Example usage for java.io FileWriter FileWriter

Introduction

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

Prototype

public FileWriter(FileDescriptor fd) 

Source Link

Document

Constructs a FileWriter given a file descriptor, using the platform's java.nio.charset.Charset#defaultCharset() default charset .

Usage

From source file:gov.nih.nci.caarray.plugins.agilent.EndOfLineCorrectingReaderTest.java

private File createTestFile() throws IOException {
    File file = File.createTempFile("EndOfLineCorrectingReaderTest", null);
    file.deleteOnExit();//from   w  ww.j ava2 s  .c o  m

    final FileWriter fileWriter = new FileWriter(file);
    try {
        IOUtils.copy(new StringReader(originalData), fileWriter);
    } finally {
        fileWriter.close();
    }

    return file;
}

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From source file:com.shazam.fork.listeners.RawLogCatWriter.java

@Override
public void writeLogs(TestIdentifier test, List<LogCatMessage> logCatMessages) {
    File file = fileManager.createFile(RAW_LOG, pool, serial, test);
    FileWriter fileWriter = null;
    try {/*from w  ww  . j a v  a2  s . com*/
        fileWriter = new FileWriter(file);
        for (LogCatMessage logCatMessage : logCatMessages) {
            write(logCatMessage.toString(), fileWriter);
            write("\n", fileWriter);
        }
    } catch (IOException e) {
        throw new RuntimeException(e);
    } finally {
        closeQuietly(fileWriter);
    }
}

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From source file:test.gov.nih.nci.system.web.client.HardDriveClient.java

private static File marshall(HardDrive hardDrive) throws IOException, XMLUtilityException {
    String namespacePrefix = "gme://caCORE.caCORE/3.2/";
    String jaxbContextName = "gov.nih.nci.cacoresdk.domain.onetomany.bidirectional";
    Marshaller marshaller = new JAXBMarshaller(true, jaxbContextName, namespacePrefix);
    Unmarshaller unmarshaller = new JAXBUnmarshaller(true, jaxbContextName);
    XMLUtility myUtil = new XMLUtility(marshaller, unmarshaller);
    File myFile = new File("HardDrive.xml");
    FileWriter myWriter = new FileWriter(myFile);
    myUtil.toXML(hardDrive, myWriter);/*  w  w w  . ja v  a2  s . c  o  m*/
    myWriter.close();
    return myFile;
}

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From source file:de.ipbhalle.metfrag.main.CommandLineTool.java

/**
 * @param args//ww  w  .  j  ava  2  s .  com
 * @throws Exception 
 */
public static void main(String[] args) {

    CommandLineParser parser = new PosixParser();

    // create the Options
    Options options = new Options();

    options.addOption("d", "database", true, "database: " + Databases.getString() + " (default: kegg)");
    options.addOption("l", "localdb", true,
            "use a local database together with a settings file for candidate search (default: not used) note: only usable if pubchem database is selected (-d)");
    options.addOption("a", "mzabs", true,
            "allowed absolute (Da) mass deviation of fragment and peak masses (default: 0.01)");
    options.addOption("p", "mzppm", true,
            "allowed relative (ppm) mass deviation of fragment and peak masses (default: 10)");
    options.addOption("s", "searchppm", true,
            "relative (ppm) mass deviation used for candidate search in given compound database (-d) (default: 10; not used by default if sdf database is selected (-d))\n");
    options.addOption("n", "exactmass", true,
            "neutral mass of measured compound used for candidate search in database (-d) (mandatory)");
    options.addOption("b", "biological", false,
            "only consider compounds including CHNOPS atoms (not used by default)");
    options.addOption("i", "databaseids", true,
            "database ids of compounds used for in silico fragmentation (separated by ,) (not used by default; not used if sdf database is selected (-d)) note: given ids must be valid ids of given database (-d)");
    options.addOption("t", "treedepth", true,
            "treedepth used for in silico fragmentation (default: 2) note: high values result in high computation time");
    options.addOption("M", "mode", true,
            "mode used for measured ms/ms spectrum:\n" + Modes.getString() + "(default: 3)");
    options.addOption("f", "formula", true,
            "molecular formula of measured compound used for candidate search in database (-d) (not used by default; not used if sdf database is selected (-d))");
    options.addOption("B", "breakrings", false,
            "allow splitting of aromatic rings of candidate structures during in silico fragmentation (not used by default)");
    options.addOption("F", "storefragments", false,
            "store in silico generated fragments of candidate molecules (not used by default)");
    options.addOption("R", "resultspath", true, "directory where result files are stored (default: /tmp)");
    options.addOption("L", "sdffile", true,
            "location of the local sdf file (mandatory if sdf database (-d) is selected)");
    options.addOption("h", "help", false, "print help");
    options.addOption("D", "spectrumfile", true,
            "file containing peak data (mandatory) note: commandline options overwrite parameters given in the spectrum data file");
    options.addOption("T", "threads", true,
            "number of threads used for fragment calculation (default: number of available cpu cores)");
    options.addOption("c", "chemspidertoken", true,
            "Token for ChemSpider database search (not used by default; only necessary (mandatory) if ChemSpider database (-d) is selected)");
    options.addOption("v", "verbose", false,
            "get more output information during the processing (not used by default)");
    options.addOption("S", "samplename", true,
            "name of the sample measured (mandatory) note: result files are stored with given value");
    options.addOption("P", "saveparameters", false, "save used parameters (not used by default)");
    options.addOption("e", "printexamplespecfile", false,
            "print an example spectrum data file (not used by default)");
    options.addOption("C", "charge", true,
            "charge used in combination with mode (-M):\n" + Charges.getString() + " (default: 1)");
    options.addOption("r", "range", true,
            "range of candidates that will be processed: N (first N), M-N (from M to N), M- (from M), -N (till N); if N is greater than the number of candidates it will be set accordingly");

    // parse the command line arguments
    CommandLine line = null;
    try {
        line = parser.parse(options, args);
    } catch (ParseException e1) {
        System.out.println(e1.getMessage());
        System.out.println("Error: Could not parse option parameters.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }

    if (line == null) {
        System.out.println("Error: Could not parse option parameters.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }
    if (checkInitialParamsPresent(line, options))
        System.exit(0);

    if (!checkSpectrumFile(line)) {
        System.out.println("Error: Option parameters are not set correctly.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }
    if (!parseSpectrumFile(spectrumfile)) {
        System.out.println("Error: Could not correctly parse the spectrum data file.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }

    int successfulSet = setParameters(line, options);
    if (successfulSet == 2)
        System.exit(0);
    if (successfulSet != 0) {
        System.out.println("Error: Option parameters are not set correctly.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }

    boolean successfulChecked = true;
    if (successfulSet == 0)
        successfulChecked = checkParameters();
    if (saveParametersIsSet) {
        try {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(
                    resultspath + System.getProperty("file.separator") + "parameters_" + sampleName + ".txt")));
            bwriter.write(getParameters());
            bwriter.close();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }

    try {
        boolean isPositive = true;
        if (charge.getValue() == 2)
            isPositive = false;
        spec = new WrapperSpectrum(peaksString, mode.getValueWithOffset(), exactMass.getValue(), isPositive);
    } catch (Exception e) {
        System.out.println("Error: Could not parse spectrum correctly. Check the given peak list.");
        System.exit(1);
    }

    if (!successfulChecked) {
        System.out.println("Error: Option parameters are not set correctly.");
        System.out.println("Use help -h (--help) for information.");
        System.exit(1);
    }

    List<MetFragResult> results = null;
    String pathToStoreFrags = "";
    if (storeFragments)
        pathToStoreFrags = resultspath;
    //run metfrag when all checks were successful

    if (usesdf) {
        try {
            if (verbose) {
                System.out.println("start fragmenter with local database");
                System.out.println("using database " + database);
            }
            results = MetFrag.startConvenienceSDF(spec, mzabs.getValue(), mzppm.getValue(),
                    searchppm.getValue(), true, breakRings, treeDepth.getValue(), true, true, true, false,
                    Integer.MAX_VALUE, true, sdfFile, "", null, searchppmIsSet, pathToStoreFrags,
                    numberThreads.getValue(), verbose, sampleName, onlyBiologicalCompounds);
        } catch (Exception e) {
            System.out.println("Error: " + e.getMessage());
            System.out.println("Error: Could not perform in silico fragmentation step.");
            System.exit(1);
        }
    } else {
        try {
            if (verbose) {
                if (!localdbIsSet)
                    System.out.println("start fragmenter with web database");
                else
                    System.out.println("start fragmenter with local database");
                System.out.println("using database " + database);
            }
            results = MetFrag.startConvenience(database, databaseIDs, formula, exactMass.getValue(), spec,
                    useProxy, mzabs.getValue(), mzppm.getValue(), searchppm.getValue(), true, breakRings,
                    treeDepth.getValue(), true, false, true, false, startindex.getValue(), endindex.getValue(),
                    true, pathToStoreFrags, numberThreads.getValue(), chemSpiderToken, verbose, sampleName,
                    localdb, onlyBiologicalCompounds, dblink, dbuser, dbpass, uniquebyinchi);
        } catch (Exception e) {
            e.printStackTrace();
            System.out.println("Error: " + e.getMessage());
            System.out.println("Error: Could not perform in silico fragmentation step.");
            System.exit(1);
        }
    }

    saveResults(results);

}

---

From source file:io.proleap.cobol.TestGenerator.java

public static void generateTestClass(final File cobolInputFile, final File outputDirectory,
        final String packageName) throws IOException {
    final File parentDirectory = cobolInputFile.getParentFile();
    final String inputFilename = getInputFilename(cobolInputFile);
    final File outputFile = new File(
            outputDirectory + "/" + inputFilename + OUTPUT_FILE_SUFFIX + JAVA_EXTENSION);

    final boolean createdNewFile = outputFile.createNewFile();

    if (createdNewFile) {
        LOG.info("Creating unit test {}.", outputFile);

        final PrintWriter pWriter = new PrintWriter(new FileWriter(outputFile));
        final String cobolInputFileName = cobolInputFile.getPath().replace("\\", "/");
        final CobolSourceFormat format = getCobolSourceFormat(parentDirectory);

        pWriter.write("package " + packageName + ";\n");
        pWriter.write("\n");
        pWriter.write("import java.io.File;\n");
        pWriter.write("\n");
        pWriter.write("import io.proleap.cobol.applicationcontext.CobolGrammarContextFactory;\n");
        pWriter.write("import io.proleap.cobol.preprocessor.CobolPreprocessor.CobolSourceFormatEnum;\n");
        pWriter.write("import io.proleap.cobol.runner.CobolParseTestRunner;\n");
        pWriter.write("import io.proleap.cobol.runner.impl.CobolParseTestRunnerImpl;\n");
        pWriter.write("import org.junit.Test;\n");
        pWriter.write("\n");
        pWriter.write("public class " + inputFilename + "Test {\n");
        pWriter.write("\n");
        pWriter.write("   @Test\n");
        pWriter.write("   public void test() throws Exception {\n");
        pWriter.write("      CobolGrammarContextFactory.configureDefaultApplicationContext();\n");
        pWriter.write("\n");
        pWriter.write("      final File inputFile = new File(\"" + cobolInputFileName + "\");\n");
        pWriter.write("      final CobolParseTestRunner runner = new CobolParseTestRunnerImpl();\n");
        pWriter.write("      runner.parseFile(inputFile, CobolSourceFormatEnum." + format + ");\n");
        pWriter.write("   }\n");
        pWriter.write("}");

        pWriter.flush();//from w ww .  j  a v a2 s  .c om
        pWriter.close();
    }
}

---

From source file:com.amazonaws.util.FileUtils.java

/**
 * Appends the given data to the file specified in the input and returns the
 * reference to the file./*w ww.  j a  v  a 2  s.  c o  m*/
 * 
 * @param file
 * @param dataToAppend
 * @return reference to the file.
 * @throws IOException
 */
public static File appendDataToTempFile(File file, String dataToAppend) throws IOException {
    FileWriter outputWriter = new FileWriter(file);

    try {
        outputWriter.append(dataToAppend);
    } finally {
        outputWriter.close();
    }

    return file;
}

---

From source file:com.wso2telco.services.bw.FileUtil.java

public static void fileWrite(String filePath, String data) throws IOException {
    BufferedWriter out = null;//from  ww w  .  j  av a  2 s .  c  om
    try {
        out = new BufferedWriter(new FileWriter(filePath));
        out.write(data);
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        out.close();
    }

}

---

From source file:WarUtil.java

private static void writeLastModifiled(File file, long time) {
    BufferedWriter writer = null;
    try {//from   w w w . ja va  2  s .  co  m
        if (!file.exists()) {
            file.createNewFile();
        }
        writer = new BufferedWriter(new FileWriter(file));
        writer.write(Long.toString(time));
        writer.flush();
    } catch (Exception e) {

    }
}

---

From source file:com.spike.tg4w.htmlunit.XmlTestResultImpl.java

public XmlTestResultImpl(String filename, String encoding) throws IOException {
    this.writer = new FileWriter(filename);
    if (encoding == null) {
        encoding = "ISO-8859-1";
    }/*from   w  ww . ja  va  2  s . c om*/
    write("<?xml version='1.0' encoding='" + encoding + "'?>");
    write("<tests>");
    this.writeDir = (new File(filename)).getParent();

    Runtime.getRuntime().addShutdownHook(new ShutDownHook(this));
}

---

From source file:biz.c24.batchdemo.writers.SplittingFileWriterSource.java

@Override
public void initialise(StepExecution stepExecution) {
    // Extract the name of the file we're supposed to be writing to
    String fileName = stepExecution.getJobParameters().getString("output.file");

    // Remove any leading file:// if it exists
    if (fileName.startsWith("file://")) {
        fileName = fileName.substring("file://".length());
    }//from  ww  w  .j  a  v  a 2s .c om

    try {
        outputFile = new FileWriter(fileName);
    } catch (IOException ioEx) {
        throw new RuntimeException(ioEx);
    }

}

---

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