Example usage for java.io FileReader FileReader

List of usage examples for java.io FileReader FileReader

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Introduction

In this page you can find the example usage for java.io FileReader FileReader.

Prototype

public FileReader(FileDescriptor fd)

Source Link

Document

Creates a new FileReader , given the FileDescriptor to read, using the platform's java.nio.charset.Charset#defaultCharset() default charset .

Usage

From source file:currencyexchange.JSONCurrency.java

public static ArrayList<CurrencyUnit> getCurrencyUnitsJSON() {
    try {//  www  .j a  va 2 s .  c o m
        FileReader reader = new FileReader(filePath);

        JSONParser jsonParser = new JSONParser();
        JSONObject jsonObject = (JSONObject) jsonParser.parse(reader);

        JSONArray currencyUnits = (JSONArray) jsonObject.get("units");

        ArrayList<CurrencyUnit> currencies = new ArrayList<CurrencyUnit>();

        Iterator i = currencyUnits.iterator();
        while (i.hasNext()) {
            JSONObject e = (JSONObject) i.next();
            CurrencyUnit currency = new CurrencyUnit((String) e.get("CountryCurrency"),
                    (String) e.get("Units"));

            currencies.add(currency);
        }
        return currencies;

    } catch (FileNotFoundException ex) {
        ex.printStackTrace();
    } catch (IOException ex) {
        ex.printStackTrace();
    } catch (ParseException | NullPointerException ex) {
        ex.printStackTrace();
    }

    return null;
}

From source file:Main.java

/**
 * Converts a PEM formatted cert in a given file to the binary DER format.
 *
 * @param pemPathname the location of the certificate to convert.
 * @return array of bytes that represent the certificate in DER format.
 * @throws IOException if the file cannot be read.
 *///  w  w  w.ja v  a  2s  .c  o  m
public static byte[] pemToDer(String pemPathname) throws IOException {
    BufferedReader reader = new BufferedReader(new FileReader(pemPathname));
    StringBuilder builder = new StringBuilder();

    // Skip past leading junk lines, if any.
    String line = reader.readLine();
    while (line != null && !line.contains(BEGIN_MARKER))
        line = reader.readLine();

    // Then skip the BEGIN_MARKER itself, if present.
    while (line != null && line.contains(BEGIN_MARKER))
        line = reader.readLine();

    // Now gather the data lines into the builder.
    while (line != null && !line.contains(END_MARKER)) {
        builder.append(line.trim());
        line = reader.readLine();
    }

    reader.close();
    return Base64.decode(builder.toString(), Base64.DEFAULT);
}

From source file:eqtlmappingpipeline.util.ModuleEqtlGeuvadisReplication.java

/**
 * @param args the command line arguments
 *//*from w  w  w  .ja  va 2  s  . c o m*/
public static void main(String[] args) throws IOException, LdCalculatorException {

    System.out.println(HEADER);
    System.out.println();
    System.out.flush(); //flush to make sure header is before errors
    try {
        Thread.sleep(25); //Allows flush to complete
    } catch (InterruptedException ex) {
    }

    CommandLineParser parser = new PosixParser();
    final CommandLine commandLine;
    try {
        commandLine = parser.parse(OPTIONS, args, true);
    } catch (ParseException ex) {
        System.err.println("Invalid command line arguments: " + ex.getMessage());
        System.err.println();
        new HelpFormatter().printHelp(" ", OPTIONS);
        System.exit(1);
        return;
    }

    final String[] genotypesBasePaths = commandLine.getOptionValues("g");
    final RandomAccessGenotypeDataReaderFormats genotypeDataType;
    final String replicationQtlFilePath = commandLine.getOptionValue("e");
    final String interactionQtlFilePath = commandLine.getOptionValue("i");
    final String outputFilePath = commandLine.getOptionValue("o");
    final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld"));
    final int window = Integer.parseInt(commandLine.getOptionValue("w"));

    System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths));
    System.out.println("Interaction file: " + interactionQtlFilePath);
    System.out.println("Replication file: " + replicationQtlFilePath);
    System.out.println("Output: " + outputFilePath);
    System.out.println("LD: " + ldCutoff);
    System.out.println("Window: " + window);

    try {
        if (commandLine.hasOption("G")) {
            genotypeDataType = RandomAccessGenotypeDataReaderFormats
                    .valueOf(commandLine.getOptionValue("G").toUpperCase());
        } else {
            if (genotypesBasePaths[0].endsWith(".vcf")) {
                System.err.println(
                        "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file.");
                System.exit(1);
                return;
            }
            try {
                genotypeDataType = RandomAccessGenotypeDataReaderFormats
                        .matchFormatToPath(genotypesBasePaths[0]);
            } catch (GenotypeDataException e) {
                System.err
                        .println("Unable to determine input 1 type based on specified path. Please specify -G");
                System.exit(1);
                return;
            }
        }
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G")
                + "\" is not a valid input data format");
        System.exit(1);
        return;
    }

    final RandomAccessGenotypeData genotypeData;

    try {
        genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null,
                0.8);
    } catch (TabixFileNotFoundException e) {
        LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n"
                + "Please see README on how to create a tabix file");
        System.exit(1);
        return;
    } catch (IOException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (IncompatibleMultiPartGenotypeDataException e) {
        LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (GenotypeDataException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    }

    ChrPosTreeMap<ArrayList<EQTL>> replicationQtls = new QTLTextFile(replicationQtlFilePath, false)
            .readQtlsAsTreeMap();

    int interactionSnpNotInGenotypeData = 0;
    int noReplicationQtlsInWindow = 0;
    int noReplicationQtlsInLd = 0;
    int multipleReplicationQtlsInLd = 0;
    int replicationTopSnpNotInGenotypeData = 0;

    final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0');
    final String[] outputLine = new String[14];
    int c = 0;
    outputLine[c++] = "Chr";
    outputLine[c++] = "Pos";
    outputLine[c++] = "SNP";
    outputLine[c++] = "Gene";
    outputLine[c++] = "Module";
    outputLine[c++] = "DiscoveryZ";
    outputLine[c++] = "ReplicationZ";
    outputLine[c++] = "DiscoveryZCorrected";
    outputLine[c++] = "ReplicationZCorrected";
    outputLine[c++] = "DiscoveryAlleleAssessed";
    outputLine[c++] = "ReplicationAlleleAssessed";
    outputLine[c++] = "bestLd";
    outputLine[c++] = "bestLd_dist";
    outputLine[c++] = "nextLd";
    outputWriter.writeNext(outputLine);

    HashSet<String> notFound = new HashSet<>();

    CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t');
    interactionQtlReader.readNext();//skip header
    String[] interactionQtlLine;
    while ((interactionQtlLine = interactionQtlReader.readNext()) != null) {

        String snp = interactionQtlLine[1];
        String chr = interactionQtlLine[2];
        int pos = Integer.parseInt(interactionQtlLine[3]);
        String gene = interactionQtlLine[4];
        String alleleAssessed = interactionQtlLine[9];
        String module = interactionQtlLine[12];
        double discoveryZ = Double.parseDouble(interactionQtlLine[10]);

        GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos);

        if (interactionQtlVariant == null) {
            System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos);
            ++interactionSnpNotInGenotypeData;
            continue;
        }

        EQTL bestMatch = null;
        double bestMatchR2 = Double.NaN;
        Ld bestMatchLd = null;
        double nextBestR2 = Double.NaN;

        ArrayList<EQTL> sameSnpQtls = replicationQtls.get(chr, pos);

        if (sameSnpQtls != null) {
            for (EQTL sameSnpQtl : sameSnpQtls) {
                if (sameSnpQtl.getProbe().equals(gene)) {
                    bestMatch = sameSnpQtl;
                    bestMatchR2 = 1;
                }
            }
        }

        NavigableMap<Integer, ArrayList<EQTL>> potentionalReplicationQtls = replicationQtls.getChrRange(chr,
                pos - window, true, pos + window, true);

        for (ArrayList<EQTL> potentialReplicationQtls : potentionalReplicationQtls.values()) {

            for (EQTL potentialReplicationQtl : potentialReplicationQtls) {

                if (!potentialReplicationQtl.getProbe().equals(gene)) {
                    continue;
                }

                GeneticVariant potentialReplicationQtlVariant = genotypeData.getSnpVariantByPos(
                        potentialReplicationQtl.getRsChr().toString(), potentialReplicationQtl.getRsChrPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getRsChr().toString() + ":"
                            + potentialReplicationQtl.getRsChrPos());
                    ++replicationTopSnpNotInGenotypeData;
                    continue;
                }

                Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant);
                double r2 = ld.getR2();

                if (r2 > 1) {
                    r2 = 1;
                }

                if (bestMatch == null) {
                    bestMatch = potentialReplicationQtl;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                } else if (r2 > bestMatchR2) {
                    bestMatch = potentialReplicationQtl;
                    nextBestR2 = bestMatchR2;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                }

            }
        }

        double replicationZ = Double.NaN;
        double replicationZCorrected = Double.NaN;
        double discoveryZCorrected = Double.NaN;

        String replicationAlleleAssessed = null;

        if (bestMatch != null) {
            replicationZ = bestMatch.getZscore();
            replicationAlleleAssessed = bestMatch.getAlleleAssessed();

            if (pos != bestMatch.getRsChrPos()) {

                String commonHap = null;
                double commonHapFreq = -1;
                for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) {

                    double f = hapFreq.getValue();

                    if (f > commonHapFreq) {
                        commonHapFreq = f;
                        commonHap = hapFreq.getKey();
                    }

                }

                String[] commonHapAlleles = StringUtils.split(commonHap, '/');

                discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1;
                replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            } else {

                discoveryZCorrected = discoveryZ;
                replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            }

        }

        c = 0;
        outputLine[c++] = chr;
        outputLine[c++] = String.valueOf(pos);
        outputLine[c++] = snp;
        outputLine[c++] = gene;
        outputLine[c++] = module;
        outputLine[c++] = String.valueOf(discoveryZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected);
        outputLine[c++] = alleleAssessed;
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAlleleAssessed());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getRsChrPos()));
        outputLine[c++] = String.valueOf(nextBestR2);
        outputWriter.writeNext(outputLine);

    }

    outputWriter.close();

    for (String e : notFound) {
        System.err.println("Not found: " + e);
    }

    System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData);
    System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow);
    System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd);
    System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd);
    System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData);

}

From source file:client.communication.SocketClient.java

public static void init() {
    BufferedReader buf;//from www  . ja  va  2  s. c  o  m

    try {
        buf = new BufferedReader(new FileReader("src/ip.txt"));

        serverAddress = buf.readLine();

        //            System.out.println("Address: " + serverAddress);

        buf.close();
    } catch (FileNotFoundException e) {
        System.err.println(e.getMessage());
    } catch (IOException e) {
        System.err.println(e.getMessage());
    }
}

From source file:Main.java

public static XMLStreamReader parse(File xmlFile) throws IOException, XMLStreamException {
    FileReader input = new FileReader(xmlFile);
    XMLInputFactory xif = XMLInputFactory.newInstance();
    XMLStreamReader xmlStreamReader = xif.createXMLStreamReader(input);

    return xmlStreamReader;
}

From source file:Main.java

public static String readFileContent(String file) throws IOException {
    BufferedReader reader = new BufferedReader(new FileReader(file));
    String line = null;//from   ww w  .  j  a v a2  s  . co m
    StringBuilder stringBuilder = new StringBuilder();
    String ls = System.getProperty("line.separator");

    while ((line = reader.readLine()) != null) {
        stringBuilder.append(line);
        stringBuilder.append(ls);
    }

    return stringBuilder.toString();
}

From source file:Main.java

/**
 * read file to string list, a element of list is a line
 *
 * @param filePath/*from  ww w  .  ja  v  a 2  s. co  m*/
 * @return if file not exist, return null, else return content of file
 * @throws IOException
 *             if an error occurs while operator BufferedReader
 */
public static List<String> readFileToList(String filePath) {
    File file = new File(filePath);
    List<String> fileContent = new ArrayList<String>();
    if (file == null || !file.isFile()) {
        return null;
    }

    BufferedReader reader = null;
    try {
        reader = new BufferedReader(new FileReader(file));
        String line = null;
        while ((line = reader.readLine()) != null) {
            fileContent.add(line);
        }
        reader.close();
        return fileContent;
    } catch (IOException e) {
        throw new RuntimeException("IOException occurred. ", e);
    } finally {
        if (reader != null) {
            try {
                reader.close();
            } catch (IOException e) {
                throw new RuntimeException("IOException occurred. ", e);
            }
        }
    }
}

From source file:Main.java

/**
 * Read file, one line as a element of the String List
 * //from w w w.j a  v a 2 s  .co  m
 * @param filePath
 *            The path of the file
 * @return List<String> Return file content as a String List, if the file
 *         doesn't exist return null
 */
public static List<String> readFileToList(String filePath) {
    File file = new File(filePath);
    List<String> fileContent = new ArrayList<String>();
    if (file != null && file.isFile()) {
        BufferedReader reader = null;
        try {
            reader = new BufferedReader(new FileReader(file));
            String line = null;
            while ((line = reader.readLine()) != null) {
                fileContent.add(line);
            }
            reader.close();
            return fileContent;
        } catch (IOException e) {
            throw new RuntimeException("IOException occurred. ", e);
        } finally {
            if (reader != null) {
                try {
                    reader.close();
                } catch (IOException e) {
                    throw new RuntimeException("IOException occurred. ", e);
                }
            }
        }
    }
    return null;
}

From source file:Main.java

public static String readFromFile(final File file) {
    final StringBuilder ret = new StringBuilder();
    try {//from w  ww.ja v a  2  s  .  c  om
        final BufferedReader input = new BufferedReader(new FileReader(file), 4096);
        int len;
        final char buff[] = new char[4096];
        while ((len = input.read(buff, 0, 4096)) != -1) {
            ret.append(buff, 0, len);
        }
        input.close();
    } catch (final IOException exception) {
        exception.printStackTrace();
    }
    return ret.toString();
}

From source file:Main.java

/**
 * Converts a plain text file into TE3-input file
 *
 * @param plainfile//from   w  w w. j  a  v  a  2  s .  c  om
 * @return
 */
public static String Plain2TE3(String plainfile) {
    String outputfile = null;
    try {
        String line;
        boolean textfound = false;
        String header = "";
        String footer = "";
        String text = "";

        //process header (and dct)/text/footer
        outputfile = plainfile + ".TE3input";
        BufferedWriter te3writer = new BufferedWriter(new FileWriter(new File(outputfile)));
        BufferedReader inputReader = new BufferedReader(new FileReader(new File(plainfile)));

        try {

            SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
            String dctvalue = sdf.format(new Date());

            te3writer.write("<?xml version=\"1.0\" ?>");
            te3writer.write(
                    "\n<TimeML xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://timeml.org/timeMLdocs/TimeML_1.2.1.xsd\">\n");
            te3writer.write("\n<DOCID>" + (new File(plainfile)).getName() + "</DOCID>\n");
            te3writer.write("\n<DCT><TIMEX3 tid=\"t0\" type=\"DATE\" value=\"" + dctvalue
                    + "\" temporalFunction=\"false\" functionInDocument=\"CREATION_TIME\">" + dctvalue
                    + "</TIMEX3></DCT>\n");

            // read out text
            while ((line = inputReader.readLine()) != null) {
                text += line + "\n";
            }

            te3writer.write("\n<TEXT>\n" + text + "</TEXT>\n");
            te3writer.write("</TimeML>\n");

        } finally {
            if (inputReader != null) {
                inputReader.close();
            }
            if (te3writer != null) {
                te3writer.close();
            }
        }
    } catch (Exception e) {
        System.err.println("Errors found (TML_file_utils):\n\t" + e.toString() + "\n");
        if (System.getProperty("DEBUG") != null && System.getProperty("DEBUG").equalsIgnoreCase("true")) {
            e.printStackTrace(System.err);
        }
        return null;
    }
    return outputfile;
}