Example usage for java.io BufferedWriter append

Introduction

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

Prototype

public Writer append(CharSequence csq) throws IOException 

Source Link

Document

Appends the specified character sequence to this writer.

Usage

From source file:edu.rice.cs.bioinfo.programs.phylonet.algos.network.InferMLNetworkFromSequences.java

public List<Tuple<Network, Double>> inferNetwork(String[] gtTaxa, List<char[][]> sequences,
        Map<String, String> allele2species, RateModel gtrsm, double theta, int maxReticulations, int numSol) {
    if (_optimalNetworks == null) {
        _optimalNetworks = new Network[numSol];
        _optimalScores = new double[numSol];
        Arrays.fill(_optimalScores, Double.NEGATIVE_INFINITY);
    }/*  www. ja  va  2 s .c o  m*/

    List<Tuple<char[], Integer>> distinctSequences = summarizeSquences(sequences);
    String startingNetwork = _startNetwork.toString();

    for (int i = 0; i < _numRuns; i++) {
        System.out.println("Run #" + i);
        DirectedGraphToGraphAdapter<String, PhyloEdge<String>> speciesNetwork = makeNetwork(startingNetwork);
        NetworkNeighbourhoodRandomWalkGenerator<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, String, PhyloEdge<String>> allNeighboursStrategy = new NetworkNeighbourhoodRandomWalkGenerator<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, String, PhyloEdge<String>>(
                _operationWeight, makeNode, makeEdge, _seed);
        AllNeighboursHillClimberFirstBetter<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, String, PhyloEdge<String>, Double> searcher = new AllNeighboursHillClimberFirstBetter<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, String, PhyloEdge<String>, Double>(
                allNeighboursStrategy);
        Func1<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, Double> scorer = getScoreFunction(gtTaxa,
                allele2species, distinctSequences, gtrsm, theta);
        Comparator<Double> comparator = getDoubleScoreComparator();
        HillClimbResult<DirectedGraphToGraphAdapter<String, PhyloEdge<String>>, Double> result = searcher
                .search(speciesNetwork, scorer, comparator, _maxExaminations, maxReticulations, _maxFailure,
                        _diameterLimit); // search starts here
        if (resultFile != null) {
            try {
                BufferedWriter bw = new BufferedWriter(new FileWriter(resultFile, true));
                bw.append("Run #" + i + "\n");
                for (int j = 0; j < _optimalNetworks.length; j++) {
                    bw.append(_optimalScores[j] + ": " + _optimalNetworks[j].toString() + "\n");
                }
                bw.newLine();
                bw.close();
            } catch (Exception e) {
                System.err.println(e.getMessage());
                e.getStackTrace();
            }
        }
    }

    List<Tuple<Network, Double>> resultList = new ArrayList<Tuple<Network, Double>>();
    for (int i = 0; i < numSol; i++) {
        if (_optimalNetworks[i] != null)
            resultList.add(new Tuple<Network, Double>(_optimalNetworks[i], _optimalScores[i]));
    }
    //System.out.println("\n #Networks " + result.ExaminationsCount);
    return resultList;
}

---

From source file:com.ideateam.plugin.Version.java

public void writeLocaleToFile(String fileName, String msg) {

    try {/*from   w w  w.j  a  v  a 2  s  .co  m*/
        String path = Environment.getExternalStorageDirectory().getAbsolutePath() + "/UAR2015/" + fileName;

        File file = new File(path);

        if (!file.exists()) {
            File f = new File(Environment.getExternalStorageDirectory().getAbsolutePath() + "/UAR2015/");
            f.mkdirs();
            file.createNewFile();

        }

        BufferedWriter buf = new BufferedWriter(new FileWriter(file, true));
        buf.append(msg);
        buf.newLine();
        buf.close();
        // callbackContext.sendPluginResult(new PluginResult(PluginResult.Status.OK, "writed to file"));
        Log.d(TAG, "..callBackPlugin");
        activity.sendJavascript("UART.system.Helper.callBackPlugin('ok')");

    } catch (IOException e) {
        Log.d(TAG, e.getMessage());
    }

}

---

From source file:ie.pars.nlp.sketchengine.interactions.FreqSKEInteraction.java

/**
 * Get all the results and dump it into files this method can be changed so
 * Here the difference is that all the res are written into one
 *
 *
 * @throws UnsupportedEncodingException/*from w w  w . j  a v  a  2 s  .c  om*/
 * @throws IOExceptionsket
 * @throws Exception
 */
public void getFrequencyContextSingle() throws UnsupportedEncodingException, IOException, Exception {
    HttpClient sessionID = super.getSessionID();

    BufferedWriter writer;// this.writer;
    //append to the end of file
    OutputStreamWriter outputStreamWriter = new OutputStreamWriter(new FileOutputStream(this.fileOutput),
            StandardCharsets.UTF_8);
    writer = new BufferedWriter(outputStreamWriter);

    if (!writeParsed) {
        writer.append("{\"results\": [\n");
    }
    int pageNumer = 0;
    while (true) {
        JSONObject jsonObjP = super.getHTTP(sessionID, encodeFreqQuery(pageNumer));
        if (!writeParsed) {
            writer.append(jsonObjP.toString(1));
        } else {
            FreqMethodJsonParser fjpm = new FreqMethodJsonParser(jsonObjP.toString());
            FrequencyLine fl;

            while ((fl = fjpm.getNext()) != null) {
                // just to make sure that the output won't be messed up
                // I may need to change this to a better solution

                // at least with the current hardware the writer sis not a bottleneck
                writer.append(fl.toStringLine()).append("\n");

            }
            //   writer.flush();

        }
        boolean hasError = jsonObjP.has("error");
        if (hasError) {
            String message = (String) jsonObjP.get("error");
            if ("Empty list".equals(message)) {
                System.out.println("No result for current query: " + this.query); // retrun null etc
                break;
            } else {
                System.out.println("* NOT SEEN * " + jsonObjP.toString(1));
                throw new Exception("not seen " + jsonObjP.toString(1));
            }
        } else {
            int isLastPage = 0;

            //                int finished = (int) jsonObjP.get("finished");
            if (jsonObjP.has("lastpage")) {
                isLastPage = (int) jsonObjP.get("lastpage");
                //System.out.println("** IS Last TO GO  " + isLastPage);
                if (isLastPage == 0) {
                    if (!writeParsed) {
                        writer.append(",");
                    }
                    pageNumer++;
                } else {
                    //System.out.println("Going to break because last page is not 0");
                    break;
                }
            }

        }
    }
    if (!writeParsed) {
        writer.append("]" + "}"); // to the end the json file}
    }
    writer.flush();
    writer.close();

}

---

From source file:com.pieframework.runtime.utils.azure.CsdefGenerator.java

private List<String> printEndpoints(BufferedWriter out, Role r) {
    //print Endpoints
    List<String> epList = null;
    try {//from   w  w w. j ava 2s  .  com
        AzureKey ssl = (AzureKey) r.getResources().get("sslCert");
        AzureEndpoint ap = (AzureEndpoint) r.getResources().get("endpoints");
        String certName = ssl.getCertificateName();
        out.append("<Endpoints>");
        if (ap != null) {
            epList = new ArrayList<String>();
            for (String port : ap.getEndpoints().keySet()) {
                String protocol = ap.getEndpoints().get(port);
                String id = protocol + port;
                out.append("<InputEndpoint name=\"" + id + "\" protocol=\"" + protocol + "\" port=\"" + port
                        + "\" ");
                if (protocol.equalsIgnoreCase("https")) {
                    if (!StringUtils.empty(certName)) {
                        out.append(" certificate=\"" + certName + "\" ");
                    } else {
                        throw new RuntimeException(
                                "Certificate name is not configured in resource " + ssl.getId());
                    }
                }
                out.append("/>");

                //Save the endpoint in the map
                epList.add(id);
            }
        }

        out.append("</Endpoints>");
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return epList;
}

---

From source file:org.balloon_project.overflight.task.indexing.IndexingTask.java

private void dumpIndexedTriples(List<Triple> results) throws IOException {
    Stopwatch storeTimer = Stopwatch.createStarted();

    if (results.size() > 0) {
        BufferedWriter writer = new BufferedWriter(new FileWriter(file, true));

        try {//from   www  .j  a  va2 s  .co  m
            for (Triple triple : results) {
                StringBuilder sb = new StringBuilder();
                sb.append("<").append(triple.getSubject()).append("> <")
                        .append(triple.getRelEntity().getPredicate()).append("> <").append(triple.getObject())
                        .append(">.\n");
                writer.append(sb.toString());
            }
        } finally {
            writer.flush();
            writer.close();
        }
    }

    logger.debug(this.endpoint.getEndpointID() + ": Intermediate result persisted (Size = " + results.size()
            + ") Continue query process" + " (save duration: "
            + storeTimer.stop().elapsed(TimeUnit.MILLISECONDS) + " ms) predicate " + relEntity.getPredicate());
}

---

From source file:com.termmed.statistics.Processor.java

private void printExcluyentList(IReportDetail file, HashSet<Long> conceptList, File outputFold)
        throws IOException {
    File exclFile = new File(I_Constants.EXCLUYENT_OUTPUT_FOLDER + "/" + file.getFile()
            + (file.getFile().toLowerCase().endsWith(".csv") ? "" : ".csv"));
    File completeDetailFile = new File(I_Constants.STATS_OUTPUT_FOLDER + "/" + file.getFile()
            + (file.getFile().toLowerCase().endsWith(".csv") ? "" : ".csv"));

    BufferedReader br = FileHelper.getReader(completeDetailFile);
    BufferedWriter bw = FileHelper.getWriter(exclFile);

    Integer sctIdIndex = file.getSctIdIndex();
    if (sctIdIndex == null) {
        sctIdIndex = 1;//from   ww w . jav  a 2s  . com
    }
    bw.append(br.readLine());
    bw.append("\r\n");
    String line;
    String[] spl;
    while ((line = br.readLine()) != null) {
        spl = line.split(",", -1);
        Long cid = Long.parseLong(spl[sctIdIndex]);
        if (conceptList.contains(cid)) {
            continue;
        }
        bw.append(line);
        bw.append("\r\n");
        conceptList.add(cid);
    }
    br.close();
    bw.close();
}

---

From source file:analytics.storage.store2csv.java

private void createHeaders(BufferedWriter writer, String metricName, String element) {

    try {/*from   www.  ja v a2s  . c o  m*/
        writer.append(element);
        writer.append(',');
        writer.append(metricName);
        writer.newLine();
        // writer.close();

    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    // finally {
    // try {
    // if (writer != null)
    // writer.close();
    // } catch (IOException ex) {
    // ex.printStackTrace();
    // }
    // }

}

---

From source file:com.itemanalysis.jmetrik.workspace.JmetrikPreferencesManager.java

private void createLogProperties(String logHome) {
    //directory should already exist
    //create log4j properties file if it does not exist
    String header = "#DO NOT EDIT - JMETRIK LOG PROPERTIES FILE - DO NOT EDIT";
    String fullPropertiesName = (logHome + "/" + DEFAULT_LOG_PROPERTY_FILE_V4);
    String fullLogFileName = (logHome + "/" + DEFAULT_LOG_NAME);
    String fullScriptLogFileName = (logHome + "/" + DEFAULT_SCRIPT_LOG_NAME);
    File f = new File(fullPropertiesName);
    if (!f.exists()) {
        try {/*from w w  w . j  a v  a2s .c o  m*/
            createLogHome(logHome);
            f.createNewFile();
            BufferedWriter bw = new BufferedWriter(new FileWriter(f));
            bw.append(header);
            bw.newLine();
            bw.append("log4j.logger.jmetrik-logger=ALL, adminAppender");
            bw.newLine();
            bw.append("log4j.logger.jmetrik-script-logger=INFO, scriptAppender");
            bw.newLine();
            bw.append("log4j.additivity.jmetrik-logger=false");
            bw.newLine();
            bw.append("log4j.additivity.jmetrik-script-logger=false");
            bw.newLine();

            //Main appender processes all levels
            bw.append("log4j.appender.adminAppender=org.apache.log4j.FileAppender");
            bw.newLine();
            bw.append("log4j.appender.adminAppender.layout=org.apache.log4j.PatternLayout");
            bw.newLine();
            bw.append("log4j.appender.adminAppender.File=" + fullLogFileName);
            bw.newLine();
            bw.append("log4j.appender.adminAppender.Append=false");
            bw.newLine();
            bw.append("log4j.appender.adminAppender.layout.ConversionPattern=[%p] %d{DATE} %n%m%n%n");
            bw.newLine();

            //Script appender processes scripts only
            bw.append("log4j.appender.scriptAppender=org.apache.log4j.FileAppender");
            bw.newLine();
            bw.append("log4j.appender.scriptAppender.layout=org.apache.log4j.PatternLayout");
            bw.newLine();
            bw.append("log4j.appender.scriptAppender.File=" + fullScriptLogFileName);
            bw.newLine();
            bw.append("log4j.appender.scriptAppender.Append=false");
            bw.newLine();
            bw.append("log4j.appender.scriptAppender.layout.ConversionPattern=%m%n%n");
            bw.newLine();

            bw.close();
        } catch (IOException ex) {
            firePropertyChange("error", "", "Error - Log properties file could not be created.");
        }
    }
}

---

From source file:de.tudarmstadt.ukp.clarin.webanno.automation.util.AutomationUtil.java

public static void generatePredictDocument(MiraTemplate aTemplate, RepositoryService aRepository,
        AnnotationService aAnnotationService, AutomationService aAutomationService, UserDao aUserDao)
        throws IOException, UIMAException, ClassNotFoundException {
    File miraDir = aAutomationService.getMiraDir(aTemplate.getTrainFeature());
    if (!miraDir.exists()) {
        FileUtils.forceMkdir(miraDir);// ww  w  .j  av a  2  s . c  o  m
    }

    String username = SecurityContextHolder.getContext().getAuthentication().getName();
    User user = aUserDao.get(username);
    AnnotationFeature feature = aTemplate.getTrainFeature();
    boolean documentChanged = false;
    for (SourceDocument document : aRepository.listSourceDocuments(feature.getProject())) {
        if (!document.isProcessed() && !document.isTrainingDocument()) {
            documentChanged = true;
            break;
        }
    }
    if (!documentChanged) {
        return;
    }
    AutomationTypeAdapter adapter = (AutomationTypeAdapter) TypeUtil.getAdapter(aAnnotationService,
            feature.getLayer());
    for (SourceDocument document : aRepository.listSourceDocuments(feature.getProject())) {
        if (!document.isProcessed() && !document.isTrainingDocument()) {
            File predFile = new File(miraDir, document.getId() + ".pred.ft");
            BufferedWriter predOut = new BufferedWriter(new FileWriter(predFile));
            JCas jCas;
            try {
                jCas = aRepository.readCorrectionCas(document);
            } catch (Exception e) {
                jCas = aRepository.readAnnotationCas(document, user);
            }

            for (Sentence sentence : select(jCas, Sentence.class)) {
                predOut.append(getMiraLine(sentence, null, adapter).toString() + "\n");
            }
            predOut.close();
        }
    }
}

---

From source file:de.tudarmstadt.ukp.clarin.webanno.automation.util.AutomationUtil.java

public static void addTabSepTrainDocument(MiraTemplate aTemplate, RepositoryService aRepository,
        AutomationService aAutomationService)
        throws IOException, UIMAException, ClassNotFoundException, AutomationException {
    File miraDir = aAutomationService.getMiraDir(aTemplate.getTrainFeature());
    if (!miraDir.exists()) {
        FileUtils.forceMkdir(miraDir);/*from  w w  w  . ja  v a  2s . com*/
    }

    AutomationStatus status = aAutomationService.getAutomationStatus(aTemplate);

    boolean documentChanged = false;
    for (SourceDocument document : aAutomationService
            .listTabSepDocuments(aTemplate.getTrainFeature().getProject())) {
        if (!document.isProcessed()) {
            documentChanged = true;
            break;
        }
    }
    if (!documentChanged) {
        return;
    }

    for (SourceDocument sourceDocument : aAutomationService
            .listTabSepDocuments(aTemplate.getTrainFeature().getProject())) {
        if (sourceDocument.getFeature() != null) { // This is a target layer train document
            continue;
        }
        File trainFile = new File(miraDir,
                sourceDocument.getId() + sourceDocument.getProject().getId() + ".train");
        BufferedWriter trainOut = new BufferedWriter(new FileWriter(trainFile));
        File tabSepFile = new File(aRepository.getDocumentFolder(sourceDocument), sourceDocument.getName());
        LineIterator it = IOUtils.lineIterator(new FileReader(tabSepFile));
        while (it.hasNext()) {
            String line = it.next();
            if (line.trim().equals("")) {
                trainOut.append("\n");
            } else {
                StringTokenizer st = new StringTokenizer(line, "\t");
                if (st.countTokens() != 2) {
                    trainOut.close();
                    throw new AutomationException("This is not a valid TAB-SEP document");
                }
                trainOut.append(getMiraLineForTabSep(st.nextToken(), st.nextToken()));
            }
        }
        sourceDocument.setProcessed(false);
        status.setTrainDocs(status.getTrainDocs() - 1);
        trainOut.close();
    }

}

---

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