Example usage for java.io BufferedWriter BufferedWriter

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:edu.pitt.dbmi.ipm.service.EntityStreamingOutput.java

/**
 * Writes to stream./*from w w w  . j a  va  2  s  .  co  m*/
 */
@Override
public void write(OutputStream output) throws IOException, WebApplicationException {

    byte[] buffer = new byte[1024];
    int read = -1;
    InputStream instream = null;

    try {

        instream = entity.getContent();
        BufferedReader br = new BufferedReader(new InputStreamReader(instream));
        Writer writer = new BufferedWriter(new OutputStreamWriter(output));

        String line = null;
        while ((line = br.readLine()) != null) {
            line = line.replaceAll("\"", "");
            writer.write(line + "\n");
            writer.flush();
        }

    } catch (IOException e) {
        throw new RuntimeException(e);
    } finally {

        if (instream != null)
            instream.close();

        if (output != null)
            output.close();

        httpclient.getConnectionManager().shutdown();
    }

}

---

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetAttribute1Listener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setAttribute1UI.getValues();
    Vector<String> samples = this.setAttribute1UI.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.setAttribute1UI.displayMessage("Error: no subject to sample mapping file");
    }/*from ww  w  . jav  a  2 s.  c om*/
    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 attribute;
                if (samples.contains(sample)) {
                    attribute = 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" + fields[5] + "\t" + attribute + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            setAttribute1UI.displayMessage("File 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.setAttribute1UI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setAttribute1UI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setAttribute1UI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

---

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetAttribute2Listener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setAttribute2UI.getValues();
    Vector<String> samples = this.setAttribute2UI.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.setAttribute2UI.displayMessage("Error: no subject to sample mapping file");
    }/*from w  w w  .  j a  va2  s .  c  o  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 attribute;
                if (samples.contains(sample)) {
                    attribute = 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" + fields[5] + "\t" + fields[6] + "\t" + attribute + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setAttribute2UI.displayMessage("File 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.setAttribute2UI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setAttribute2UI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setAttribute2UI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

---

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

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setTissueTypeUI.getValues();
    Vector<String> samples = this.setTissueTypeUI.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.setTissueTypeUI.displayMessage("Error: no subject to sample mapping file");
    }/*from w ww  . j  a v  a2  s  .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 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" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setTissueTypeUI.displayMessage("File 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.setTissueTypeUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setTissueTypeUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setTissueTypeUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

---

From source file:DiskIO.java

public static void saveStringInFile(File toFile, String insertString) throws IOException {
    BufferedWriter out;/*from   w  w w . j av  a 2 s.  co  m*/

    out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(toFile), "ISO-8859-1"));
    out.write(insertString);
    out.flush();
    out.close();
}

---

From source file:edu.indiana.d2i.htrc.util.ClusterInspection.java

@Override
public int run(String[] args) throws Exception {
    String input = args[0]; // cluster path
    String output = args[1];// w  w w . ja  v a2  s  . c o  m

    int numVector = 0;

    Configuration conf = getConf();
    FileSystem fs = FileSystem.get(conf);
    FileStatus[] status = fs.listStatus(new Path(input), Utilities.HIDDEN_FILE_FILTER);
    Text key = new Text();
    LongWritable value = new LongWritable();
    BufferedWriter writer = new BufferedWriter(new FileWriter(output));
    for (int i = 0; i < status.length; i++) {
        SequenceFile.Reader seqReader = new SequenceFile.Reader(fs, status[i].getPath(), conf);
        while (seqReader.next(key, value)) {
            numVector++;
            writer.write(key.toString() + "\n");
        }
    }
    writer.close();

    logger.info("#vector: " + numVector);

    return 0;
}

---

From source file:jatoo.exec.InputStreamExhausterWithDumpStream.java

public final void exhaust() {

    BufferedReader processInputStreamReader = null;
    BufferedWriter dumpOutputStreamWriter = null;

    try {/*from w w  w  .  j  a  v  a 2s . com*/

        processInputStreamReader = new BufferedReader(new InputStreamReader(processInputStream));
        dumpOutputStreamWriter = new BufferedWriter(new OutputStreamWriter(dumpOutputStream));

        String line = null;
        while ((line = processInputStreamReader.readLine()) != null) {

            dumpOutputStreamWriter.write(line);
            dumpOutputStreamWriter.newLine();

            dumpOutputStreamWriter.flush();
        }
    }

    catch (IOException e) {
        LOGGER.error("error exhausting the stream", e);
    }

    finally {
        if (closeDumpOutputStream && dumpOutputStreamWriter != null) {
            try {
                dumpOutputStreamWriter.close();
            } catch (IOException e) {
                LOGGER.error("error closing the dump stream", e);
            }
        }
    }
}

---

From source file:edu.indiana.d2i.htrc.util.TokensInspection.java

@Override
public int run(String[] args) throws Exception {
    String input = args[0]; // word count path
    String output = args[1];//w w  w  . j ava  2s . c o  m

    int numVector = 0;

    Configuration conf = getConf();
    FileSystem fs = FileSystem.get(conf);
    FileStatus[] status = fs.listStatus(new Path(input), Utilities.HIDDEN_FILE_FILTER);
    Text key = new Text();
    LongWritable value = new LongWritable();
    BufferedWriter writer = new BufferedWriter(new FileWriter(output));
    for (int i = 0; i < status.length; i++) {
        SequenceFile.Reader seqReader = new SequenceFile.Reader(fs, status[i].getPath(), conf);
        while (seqReader.next(key, value)) {
            numVector++;
            writer.write(key.toString() + "\n");
        }
    }
    writer.close();

    logger.info("#vector: " + numVector);

    return 0;
}

---

From source file:org.jboss.as.test.manualmode.web.valve.authenticator.ValveUtil.java

public static void createValveModule(final ManagementClient managementClient, String modulename,
        String baseModulePath, String jarName, Class valveClass) throws Exception {
    log.info("Creating a valve module " + modulename);
    String path = ValveUtil.readASPath(managementClient.getControllerClient());
    File file = new File(path);
    if (file.exists()) {
        file = new File(path + baseModulePath);
        file.mkdirs();/*from w  ww .jav a  2  s  .c  om*/
        file = new File(path + baseModulePath + "/" + jarName);
        if (file.exists()) {
            file.delete();
        }
        createJar(file, valveClass);
        file = new File(path + baseModulePath + "/module.xml");
        if (file.exists()) {
            file.delete();
        }
        FileWriter fstream = new FileWriter(path + baseModulePath + "/module.xml");
        BufferedWriter out = new BufferedWriter(fstream);
        out.write("<module xmlns=\"urn:jboss:module:1.1\" name=\"" + modulename + "\">\n");
        out.write("    <properties>\n");
        out.write("        <property name=\"jboss.api\" value=\"private\"/>\n");
        out.write("    </properties>\n");

        out.write("    <resources>\n");
        out.write("        <resource-root path=\"" + jarName + "\"/>\n");
        out.write("    </resources>\n");

        out.write("    <dependencies>\n");
        out.write("        <module name=\"sun.jdk\"/>\n");
        out.write("        <module name=\"javax.servlet.api\"/>\n");
        out.write("        <module name=\"org.jboss.as.web\"/>\n");
        out.write("       <module name=\"org.jboss.logging\"/>\n");
        out.write("    </dependencies>\n");
        out.write("</module>");
        out.close();
    }
}

---

From source file:gr.uoc.nlp.opinion.ilsptagger.POSTagDocuments.java

private void crateTxtFiles(ResultSet rs) {

    System.out.println("Creating .txt files..");
    try {/* w ww.  ja v  a2s  .com*/
        while (rs.next()) {
            try (BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(
                    new FileOutputStream(this.dir + rs.getString("comment_id") + ".txt"), "utf-8"))) {
                bw.write(rs.getString("comment"));

                bw.close();
            }
        }

        System.out.println("Done creating .txt files!");

    } catch (FileNotFoundException | UnsupportedEncodingException ex) {
        System.err.println("Abort!");
        Logger.getLogger(POSTagDocuments.class.getName()).log(Level.SEVERE, null, ex);
    } catch (SQLException | IOException ex) {
        Logger.getLogger(POSTagDocuments.class.getName()).log(Level.SEVERE, null, ex);
    }
}

---

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