Example usage for java.io BufferedWriter BufferedWriter

List of usage examples for java.io BufferedWriter BufferedWriter

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Introduction

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

Prototype

public BufferedWriter(Writer out)

Source Link

Document

Creates a buffered character-output stream that uses a default-sized output buffer.

Usage

From source file:com.orange.mmp.bind.JSONClientBinding.java

/**
 *    Sends the request to WebService and return an object built from
 *    JSON response./*from   w w w  .  j  a v a 2 s  .  c  om*/
 *    @return A binding object in a JSONObject, JSONArray or String
 */
public Object getResponse(InputStream postData) throws BindingException {
    StringWriter responseContent = new StringWriter();
    BufferedReader reader = null;
    BufferedWriter writer = null;
    //Get response
    try {
        this.getHttpConnection().init(this.buildURL(), this.timeout);
        if (postData != null)
            this.getHttpConnection().sendData(postData);
        InputStream httpIn = this.getHttpConnection().getData();
        if (httpIn != null) {
            writer = new BufferedWriter(responseContent);
            reader = new BufferedReader(new InputStreamReader(httpIn, Constants.DEFAULT_ENCODING));
            String line = null;
            while ((line = reader.readLine()) != null) {
                writer.write(line);
                writer.newLine();
                writer.flush();
            }
        } else
            return null;

    } catch (UnsupportedEncodingException uee) {
        throw new BindingException("Unsupported encoding from " + this.epr + " : " + uee.getMessage());
    } catch (IOException ioe) {
        throw new BindingException("Failed to get response : " + ioe.getMessage());
    } catch (MMPNetException mne) {
        throw new BindingException("Failed to get response : " + mne.getMessage());
    } finally {
        try {
            if (reader != null)
                reader.close();
            if (writer != null)
                writer.close();
            this.releaseConnection();
        } catch (MMPNetException mne) {
            //Nop, logs in AOP
        } catch (IOException ioe) {
            //Nop, logs in AOP
        }
    }

    //Parse response
    if (responseContent == null)
        throw new BindingException("Failed to parse response : empty result");
    String jsonString = responseContent.toString();
    if (jsonString.length() == 0)
        throw new BindingException("Failed to parse response : empty result");
    try {
        JSONTokener tokener = new JSONTokener(jsonString);
        return tokener.nextValue();
    } catch (JSONException je) {
        throw new BindingException("Failed to parse response : " + je.getMessage());
    }
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.snpData.SetTissueListener.java

@Override
public void handleEvent(Event event) {
    Vector<String> values = this.ui.getValues();
    Vector<String> samples = this.ui.getSamples();
    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".subject_mapping.tmp");
    File mappingFile = ((SnpData) this.dataType).getMappingFile();
    if (mappingFile == null) {
        this.ui.displayMessage("Error: no subject to sample mapping file");
    }//w w w.  j a  v  a 2  s. c om
    try {
        FileWriter fw = new FileWriter(file);
        BufferedWriter out = new BufferedWriter(fw);

        try {
            BufferedReader br = new BufferedReader(new FileReader(mappingFile));
            String line;
            while ((line = br.readLine()) != null) {
                String[] fields = line.split("\t", -1);
                String sample = fields[3];
                String tissueType;
                if (samples.contains(sample)) {
                    tissueType = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + fields[4]
                        + "\t" + tissueType + "\t" + fields[6] + "\t" + fields[7] + "\t" + "PLATFORM+TISSUETYPE"
                        + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.ui.displayMessage("File error: " + e.getLocalizedMessage());
            out.close();
            e.printStackTrace();
        }
        out.close();
        try {
            File fileDest;
            if (mappingFile != null) {
                String fileName = mappingFile.getName();
                mappingFile.delete();
                fileDest = new File(this.dataType.getPath() + File.separator + fileName);
            } else {
                fileDest = new File(this.dataType.getPath() + File.separator
                        + this.dataType.getStudy().toString() + ".subject_mapping");
            }
            FileUtils.moveFile(file, fileDest);
            ((SnpData) this.dataType).setMappingFile(fileDest);
        } catch (IOException ioe) {
            this.ui.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.ui.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.ui.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnJavaFieldCutter.java

public void subsetFile(InputStream in, String outfile, Set<Integer> columns, Long numCases, String delimiter) {
    try {/*from  ww  w  .j  ava2  s .  co  m*/
        Scanner scanner = new Scanner(in);

        dbgLog.fine("outfile=" + outfile);

        BufferedWriter out = new BufferedWriter(new FileWriter(outfile));
        scanner.useDelimiter("\\n");

        for (long caseIndex = 0; caseIndex < numCases; caseIndex++) {
            if (scanner.hasNext()) {
                String[] line = (scanner.next()).split(delimiter, -1);
                List<String> ln = new ArrayList<String>();
                for (Integer i : columns) {
                    ln.add(line[i]);
                }
                out.write(StringUtils.join(ln, "\t") + "\n");
            } else {
                throw new RuntimeException("Tab file has fewer rows than the determined number of cases.");
            }
        }

        while (scanner.hasNext()) {
            if (!"".equals(scanner.next())) {
                throw new RuntimeException(
                        "Tab file has extra nonempty rows than the determined number of cases.");

            }
        }

        scanner.close();
        out.close();

    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }

}

From source file:eu.h2020.symbiote.model.Registry.java

public void registerMapping(BigInteger mappingId, BigInteger modelId1, BigInteger modelId2, String mapping)
        throws UnsupportedEncodingException {
    // use library to parse mapping file to RDF, then read RDFXML into store
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    try (PrintWriter writer = new PrintWriter(new BufferedWriter(new OutputStreamWriter(out, "UTF-8")), true)) {
        AlignmentParser parser = new AlignmentParser(0);
        parser.initAlignment(null);//from  w  w  w.j a va2 s . co  m
        try {
            parser.parseString(mapping).render(new RDFRendererVisitor(writer));
        } catch (AlignmentException e) {
            log.error("Couldn't load the alignment:", e);
        }
        writer.flush();
    }
    String mappingRDF = out.toString();
    Model model = ModelFactory.createDefaultModel();
    model.read(new ByteArrayInputStream(out.toByteArray()), null, RDFFormat.RDFXML.toString());

    tripleStore.insertGraph(Ontology.getMappingGraphURI(mappingId), model, RDFFormat.RDFXML);
    tripleStore.insertGraph(Ontology.MAPPING_GRAPH, Ontology.getMappingMetadata(modelId1, modelId2, mappingId),
            RDFFormat.NTriples);
    log.debug(String.format("mapping registered: modelId1={}, modelId2={}, mapping={}", modelId1, modelId2,
            mappingRDF));
}

From source file:edu.cmu.cs.lti.ark.fn.data.prep.ParsePreparation.java

/**
 * Converts a POS tagged file into conll format
 * @param posFile/*  ww w .  j  a  v  a2  s  . c om*/
 * @param conllInputFile
 */
public static void printCoNLLTypeInput(String posFile, String conllInputFile) throws IOException {
    List<String> posSentences = readLines(posFile);
    BufferedWriter bWriter = new BufferedWriter(new FileWriter(conllInputFile));
    try {
        for (String posSentence : posSentences) {
            posSentence = replaceSentenceWithPTBWords(posSentence);
            ArrayList<String> words = new ArrayList<String>();
            ArrayList<String> pos = new ArrayList<String>();
            ArrayList<String> parents = new ArrayList<String>();
            ArrayList<String> labels = new ArrayList<String>();
            StringTokenizer st = new StringTokenizer(posSentence.trim());
            while (st.hasMoreTokens()) {
                String token = st.nextToken();
                int lastIndex = token.lastIndexOf('_');
                String word = token.substring(0, lastIndex);
                String POS = token.substring(lastIndex + 1);
                words.add(word);
                pos.add(POS);
                parents.add("0");
                labels.add("SUB");
            }
            writeStuff(bWriter, words, pos, parents, labels);
        }
    } finally {
        IOUtils.closeQuietly(bWriter);
    }
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetSiteIdListener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setSiteIdUI.getValues();
    Vector<String> samples = this.setSiteIdUI.getSamples();
    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".subject_mapping.tmp");
    File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
    if (stsmf == null) {
        this.setSiteIdUI.displayMessage("Error: no subject to sample mapping file");
    }//from w  w  w.j  a  v  a 2  s  .  com
    try {
        FileWriter fw = new FileWriter(file);
        BufferedWriter out = new BufferedWriter(fw);
        out.write(
                "study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");

        try {
            BufferedReader br = new BufferedReader(new FileReader(stsmf));
            String line = br.readLine();
            while ((line = br.readLine()) != null) {
                String[] fields = line.split("\t", -1);
                String sample = fields[3];
                String site;
                if (samples.contains(sample)) {
                    site = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + site + "\t" + fields[2] + "\t" + sample + "\t" + fields[4] + "\t"
                        + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setSiteIdUI.displayMessage("Error: " + e.getLocalizedMessage());
            out.close();
            e.printStackTrace();
        }
        out.close();
        try {
            File fileDest;
            if (stsmf != null) {
                String fileName = stsmf.getName();
                stsmf.delete();
                fileDest = new File(this.dataType.getPath() + File.separator + fileName);
            } else {
                fileDest = new File(this.dataType.getPath() + File.separator
                        + this.dataType.getStudy().toString() + ".subject_mapping");
            }
            FileUtils.moveFile(file, fileDest);
            ((GeneExpressionData) this.dataType).setSTSMF(fileDest);
        } catch (IOException ioe) {
            this.setSiteIdUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setSiteIdUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setSiteIdUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:net.mohatu.bloocoin.miner.Miner.java

public void mine() throws NoSuchAlgorithmException {
    // String testString = "dx3NAa"; //dx3NAa257363
    while (Main.getStatus()) {
        String startString = randomString();
        System.out.println("Starting: " + startString);

        for (int counter = 0; counter <= 10000000; counter++) {
            Main.updateCounter();//from   www  . j a  v  a 2  s .  c om
            String currentString = startString + counter;
            String hash = DigestUtils.sha512Hex(currentString);

            if (hash.startsWith(difficulty)) {
                new Thread(new Submitter(hash, currentString)).start();

                Main.updateSolved(currentString);
                System.out.println("Success: " + currentString);

                try {
                    PrintWriter out = new PrintWriter(new BufferedWriter(
                            new FileWriter(System.getProperty("user.home") + "/.bloocoin/solved.dat", true)));
                    out.println(currentString);
                    out.close();
                } catch (IOException e) {
                    // Error
                    System.out.println("Unable to save to BLC_Solved.txt, check permissions.");
                }

            }

            if (!Main.getStatus()) {
                counter = 10000000;
                System.out.println("STOPPING");
            }
        }
    }
}

From source file:io.druid.data.input.impl.PrefetchableTextFilesFirehoseFactoryTest.java

@BeforeClass
public static void setup() throws IOException {
    testDir = File.createTempFile(PrefetchableTextFilesFirehoseFactoryTest.class.getSimpleName(), "testDir");
    FileUtils.forceDelete(testDir);//from  ww w.j  a v  a2 s . c o  m
    FileUtils.forceMkdir(testDir);

    firehoseTempDir = File.createTempFile(PrefetchableTextFilesFirehoseFactoryTest.class.getSimpleName(),
            "baseDir");
    FileUtils.forceDelete(firehoseTempDir);
    FileUtils.forceMkdir(firehoseTempDir);

    for (int i = 0; i < 10; i++) {
        // Each file is 1390 bytes
        try (final Writer writer = new BufferedWriter(new FileWriter(new File(testDir, "test_" + i)))) {
            for (int j = 0; j < 100; j++) {
                final String a = (20171220 + i) + "," + i + "," + j + "\n";
                writer.write(a);
            }
        }
    }
}

From source file:chibi.gemmaanalysis.ExpressionDataLoader.java

public void writeExpressionDataToFile(String paraFileName) {
    try (BufferedWriter writer = new BufferedWriter(new FileWriter(this.analysisResultsPath + paraFileName))) {
        writer.write("Experiment Name: " + this.experimentName + "\n");
        writer.write("Accession: " + this.experiment.getAccession().getAccession() + "\n");
        writer.write("Name: " + this.experiment.getName() + "\n");
        writer.write("Description: " + this.experiment.getDescription() + "\n");
        writer.write("Source: " + this.experiment.getSource() + "\n");

        for (DesignElementDataVector dataVector : this.designElementDataVectors) {
            CompositeSequence designElement = dataVector.getDesignElement();
            String probId = designElement.getName();
            byte[] expressionByteData = dataVector.getData();
            ByteArrayConverter byteConverter = new ByteArrayConverter();
            double[] expressionData = byteConverter.byteArrayToDoubles(expressionByteData);
            writer.write(probId + "\t");
            for (int i = 0; i < expressionData.length; i++)
                writer.write(expressionData[i] + "\t");
            writer.write(dataVector.getQuantitationType().getName() + "\t");
            writer.write(dataVector.getQuantitationType().getRepresentation() + "\t");
            writer.write(dataVector.getQuantitationType().getScale().getValue() + "\t");
            writer.write(dataVector.getQuantitationType().getType().getValue() + "\t");
            writer.write("\n");
        }//from   w  ww. ja  va  2s  . c  o  m
    } catch (IOException e) {
        log.error("Error in write data into file");
    }
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetPlatformsListener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setPlatformsUI.getValues();
    Vector<String> samples = this.setPlatformsUI.getSamples();
    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".subject_mapping.tmp");
    File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
    if (stsmf == null) {
        this.setPlatformsUI.displayMessage("Error: no subject to sample mapping file");
    }//  w ww  .j a  va  2s  .co  m
    try {
        FileWriter fw = new FileWriter(file);
        BufferedWriter out = new BufferedWriter(fw);
        out.write(
                "study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");

        try {
            BufferedReader br = new BufferedReader(new FileReader(stsmf));
            String line = br.readLine();
            while ((line = br.readLine()) != null) {
                String[] fields = line.split("\t", -1);
                String sample = fields[3];
                String platform;
                if (samples.contains(sample)) {
                    platform = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform
                        + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
            out.close();
            e.printStackTrace();
        }
        out.close();
        try {
            File fileDest;
            if (stsmf != null) {
                String fileName = stsmf.getName();
                stsmf.delete();
                fileDest = new File(this.dataType.getPath() + File.separator + fileName);
            } else {
                fileDest = new File(this.dataType.getPath() + File.separator
                        + this.dataType.getStudy().toString() + ".subject_mapping");
            }
            FileUtils.moveFile(file, fileDest);
            ((GeneExpressionData) this.dataType).setSTSMF(fileDest);
        } catch (IOException ioe) {
            this.setPlatformsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setPlatformsUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}