            Indexer indexing_ = new Indexer(reference_file);
            indexing_.Make_Index(B2, bedfile_,
                    Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString());
            B2.close();

        }
    } else if (comparing == true) {
        if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1")
                || cmd.hasOption("2"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String folder_loc = cmd.getOptionValue("o");
        int window_ = Integer.parseInt(cmd.getOptionValue("w"));
        //int window_=600;

        int slide_ = Integer.parseInt(cmd.getOptionValue("s"));

        String first = cmd.getOptionValue("1").replace("_BDB", "");
        String second = cmd.getOptionValue("2").replace("_BDB", "");
        String reference_file = cmd.getOptionValue("r");
        //String folder_loc=cmd.getOptionValue("o");

        String sample_name_first = FilenameUtils.getBaseName(first);
        String sample_name_second = FilenameUtils.getBaseName(second);

        Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first);
        Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second);

        List<String> first_condition_genes = Files
                .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        List<String> second_condition_genes = Files
                .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        System.out.println("First and second condition are loaded!!! ");
        List<String> intersection_ = new ArrayList<>(first_condition_genes);
        intersection_.retainAll(second_condition_genes);

        BufferedWriter output = new BufferedWriter(
                new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt")
                        .toAbsolutePath().toString(), false));
        List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>());
        Worker_New worker_class = new Worker_New();
        worker_class.Read_Reference(reference_file);

        while (!intersection_.isEmpty()) {
            List<String> selected_genes = new ArrayList<>();
            //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));}
            //else selected_genes.addAll(intersection_.subList(0, 10000));
            if (intersection_.size() <= intersection_.size()) {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            } else {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            }
            intersection_.removeAll(selected_genes);
            //System.out.println("Intersection count is:"+intersection_.size());
            //final List<Result_Window> resultssss_=new ArrayList<>();
            IntStream.range(0, selected_genes.size()).parallel().forEach(i -> {
                System.out.println(selected_genes.get(i) + "\tprocessing......");
                String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2";
                int start = worker_class.dic_genes.get(gene_of_interest).start_loc;
                int end = worker_class.dic_genes.get(gene_of_interest).end_loc;

                Map<Integer, Integer> first_ = Collections.EMPTY_MAP;
                try {
                    first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }

                Map<Integer, Integer> second_ = Collections.EMPTY_MAP;
                try {
                    second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }
                List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_);
                List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_);
                //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i));
                // System.out.println("top_window_first_Count\t"+top_windows_first.size());
                // System.out.println("top_window_second_Count\t"+top_windows_second.size());
                if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) {
                    return;
                }

                List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start,
                        end, top_windows_first, top_windows_second, second_, first_, sample_name_first,
                        sample_name_second, 0.01);
                if (!res_temp.isEmpty()) {
                    final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01));

                } //System.out.println(selected_genes.get(i)+"\tprocessed.");

            });

            /*selected_genes.parallelStream().forEach(i ->
             {
                    
                    
             });*/
            List<Double> pvals = new ArrayList<>();

            for (int i = 0; i < final_results.size(); i++) {
                pvals.add(final_results.get(i).p_value);
            }
            List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals);

            System.out.println("Writing to file...");
            output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR");
            output.newLine();

            for (int i = 0; i < final_results.size(); i++) {
                Result_Window item = final_results.get(i);
                output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t"
                        + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value
                        + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
                output.newLine();
            }

            /* for (Result_Window item : final_results)
             {
            output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
            output.newLine();
             }
               */
            final_results.clear();

        }
        output.close();

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

}

From source file:com.act.analysis.similarity.SimilarityAnalysis.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//from   w w  w .  ja  v  a  2 s. c  om
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    LicenseManager.setLicenseFile(cl.getOptionValue(OPTION_LICENSE_FILE));

    if (cl.hasOption(OPTION_TARGET_INCHI) && cl.hasOption(OPTION_TARGET_FILE)) {
        System.err.format("Specify only one of -%s or -%s\n", OPTION_TARGET_INCHI, OPTION_TARGET_FILE);
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    List<SimilarityOperator> querySimilarityOperators = new ArrayList<>();
    List<String> header = new ArrayList<>();
    header.add("name");
    header.add("id");
    header.add("inchi");

    if (cl.hasOption(OPTION_QUERY_INCHI) && !cl.hasOption(OPTION_QUERY_FILE)) {
        SimilarityOperator so = makeSimilarityOperators("from inchi", cl.getOptionValue(OPTION_QUERY_INCHI));
        so.init();
        querySimilarityOperators.add(so);
        header.addAll(so.getResultFields());
    } else if (cl.hasOption(OPTION_QUERY_FILE) && !cl.hasOption(OPTION_QUERY_INCHI)) {
        TSVParser parser = new TSVParser();
        parser.parse(new File(cl.getOptionValue(OPTION_QUERY_FILE)));
        for (Map<String, String> row : parser.getResults()) {
            System.out.format("Compiling query for %s, %s\n", row.get("name"), row.get("inchi"));
            SimilarityOperator so = makeSimilarityOperators(row.get("name"), row.get("inchi"));
            so.init();
            querySimilarityOperators.add(so);
            header.addAll(so.getResultFields());
        }
    } else {
        System.err.format("Specify exactly one of -%s or -%s\n", OPTION_QUERY_INCHI, OPTION_QUERY_FILE);
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    List<Map<String, String>> targetChemicals = null;
    if (cl.hasOption(OPTION_TARGET_INCHI) && !cl.hasOption(OPTION_TARGET_FILE)) {
        String inchi = cl.getOptionValue(OPTION_TARGET_INCHI);
        targetChemicals = Collections.singletonList(new HashMap<String, String>() {
            {
                put("name", "direct-input");
                put("id", null);
                put("inchi", inchi);
            }
        });
    } else if (cl.hasOption(OPTION_TARGET_FILE) && !cl.hasOption(OPTION_TARGET_INCHI)) {
        TSVParser parser = new TSVParser();
        parser.parse(new File(cl.getOptionValue(OPTION_TARGET_FILE)));
        targetChemicals = parser.getResults();
    } else {
        System.err.format("Specify exactly one of -%s or -%s\n", OPTION_TARGET_INCHI, OPTION_TARGET_FILE);
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    AlignmentMoleculeFactory alignmentMoleculeFactory = new AlignmentMoleculeFactory();

    // TODO: add symmetric computations for target as query and each query as target.
    TSVWriter<String, String> writer = new TSVWriter<>(header);
    writer.open(new File(cl.getOptionValue(OPTION_OUTPUT_FILE)));
    try {
        for (Map<String, String> row : targetChemicals) {
            Molecule targetMol = MolImporter.importMol(row.get("inchi"));
            Cleaner.clean(targetMol, 3); // This will assign 3D atom coordinates to the MolAtoms in targetMol.
            Molecule targetFragment = findLargestFragment(targetMol.convertToFrags());
            AlignmentMolecule am = alignmentMoleculeFactory.create(targetFragment,
                    AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE);
            Map<String, String> outputRow = new HashMap<>(row);
            System.out.format("Processing target %s\n", row.get("name"));
            for (SimilarityOperator so : querySimilarityOperators) {
                System.out.format("  running query %s\n", so.getName());
                Map<String, Double> results = so.calculateSimilarity(am);
                outputRow.putAll(doubleMapToStringMap(results));
            }
            writer.append(outputRow);
            writer.flush();
        }
    } finally {
        if (writer != null) {
            writer.close();
        }
    }
    System.out.format("Done\n");
}