Example usage for java.io PrintWriter write

List of usage examples for java.io PrintWriter write

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Introduction

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

Prototype

public void write(String s)

Source Link

Document

Writes a string.

Usage

From source file:com.isecpartners.gizmo.FourthIdea.java

private void executeCommand(final String text) {
    final InputStream procInput;
    new Thread(new Runnable() {

        public void run() {
            String newRequestText = "";
            try {
                temp_files_to_clean_up.add(buffer_file.getCanonicalPath());
                PrintWriter out = new PrintWriter(new FileOutputStream(buffer_file));
                byte[] requestBuf = null;
                if (jTextPane1.getSelectedText() != null && jTextPane1.getSelectedText().length() > 0) {
                    out.write(jTextPane1.getSelectedText());
                    requestBuf = jTextPane1.getSelectedText().getBytes();
                } else {
                    out.write(jTextPane1.getText());
                    requestBuf = jTextPane1.getText().getBytes();
                }/* w ww. j  a va2s.c o  m*/

                out.close();
                String env[] = getenv(1);
                env[0] = "BUF=" + buffer_file.getCanonicalPath();
                String cmd = "";
                if (System.getProperty("os.name").toUpperCase().contains("WINDOWS")) {
                    cmd = "type " + buffer_file + "|" + text;
                } else {
                    cmd = "cat " + buffer_file + "|" + text;
                }

                newRequestText = exec(cmd, env, requestBuf);

            } catch (IOException ex) {
                Logger.getLogger(FourthIdea.class.getName()).log(Level.SEVERE, null, ex);

            } finally {
                if (jTextPane1.getSelectedText() != null && jTextPane1.getSelectedText().length() > 0) {
                    jTextPane1.replaceSelection(newRequestText);
                } else {
                    FourthIdea.this.jTextPane1.setText(newRequestText);
                }
            }

        }

        private String readWholeFile(File file) {
            InputStream in = null;
            String ret = "";
            try {
                in = new FileInputStream(file);
                int file_size = Integer.MAX_VALUE;
                if (file.length() < Integer.MAX_VALUE) {
                    file_size = (int) file.length();
                }
                byte[] buf = new byte[file_size];
                // truncated because for some reason, a byte array is initialized with an int instead of a long
                // so this's a bit awful, but if you're editing a request bigger than 2G in size, then don't
                in.read(buf);
                ret = new String(buf);
            } catch (IOException ex) {
                Logger.getLogger(FourthIdea.class.getName()).log(Level.SEVERE, null, ex);
            } finally {
                try {
                    in.close();
                } catch (IOException ex) {
                    Logger.getLogger(FourthIdea.class.getName()).log(Level.SEVERE, null, ex);
                }
            }
            return ret;
        }
    }).start();

}

From source file:edu.cornell.med.icb.goby.modes.WithinGroupVariabilityMode.java

private void processTranscriptAlignment(final String basename) throws IOException {
    final AlignmentReaderImpl reader = new AlignmentReaderImpl(basename);
    PrintWriter outputWriter = null;
    try {/* ww w.jav  a 2s .co m*/
        outputWriter = new PrintWriter(new FileWriter(outputFile));

        // outputWriter.write("# One line per reference id. Count indicates the number of times a query \n" +
        //         "# partially overlaps a target, given the various quality filters used to create the alignment.\n");
        outputWriter.write("sampleId\treferenceId\tcount\tlog10(count+1)\tcumulativeBasesAligned\n");

        reader.readHeader();

        final int numberOfReferences = reader.getNumberOfTargets();
        final int[] numberOfReadsPerReference = new int[numberOfReferences];
        final int[] cumulativeBasesPerReference = new int[numberOfReferences];

        System.out.printf("Scanning alignment %s%n", basename);
        for (final Alignments.AlignmentEntry alignmentEntry : reader) {
            ++numberOfReadsPerReference[alignmentEntry.getTargetIndex()];

            cumulativeBasesPerReference[alignmentEntry.getTargetIndex()] += Math
                    .min(alignmentEntry.getQueryAlignedLength(), alignmentEntry.getTargetAlignedLength());
        }
        final IndexedIdentifier targetIds = reader.getTargetIdentifiers();

        final DoubleIndexedIdentifier targetIdBackward = new DoubleIndexedIdentifier(targetIds);

        final String sampleId = FilenameUtils.getBaseName(basename);
        deCalculator.reserve(numberOfReferences, inputFiles.length);
        int numAlignedReadsInSample = 0;
        // define elements that will be tested for differential expression:
        for (int referenceIndex = 0; referenceIndex < numberOfReferences; ++referenceIndex) {

            final String transcriptId = targetIdBackward.getId(referenceIndex).toString();
            final int index = deCalculator.defineElement(transcriptId,
                    DifferentialExpressionCalculator.ElementType.TRANSCRIPT);

            deCalculator.defineElementLength(index, reader.getTargetLength(referenceIndex));
        }

        // observe elements:
        for (int referenceIndex = 0; referenceIndex < numberOfReferences; ++referenceIndex) {

            outputWriter.printf("%s\t%s\t%d\t%g\t%d%n", basename, targetIdBackward.getId(referenceIndex),
                    numberOfReadsPerReference[referenceIndex],
                    Math.log10(numberOfReadsPerReference[referenceIndex] + 1),
                    cumulativeBasesPerReference[referenceIndex]);

            final String transcriptId = targetIdBackward.getId(referenceIndex).toString();

            deCalculator.observe(sampleId, transcriptId, numberOfReadsPerReference[referenceIndex]);
            numAlignedReadsInSample += numberOfReadsPerReference[referenceIndex];
        }
        deCalculator.setNumAlignedInSample(sampleId, numAlignedReadsInSample);
        outputWriter.flush();

    } finally {
        IOUtils.closeQuietly(outputWriter);
        reader.close();
    }
}

From source file:de.xwic.appkit.core.remote.server.RemoteDataAccessServlet.java

/**
 * @param entityType/*from   w ww .  jav a 2  s  . c  o  m*/
 * @param req
 * @param resp
 * @param pwOut
 * @throws DocumentException
 * @throws TransportException
 * @throws ConfigurationException
 * @throws IOException
 */
private void handleUpdateEntity(final String entityType, final HttpServletRequest req,
        final HttpServletResponse resp, final PrintWriter pwOut)
        throws DocumentException, TransportException, ConfigurationException, IOException {

    String strEto = req.getParameter(PARAM_ETO);

    EntityTransferObject eto = EtoSerializer.deserialize(strEto, true);

    EntityTransferObject result = accessHandler.updateETO(eto);

    if (result == null) {
        throw new IllegalStateException("Result ETO is null");
    }

    String strResult = EtoSerializer.serialize(entityType, result, true);

    pwOut.write(strResult);
    pwOut.flush();
}

From source file:com.ephesoft.gxt.admin.server.ImportTableUploadServlet.java

/**
 * This API is used to write content in temp file.
 * /*from ww w  .j a  va 2 s  . co  m*/
 * @param item {@link FileItem} uploaded file item.
 * @param filePath {@link String} to create temporary file.
 * @param printWriter {@link PrintWriter}.
 * @return {@link File} temporary file.
 */
private File copyItemContentInFile(final FileItem item, final String filePath, final PrintWriter printWriter) {
    File tempTableFile = null;
    OutputStream out = null;
    InputStream instream = null;
    try {
        instream = item.getInputStream();
        tempTableFile = new File(filePath);
        //         if (tempTableFile.exists()) {
        //            tempTableFile.delete();
        //         }
        out = new FileOutputStream(tempTableFile);
        final byte buf[] = new byte[1024];
        int len;
        while ((len = instream.read(buf)) > 0) {
            out.write(buf, 0, len);
        }
    } catch (final FileNotFoundException e) {
        printWriter.write("Unable to create the export folder.Please try again.");
    } catch (final IOException e) {
        printWriter.write("Unable to read the file.Please try again.");
    } finally {
        if (out != null) {
            try {
                out.close();
            } catch (final IOException ioe) {
                log.error("Could not close stream for file." + tempTableFile);
            }
        }
        if (instream != null) {
            try {
                instream.close();
            } catch (final IOException ioe) {
                log.error("Could not close stream for file." + filePath);
            }
        }
    }
    return tempTableFile;
}

From source file:com.ephesoft.dcma.gwt.customworkflow.server.ImportPluginUploadServlet.java

/**
 * @param tempZipFile//  w w w . ja va2  s.co  m
 * @param exportSerailizationFolderPath
 * @param printWriter 
 * @return
 * @throws FileNotFoundException
 * @throws IOException
 */
private String processZipFileEntries(File tempZipFile, String exportSerailizationFolderPath,
        PrintWriter printWriter) throws FileNotFoundException, IOException {
    String errorMessageString;
    ZipInputStream zipInputStream;
    List<ZipEntry> zipEntries;
    tempOutputUnZipDir = exportSerailizationFolderPath + File.separator + zipFileName;
    File tempOutputUnZipDirFile = new File(tempOutputUnZipDir);
    try {
        FileUtils.copyFile(tempZipFile, tempOutputUnZipDirFile);

        // FileUtils.unzip(tempZipFile, tempOutputUnZipDir);
    } catch (Exception e) {
        LOG.error("Unable to copy the file." + e, e);
        printWriter.write("Unable to copy the file.Please try again.");
        tempZipFile.delete();
    }

    zipInputStream = new ZipInputStream(new FileInputStream(tempOutputUnZipDir));
    // new ZipInputStream(new FileInputStream(tempOutputUnZipDir)).getNextEntry();

    zipEntries = new ArrayList<ZipEntry>();
    ZipEntry nextEntry = zipInputStream.getNextEntry();
    while (nextEntry != null) {
        zipEntries.add(nextEntry);
        nextEntry = zipInputStream.getNextEntry();
    }
    errorMessageString = processZipFileContents(zipEntries);
    return errorMessageString;
}

From source file:com.ijuru.kumva.sms.web.SearchServlet.java

/**
 * @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
 *//*from w  w w .ja  v  a2 s .c  om*/
@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    PrintWriter out = response.getWriter();
    String query = request.getParameter("q");

    if (query == null || query.length() == 0)
        return;

    query = query.trim();

    String keyword = Context.getOptions().getInputKeyword();

    // Strip keyword if one is specified
    if (StringUtils.isNotEmpty(keyword) && query.toLowerCase().startsWith(keyword + " ")) {
        query = query.substring((keyword + " ").length());
    }

    int timeout = Context.getOptions().getConnectionTimeout();
    String searchRef = Context.getOptions().getSearchRef();

    try {
        Search search = new RemoteSearch(Context.getDictionary(), timeout);
        SearchResult result = search.execute(query, 10, searchRef);
        String message = Messages.searchResult(result, query);

        out.write(message);
    } catch (Exception ex) {
        out.write(Messages.errorOccurred());

        log.warn("Remote search failed");
    }
}

From source file:com.browseengine.bobo.api.BoboIndexReader.java

/**
 * Utility method to dump out all fields (name and terms) for a given index.
 * /*  w  w w  .  ja  v  a  2 s  .co  m*/
 * @param outFile
 *          File to dump to.
 * @throws IOException
 */
public void dumpFields(File outFile) throws IOException {
    FileWriter writer = null;
    try {
        writer = new FileWriter(outFile);
        PrintWriter out = new PrintWriter(writer);
        Set<String> fieldNames = getFacetNames();
        for (String fieldName : fieldNames) {
            TermEnum te = terms(new Term(fieldName, ""));
            out.write(fieldName + ":\n");
            while (te.next()) {
                Term term = te.term();
                if (!fieldName.equals(term.field())) {
                    break;
                }
                out.write(term.text() + "\n");
            }
            out.write("\n\n");
        }
    } finally {
        if (writer != null) {
            writer.close();
        }
    }
}

From source file:eu.stratosphere.nephele.jobmanager.web.JobmanagerInfoServlet.java

/**
 * Writes infos about one particular archived groupvertex in a job, including all groupmembers, their times and status
 * /*from   w  ww.  j  av a 2 s  . c om*/
 * @param wrt
 * @param jobEvent
 * @param groupvertexId
 */
private void writeJsonForArchivedJobGroupvertex(PrintWriter wrt, RecentJobEvent jobEvent,
        ManagementGroupVertexID groupvertexId) {

    try {

        ManagementGraph jobManagementGraph = jobmanager.getManagementGraph(jobEvent.getJobID());

        ManagementGroupVertex groupvertex = jobManagementGraph.getGroupVertexByID(groupvertexId);

        // Serialize ManagementGraph to json
        wrt.write("{\"groupvertex\": " + groupvertex.toJson() + ",");

        wrt.write("\"verticetimes\": {");
        boolean first = true;
        for (ManagementGroupVertex groupVertex : jobManagementGraph.getGroupVerticesInTopologicalOrder()) {

            for (int j = 0; j < groupVertex.getNumberOfGroupMembers(); j++) {
                ManagementVertex vertex = groupVertex.getGroupMember(j);

                if (first) {
                    first = false;
                } else {
                    wrt.write(",");
                }

                wrt.write("\"" + vertex.getID() + "\": {");
                wrt.write("\"vertexid\": \"" + vertex.getID() + "\",");
                wrt.write("\"vertexname\": \"" + vertex + "\",");
                wrt.write("\"CREATED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.CREATED) + ",");
                wrt.write("\"SCHEDULED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.SCHEDULED) + ",");
                wrt.write("\"ASSIGNED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.ASSIGNED) + ",");
                wrt.write("\"READY\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.READY) + ",");
                wrt.write("\"STARTING\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.STARTING) + ",");
                wrt.write("\"RUNNING\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.RUNNING) + ",");
                wrt.write("\"FINISHING\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.FINISHING) + ",");
                wrt.write("\"FINISHED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.FINISHED) + ",");
                wrt.write("\"CANCELING\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.CANCELING) + ",");
                wrt.write("\"CANCELED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.CANCELED) + ",");
                wrt.write("\"FAILED\": " + jobmanager.getArchive().getVertexTime(jobEvent.getJobID(),
                        vertex.getID(), ExecutionState.FAILED) + "");
                wrt.write("}");
            }

        }
        wrt.write("}}");

    } catch (EofException eof) { // Connection closed by client
        LOG.info("Info server for jobmanager: Connection closed by client, EofException");
    } catch (IOException ioe) { // Connection closed by client   
        LOG.info("Info server for jobmanager: Connection closed by client, IOException");
    }

}

From source file:com.mycompany.trafficimportfileconverter2.Main2Controller.java

private String writeFile(String fileName, String data) {
    try {//from   w  ww .j  a  v  a2 s.  c om
        PrintWriter writer = new PrintWriter(fileName, "UTF-8");
        writer.write(data);
        writer.close();
        String newFileName = getOutputDir().getAbsolutePath() + java.io.File.separator + fileName
                + getExtension();
        if (rename(fileName, newFileName)) {
            log("Success writing: " + newFileName);
        } else {
            log("failed to write:" + newFileName);
        }
        ;
        return newFileName;
    } catch (IOException e) {
        e.printStackTrace();
        // do something
    }
    return null;

}