Example usage for java.util HashMap toString

Introduction

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

Prototype

public String toString() 

Source Link

Document

Returns a string representation of the object.

Usage

From source file:Main.java

public static void main(String[] args) {
    HashMap<Character, Integer> map = new HashMap<Character, Integer>();
    String test = "BUNANA";
    char[] chars = test.toCharArray();

    for (int i = 0; i < chars.length; i++) {
        if (!map.containsKey(chars[i])) {
            map.put(chars[i], 1);/* w  w w. j a  v a  2  s. c  o  m*/
        }
        map.put(chars[i], map.get(chars[i]) + 1);
    }

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

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From source file:nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression.ReadGenoAndAsFromIndividual.java

public static void readGenoAndAsFromIndividual(String loc_of_bam1, String genotype_loc,
        String coupling_location, String outputLocation, String snpLocation) throws IOException, Exception {

    if (GlobalVariables.verbosity >= 1) {
        //Print ASREADS header
        System.out.println("---- Starting ASREADS for the following settings: ----");
        System.out.println("\t input bam:         " + loc_of_bam1);
        System.out.println("\t genotype location: " + genotype_loc);
        System.out.println("\t coupling file:     " + coupling_location);
        System.out.println("\t output location:   " + outputLocation);
        if (!snpLocation.equals("")) {
            System.out.println("\t snp Location:      " + snpLocation);
        } else {/*from w w  w  .j  av a  2s.  c o  m*/
            System.out.println("\t snp Location:      " + "NONE");
        }

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

    //parse command line arguments
    String loc_of_bam;
    loc_of_bam = loc_of_bam1;
    System.out.println("Location of bam file: ");
    System.out.println(loc_of_bam);

    if (!new File(loc_of_bam).exists()) {
        throw new IllegalArgumentException("ERROR! Location of bam file is not an existing file. Exitting.");
    } else {
        if (GlobalVariables.verbosity >= 10) {
            System.out.println("Location of bam file is an existing file, will continue.");
        }
    }

    RandomAccessGenotypeData TTdataSet;
    VcfGenotypeData VCFdataSet;
    HashMap<String, GeneticVariant> variantIdMap;
    String[] individual_names;

    String tabixLoc = genotype_loc + ".tbi";

    //open vcf dataset
    //based on extention and existance of both files. 
    if (FilenameUtils.isExtension(genotype_loc, "gz") && new File(tabixLoc).exists()
            && new File(genotype_loc).exists()) {
        try {
            VCFdataSet = new VcfGenotypeData(new File(genotype_loc), new File(tabixLoc), 0.99);
            variantIdMap = VCFdataSet.getVariantIdMap();
            individual_names = VCFdataSet.getSampleNames();
        } catch (IOException ex) {
            System.err.println("Error reading vcf dataset: " + genotype_loc);
            throw new IllegalArgumentException();
        }

    } else if (new File(genotype_loc + "/GenotypeMatrix.dat").exists()) {
        //assuming trityper dataset based on the genotype matrix
        try {
            TTdataSet = new TriTyperGenotypeData(new File(genotype_loc));
            variantIdMap = TTdataSet.getVariantIdMap();
            individual_names = TTdataSet.getSampleNames();
        } catch (IOException ex) {
            System.err.println("Error reading trityper dataset: " + genotype_loc);
            throw new IllegalArgumentException();
        }

    } else {
        throw new IllegalDataException("could not find a Trityper or vcf file in the genotype location");
    }

    //get the variants in the variantIdMAP

    Set<String> snpNames = variantIdMap.keySet();

    ArrayList<String> SNPsToAnalyze;
    SNPsToAnalyze = new ArrayList<String>();

    //If available, read the file with rs numbers.
    if (!snpLocation.equals("")) {

        ArrayList<String> includeSNPs = UtilityMethods.readFileIntoStringArrayList(snpLocation);

        int snpsNotFound = 0;

        for (String snp_to_include : includeSNPs) {
            if (snpNames.contains(snp_to_include)) {
                SNPsToAnalyze.add(snp_to_include);
            } else {
                snpsNotFound++;
            }
        }

        if (GlobalVariables.verbosity >= 1) {
            System.out.println("WARNING: Did not find " + Integer.toString(snpsNotFound) + " out of "
                    + Integer.toString(includeSNPs.size()) + " SNPs in the include file.");
        }
    } else {
        for (String snp_to_include : snpNames) {
            SNPsToAnalyze.add(snp_to_include);
        }
    }

    //String path = "/gcc/groups/lld/tmp01/projects/bamFiles/";
    //sample_map contains all the individuals that are in the sample file.
    HashMap sample_map = convert_individual_names(individual_names, coupling_location);

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("Sample names were loaded.");
    }
    if (GlobalVariables.verbosity >= 100) {
        System.out.println(sample_map.toString());
    }

    //Twice because my files have the .MERGED.sorted.bam suffix attached to them.
    String sample_name = FilenameUtils
            .getBaseName(FilenameUtils.getBaseName(FilenameUtils.getBaseName(loc_of_bam)));

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("sample_name: " + sample_name);
        System.out.println("sample_map:  " + sample_map.toString());
    }

    Object sample_idx = sample_map.get(sample_name);

    if (sample_idx == null) {
        throw new IllegalArgumentException("Couldn't find the filename in the sample names. Quitting.");
    }

    int sample_index = Integer.parseInt(sample_idx.toString());

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("sample_index: " + sample_index);
    }

    //bam file path and filename
    String path_and_filename = loc_of_bam;
    File sample_file = new File(path_and_filename);

    SamReader bam_file = SamReaderFactory.makeDefault().open(sample_file);

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("Initialized for reading bam file");
    }

    PrintWriter writer = new PrintWriter(outputLocation, "UTF-8");

    int i = 0;
    for (String i_snp : SNPsToAnalyze) {

        //System.out.println(i_snp);

        GeneticVariant this_variant = variantIdMap.get(i_snp);

        String chromosome = this_variant.getSequenceName();
        String position = String.valueOf(this_variant.getStartPos());

        // We only do analyses if we find a SNP and it is biallelic
        // However this is trityper data, so if we use
        // the allele count is used for the check of something. 

        //DO NOT ENTER A SEPARATED GENOMIC DATASET OTHERWISE THIS WILL BREAK.
        if (this_variant.isSnp() & this_variant.isBiallelic()) {

            String row_of_table = get_allele_specific_overlap_at_snp(this_variant, sample_index, chromosome,
                    position, bam_file);

            //commented out the phasing part.

            writer.println(chromosome + "\t" + position + "\t" + i_snp + "\t"
                    + this_variant.getVariantAlleles().getAllelesAsChars()[0] + "\t"
                    + this_variant.getVariantAlleles().getAllelesAsChars()[1] + "\t" + row_of_table + "\t"
                    + Arrays.toString(this_variant.getSampleVariants().get(sample_index).getAllelesAsChars()) //+ "\t" +
            //Boolean.toString(this_variant.getSamplePhasing().get(sample_index))
            );
        }

        i++;

        if ((i % 10000 == 0) && (GlobalVariables.verbosity >= 10)) {

            System.out.println("Finished " + Integer.toString(i) + " SNPs");

        }

    }
    writer.close();
}

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From source file:com.datatorrent.demos.ads.HdfsHashMapOutputOperator.java

@Override
public byte[] getBytesForTuple(HashMap<Object, Object> t) {
    return t.toString().getBytes();
}

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From source file:jsentvar.JsonReaderTest.java

/**
 * Test of reader method, of class JsonReader.
 * @throws java.io.IOException/*from w  ww  . j  ava2s .  com*/
 */
@Test
public void testReader() throws IOException {
    System.out.println("JsonReader.reader");
    String inputFileName = "resources/test/text_doc0.json";
    JsonReader instance = new JsonReader();
    String expResult = FileUtils.readFileToString(new File("resources/test/doc0Result.txt"), "utf8").trim();
    HashMap<String, HashMap<Integer, Integer>> result0 = instance.reader(inputFileName);
    String result = result0.toString();
    System.out.println("Esperat:\n" + expResult);
    System.out.println("Obtingut:\n" + result);
    assertEquals(expResult, result);

}

---

From source file:jsentvar.GenerateTestsResults.java

public void jsonReaderResult() throws IOException {
    String possFile = "resources/text_doc0.json";
    JsonReader jreader = new JsonReader();
    HashMap<String, HashMap<Integer, Integer>> poss = jreader.reader(possFile);
    System.out.println(poss.toString());
    FileUtils.writeStringToFile(new File("resources/test/doc0Result.txt"), poss.toString(), "utf8");

}

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From source file:org.openmrs.module.dataaggregation.web.controller.DataAggregationManageController.java

@RequestMapping(value = "/module/dataaggregation/manage", method = RequestMethod.GET)
public void manage(ModelMap model) {
    model.addAttribute("user", Context.getAuthenticatedUser());

    DataAggregationService service = Context.getService(DataAggregationService.class);
    model.addAttribute("patients", service.getAllPatientNames());

    DataAggregationService serv = Context.getService(DataAggregationService.class);
    HashMap<String, Integer> diseaseBurden = serv.getDiseaseBurden();//I have no idea why it gives this error, the method exists

    //convert the data to a string that is roughly csv   
    model.addAttribute("diseaseBurden", diseaseBurden.toString());
}

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From source file:org.apache.storm.command.rebalance.java

@SuppressWarnings("rawtypes")
public void realMain(String[] args) throws Exception {
    CmdLineParser parser = new CmdLineParser(this);
    parser.setUsageWidth(80);//from  ww w . ja  va  2 s .com
    try {
        parser.parseArgument(args);
    } catch (CmdLineException e) {
        System.err.println(e.getMessage());
        _help = true;
    }
    if (_help) {
        parser.printUsage(System.err);
        System.err.println();
        return;
    }

    if (_numWorkers <= 0) {
        throw new IllegalArgumentException("Need at least one worker");
    }
    if (_name == null || _name.isEmpty()) {
        throw new IllegalArgumentException("name must be something");
    }

    String info = "Topology " + _name + " is rebalancing ";
    NimbusClient client = null;
    Map conf = Utils.readStormConfig();
    try {
        client = NimbusClient.getConfiguredClient(conf);
        RebalanceOptions options = new RebalanceOptions();
        options.set_wait_secs(_wait);
        info += " with delaySesc " + _wait + " ";
        options.set_num_workers(_numWorkers);
        info += " number of workers " + _numWorkers;
        if (_executor != null) {
            HashMap<String, Integer> executors = parseExecutor(_executor);
            options.set_num_executors(executors);
            info += " with executor " + executors.toString() + " ";
        }
        client.getClient().rebalance(_name, options);
        System.out.println(info);
    } catch (Exception e) {
        System.out.println(CoreUtil.stringifyError(e));
        printUsage();
    } finally {
        if (client != null) {
            client.close();
        }
    }

}

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From source file:se.vgregion.service.innovationsslussen.ldap.TextFrag.java

@SuppressWarnings("unchecked")
@Override//from  w  w w .  j a  v a 2  s . c  o m
public String toString() {
    try {
        if (toStringRunning) {
            return " recursive call to " + getClass().getSimpleName() + ".toString()";
        }
        toStringRunning = true;
        HashMap hm = new HashMap(new BeanMap(this));
        hm.remove("class");
        return hm.toString();
    } finally {
        toStringRunning = false;
    }
}

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From source file:ru.apertum.qsystem.reports.formirovators.DistributionJobDay.java

@Override
public String validate(String driverClassName, String url, String username, String password,
        HttpRequest request, HashMap<String, String> params) {
    //   ?  /*from w w  w  . ja v a  2s.  c  o  m*/
    QLog.l().logger().trace("?  \"" + params.toString() + "\".");
    if (params.size() == 1) {
        // date
        Date date;
        String sdate;
        try {
            date = Uses.format_dd_MM_yyyy.parse(params.get("date"));
            sdate = (new java.text.SimpleDateFormat("yyyy-MM-dd")).format(date);
        } catch (ParseException ex) {
            return "<br>  ! ? ?    (..).";
        }
        paramMap.put("sdate", sdate);
        paramMap.put("date", date);
    } else {
        return "<br>  !";
    }
    return null;
}

---

From source file:ru.apertum.qsystem.reports.formirovators.DistributionMedDayServices.java

@Override
public String validate(String driverClassName, String url, String username, String password,
        HttpRequest request, HashMap<String, String> params) {
    //   ?  /*w  w  w.java 2s.co m*/
    QLog.l().logger().trace("?  \"" + params.toString() + "\".");
    if (params.size() == 1) {
        // date/service_id/service
        Date date;
        String sdate;
        try {
            date = Uses.format_dd_MM_yyyy.parse(params.get("date"));
            sdate = (new java.text.SimpleDateFormat("yyyy-MM-dd")).format(date);
        } catch (NumberFormatException | ParseException ex) {
            return "<br>  ! ? ?    (..).";
        }
        paramMap.put("sdate", sdate);
        paramMap.put("date", date);
    } else {
        return "<br>  !";
    }
    return null;
}

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