Example usage for java.io FileReader close

List of usage examples for java.io FileReader close

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Introduction

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

Prototype

public void close() throws IOException

Source Link

Usage

From source file:Evaluator.PerQueryRelDocs.java

void load(int startQid, int endQid, String relFileName, String irrelFileName, String vectorFolderLocation)
        throws Exception {
    FileReader fr = new FileReader(qrelsFile);
    BufferedReader br = new BufferedReader(fr);

    FileReader fr1 = new FileReader(vectorFolderLocation + startQid + ".txt");
    BufferedReader br1 = new BufferedReader(fr1);
    String line1;//from w w  w . j  av  a2s.  c om
    String line;
    Integer d1 = startQid;
    line1 = br1.readLine();
    while ((line = br.readLine()) != null) {
        if (line1 != null) {
            storeRelRcd(line, line1);
            line1 = br1.readLine();
        } else {
            d1++;
            br1.close();
            fr1.close();
            // System.out.println(vectorFolderLocation + d1 + ".txt");
            fr1 = new FileReader(vectorFolderLocation + d1 + ".txt");
            br1 = new BufferedReader(fr1);
            line1 = br1.readLine();
            storeRelRcd(line, line1);
        }
    }
    Integer d = startQid;
    for (d = startQid; d <= endQid; d++) {
        PerQueryRelDocs reldoc = perQueryRels.get(d.toString());
        // System.out.println(reldoc);
        for (int i = 0; i < reldoc.relCentroid.size(); i++) {
            reldoc.relCentroid.set(i, reldoc.relCentroid.get(i) / reldoc.relMap.size());
        }
    }
    br.close();

}

From source file:org.apache.hadoop.mapred.util.LinuxResourceCalculatorPlugin.java

/**
 * Read /proc/meminfo, parse and compute memory information
 * @param readAgain if false, read only on the first time
 *///from  www.j  a v a2 s.  c  om
private void readProcMemInfoFile(boolean readAgain) {

    if (readMemInfoFile && !readAgain) {
        return;
    }

    // Read "/proc/memInfo" file
    BufferedReader in = null;
    FileReader fReader = null;
    try {
        fReader = new FileReader(procfsMemFile);
        in = new BufferedReader(fReader);
    } catch (FileNotFoundException f) {
        // shouldn't happen....
        return;
    }

    Matcher mat = null;

    try {
        String str = in.readLine();
        while (str != null) {
            mat = PROCFS_MEMFILE_FORMAT.matcher(str);
            if (mat.find()) {
                if (mat.group(1).equals(MEMTOTAL_STRING)) {
                    ramSize = Long.parseLong(mat.group(2));
                } else if (mat.group(1).equals(SWAPTOTAL_STRING)) {
                    swapSize = Long.parseLong(mat.group(2));
                } else if (mat.group(1).equals(MEMFREE_STRING)) {
                    ramSizeFree = Long.parseLong(mat.group(2));
                } else if (mat.group(1).equals(SWAPFREE_STRING)) {
                    swapSizeFree = Long.parseLong(mat.group(2));
                } else if (mat.group(1).equals(INACTIVE_STRING)) {
                    inactiveSize = Long.parseLong(mat.group(2));
                }
            }
            str = in.readLine();
        }
    } catch (IOException io) {
        //     LOG.warn("Error reading the stream " + io);
    } finally {
        // Close the streams
        try {
            fReader.close();
            try {
                in.close();
            } catch (IOException i) {
                //        LOG.warn("Error closing the stream " + in);
            }
        } catch (IOException i) {
            //     LOG.warn("Error closing the stream " + fReader);
        }
    }

    readMemInfoFile = true;
}

From source file:org.gwaspi.reports.PlinkReportLoader.java

public static CombinedRangeXYPlot loadAssocUnadjLogPvsPos(File plinkReport, Set<String> redMarkersHS)
        throws IOException {

    XYSeriesCollection chrData = new XYSeriesCollection();

    NumberAxis sharedAxis = new NumberAxis("-log?(P)");

    CombinedRangeXYPlot combinedPlot = new CombinedRangeXYPlot(sharedAxis);
    combinedPlot.setGap(0);//from  w  w  w .  ja  v a  2  s  .c  om

    XYSeries series1 = null;
    XYSeries series2 = null;

    FileReader inputFileReader = null;
    BufferedReader inputBufferReader = null;
    String tempChr = null;
    try {
        inputFileReader = new FileReader(plinkReport);
        inputBufferReader = new BufferedReader(inputFileReader);

        // Getting data from file and subdividing to series all points by chromosome
        String l;
        tempChr = "";
        String header = inputBufferReader.readLine();
        int count = 0;
        while ((l = inputBufferReader.readLine()) != null) {

            if (count % 10000 == 0) {
                log.info("loadAssocUnadjLogPvsPos -> reader count: {}", count);
            }
            count++;

            l = l.trim().replaceAll("\\s+", ",");
            String[] cVals = l.split(",");

            String markerId = cVals[1];
            int position = Integer.parseInt(cVals[2]);
            String s_pVal = cVals[8];

            if (!s_pVal.equals("NA")) {
                double logPValue = Math.abs(Math.log(Double.parseDouble(s_pVal)) / Math.log(10));

                if (cVals[0].toString().equals(tempChr)) {
                    if (redMarkersHS.contains(markerId)) {
                        series2.add(position, logPValue);
                    } else {
                        series1.add(position, logPValue);
                    }
                    labeler.put(tempChr + "_" + position, markerId);
                } else {
                    if (!tempChr.isEmpty()) { // SKIP FIRST TIME (NO DATA YET!)
                        chrData.addSeries(series1);
                        chrData.addSeries(series2);
                        appendToCombinedRangePlot(combinedPlot, tempChr, chrData);
                    }
                    tempChr = cVals[0];
                    series1 = new XYSeries("Imputed");
                    series2 = new XYSeries("Observed");
                    labeler.put(tempChr + "_" + position, markerId);

                    if (redMarkersHS.contains(markerId)) {
                        series2.add(position, logPValue);
                    } else {
                        series1.add(position, logPValue);
                    }
                }
            }
        }
    } finally {
        if (inputBufferReader != null) {
            inputBufferReader.close();
        } else if (inputFileReader != null) {
            inputFileReader.close();
        }
    }

    chrData.addSeries(series1);
    chrData.addSeries(series2);
    appendToCombinedRangePlot(combinedPlot, tempChr, chrData); // ADD LAST CHR TO PLOT

    return combinedPlot;
}

From source file:i2p.bote.I2PBote.java

/**
 * Sets up a {@link I2PSession}, using the I2P destination stored on disk or creating a new I2P
 * destination if no key file exists./*from   www  . java2  s.  c om*/
 */
private void initializeSession() throws I2PSessionException {
    Properties sessionProperties = new Properties();
    // set tunnel names
    sessionProperties.setProperty("inbound.nickname", "I2P-Bote");
    sessionProperties.setProperty("outbound.nickname", "I2P-Bote");
    if (configuration.isI2CPDomainSocketEnabled())
        sessionProperties.setProperty("i2cp.domainSocket", "true");
    // According to sponge, muxed depends on gzip, so leave gzip enabled

    // read the local destination key from the key file if it exists
    File destinationKeyFile = configuration.getDestinationKeyFile();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(destinationKeyFile);
        char[] destKeyBuffer = new char[(int) destinationKeyFile.length()];
        fileReader.read(destKeyBuffer);
        byte[] localDestinationKey = Base64.decode(new String(destKeyBuffer));
        ByteArrayInputStream inputStream = new ByteArrayInputStream(localDestinationKey);
        socketManager = I2PSocketManagerFactory.createDisconnectedManager(inputStream, null, 0,
                sessionProperties);
    } catch (IOException e) {
        log.debug("Destination key file doesn't exist or isn't readable." + e);
    } catch (I2PSessionException e) {
        // Won't happen, inputStream != null
    } finally {
        if (fileReader != null)
            try {
                fileReader.close();
            } catch (IOException e) {
                log.debug("Error closing file: <" + destinationKeyFile.getAbsolutePath() + ">" + e);
            }
    }

    // if the local destination key can't be read or is invalid, create a new one
    if (socketManager == null) {
        log.debug("Creating new local destination key");
        try {
            ByteArrayOutputStream arrayStream = new ByteArrayOutputStream();
            i2pClient.createDestination(arrayStream);
            byte[] localDestinationKey = arrayStream.toByteArray();

            ByteArrayInputStream inputStream = new ByteArrayInputStream(localDestinationKey);
            socketManager = I2PSocketManagerFactory.createDisconnectedManager(inputStream, null, 0,
                    sessionProperties);

            saveLocalDestinationKeys(destinationKeyFile, localDestinationKey);
        } catch (I2PException e) {
            log.error("Error creating local destination key.", e);
        } catch (IOException e) {
            log.error("Error writing local destination key to file.", e);
        }
    }

    i2pSession = socketManager.getSession();
    // Throws I2PSessionException if the connection fails
    i2pSession.connect();

    Destination localDestination = i2pSession.getMyDestination();
    log.info("Local destination key (base64): " + localDestination.toBase64());
    log.info("Local destination hash (base64): " + localDestination.calculateHash().toBase64());
    log.info("Local destination hash (base32): " + Util.toBase32(localDestination));
}

From source file:org.apache.sling.maven.slingstart.ModelPreprocessor.java

/**
 * Search for dependent slingstart/slingfeature artifacts and remove them from the effective model.
 * @throws MavenExecutionException//from w w  w.ja  v a2 s  .  c  o  m
 */
private List<Model> searchSlingstartDependencies(final Environment env, final ProjectInfo info,
        final Model rawModel, final Model effectiveModel) throws MavenExecutionException {
    // slingstart or slingfeature
    final List<Model> dependencies = new ArrayList<Model>();

    for (final Feature feature : effectiveModel.getFeatures()) {
        for (final RunMode runMode : feature.getRunModes()) {
            for (final ArtifactGroup group : runMode.getArtifactGroups()) {
                final List<org.apache.sling.provisioning.model.Artifact> removeList = new ArrayList<org.apache.sling.provisioning.model.Artifact>();
                for (final org.apache.sling.provisioning.model.Artifact a : group) {
                    if (a.getType().equals(BuildConstants.PACKAGING_SLINGSTART)
                            || a.getType().equals(BuildConstants.PACKAGING_PARTIAL_SYSTEM)) {

                        final Dependency dep = new Dependency();
                        dep.setGroupId(a.getGroupId());
                        dep.setArtifactId(a.getArtifactId());
                        dep.setVersion(a.getVersion());
                        dep.setType(BuildConstants.PACKAGING_PARTIAL_SYSTEM);
                        if (a.getType().equals(BuildConstants.PACKAGING_SLINGSTART)) {
                            dep.setClassifier(BuildConstants.PACKAGING_PARTIAL_SYSTEM);
                        } else {
                            dep.setClassifier(a.getClassifier());
                        }
                        dep.setScope(Artifact.SCOPE_PROVIDED);

                        env.logger.debug("- adding dependency " + ModelUtils.toString(dep));
                        info.project.getDependencies().add(dep);

                        // if it's a project from the current reactor build, we can't resolve it right now
                        final String key = a.getGroupId() + ":" + a.getArtifactId();
                        final ProjectInfo depInfo = env.modelProjects.get(key);
                        if (depInfo != null) {
                            env.logger.debug("Found reactor " + a.getType() + " dependency : " + a);
                            final Model model = addDependencies(env, depInfo);
                            if (model == null) {
                                throw new MavenExecutionException(
                                        "Recursive model dependency list including project " + info.project,
                                        (File) null);
                            }
                            dependencies.add(model);
                            info.includedModels.put(a, depInfo.localModel);

                        } else {
                            env.logger.debug("Found external " + a.getType() + " dependency: " + a);

                            // "external" dependency, we can already resolve it
                            final File modelFile = resolveSlingstartArtifact(env, info.project, dep);
                            FileReader r = null;
                            try {
                                r = new FileReader(modelFile);
                                final Model model = ModelReader.read(r, modelFile.getAbsolutePath());

                                info.includedModels.put(a, model);

                                final Map<Traceable, String> errors = ModelUtility.validate(model);
                                if (errors != null) {
                                    throw new MavenExecutionException(
                                            "Unable to read model file from " + modelFile + " : " + errors,
                                            modelFile);
                                }
                                final Model fullModel = processSlingstartDependencies(env, info, dep, model);

                                dependencies.add(fullModel);
                            } catch (final IOException ioe) {
                                throw new MavenExecutionException("Unable to read model file from " + modelFile,
                                        ioe);
                            } finally {
                                try {
                                    if (r != null) {
                                        r.close();
                                    }
                                } catch (final IOException io) {
                                    // ignore
                                }
                            }
                        }

                        removeList.add(a);
                    }
                }
                for (final org.apache.sling.provisioning.model.Artifact r : removeList) {
                    group.remove(r);
                    final Feature localModelFeature = rawModel.getFeature(feature.getName());
                    if (localModelFeature != null) {
                        final RunMode localRunMode = localModelFeature.getRunMode(runMode.getNames());
                        if (localRunMode != null) {
                            final ArtifactGroup localAG = localRunMode.getArtifactGroup(group.getStartLevel());
                            if (localAG != null) {
                                localAG.remove(r);
                            }
                        }
                    }
                }
            }
        }
    }

    return dependencies;
}

From source file:org.agmip.ui.afsirs.frames.SWFrame.java

private void readSoilDataJsonFileForUtils(File latestFile) throws FileNotFoundException {
    SoilData soilData = utils.getSoilData();//SoilData.getSoilDataInstance();
    if (soilData.getSoilsFromFile(latestFile.getName().trim()) != null)
        return;//from   w  w  w. jav a 2  s . c o  m

    String str = "";
    SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy HH:mm:ss");
    str += "Data Date: " + sdf.format(latestFile.lastModified()) + "\n";

    ObjectMapper mapper = new ObjectMapper();
    JsonNode root = null;
    FileReader fr = null;

    try {
        fr = new FileReader(latestFile);
        root = mapper.readTree(fr);

    } catch (FileNotFoundException e) {

        throw new FileNotFoundException(Messages.FILE_NOT_FOUND_MESSAGE);

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

    } finally {
        if (fr != null) {
            try {
                fr.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }
    JsonNode soils = root.path("soils");

    int row = 0;

    int whcIndex = waterholdcapacityBox.getSelectedIndex();

    ArrayList<Soil> soilList = new ArrayList<Soil>();

    for (JsonNode n : soils) {

        String soilSeriesName = n.path("mukeyName").textValue();
        String soilSeriesKey = n.path("mukey").textValue();

        String soilName = n.path("soilName").textValue();
        String compKey = n.path("cokey").textValue();

        String soilTypeArea = n.path("compArea").textValue();

        JsonNode soilLayersNodes = n.path("soilLayer");

        int NL = 0;

        double[] wc = new double[6];
        double[] wcl = new double[6];
        double[] wcu = new double[6];
        double[] du = new double[6];
        String[] txt = new String[3];

        for (JsonNode node : soilLayersNodes) {
            //System.out.println ("NL we are looking for: " + NL);
            wcu[NL] = node.get("sldul").asDouble() / 100.00;
            du[NL] = node.get("sllb").asDouble() * 0.39370;
            du[NL] = Math.floor(du[NL] * 1000) / 1000;
            wcl[NL] = node.get("slll").asDouble() / 100.00;

            if (whcIndex == 0) {
                wc[NL] = wcl[NL];
            } else if (whcIndex == 2) {
                wc[NL] = wcu[NL];
            } else {
                wc[NL] = 0.5 * (wcl[NL] + wcu[NL]);
            }

            wc[NL] = Math.floor(wc[NL] * 1000) / 1000;
            NL++;
        }
        // soilSeriesKey
        Soil soil = new Soil(row, soilName, soilSeriesKey, compKey, soilSeriesName, NL);
        soil.setValues(wc, wcl, wcu, du, txt);

        if (soilTypeArea != null)
            soil.setSoilTypeArea(Double.valueOf(soilTypeArea));
        else
            soil.setSoilTypeArea(0.0);
        //soilData.addSoil(latestFile.getName(), soil);
        soilList.add(soil);
        row++;
    }

    if (soilList.size() > 0)
        utils.setDefaultSoil(soilList.get(0));

    // Here we prepare teh
    soilData.addSoilList(latestFile.getName(), soilList);
}

From source file:guineu.modules.filter.report.qualityReport.ReportTask.java

/**
 * Read the file with the name of the samples in order
 * @throws java.lang.Exception/* w w w  . j  a  v a2 s.  co  m*/
 */
private List<sample> readFile() throws Exception {

    List<sample> Samples = new ArrayList<sample>();
    FileReader fr = null;
    try {
        fr = new FileReader(new File(fileName));
    } catch (Exception e) {
        throw e;
    }
    CsvReader reader = new CsvReader(fr);
    String splitRow[];
    sample newSample = null;
    while (reader.readRecord()) {
        splitRow = reader.getValues();
        try {

            if (splitRow[0].matches(".*Sample Name.*")) {
                newSample = new sample();
                newSample.setSampleName(splitRow[0]);
            }

            if (splitRow[2].matches(".*lysoPC_50.*")) {
                newSample.setLysoPC(splitRow);
            } else if (splitRow[2].matches(".*PC_50.*")) {
                newSample.setPC(splitRow);
            } else if (splitRow[2].matches(".*TG_50.*")) {
                newSample.setTG(splitRow);
            } else if (splitRow[2].matches(".*LPC.*")) {
                newSample.setLPC(splitRow);
            } else if (splitRow[2].matches(".*PCD.*")) {
                newSample.setPCD(splitRow);
            } else if (splitRow[2].matches(".*TGC.*")) {
                newSample.setTGC(splitRow);
                Samples.add(newSample);
            }
        } catch (Exception e) {
        }
    }
    reader.close();
    fr.close();
    return Samples;
}

From source file:org.kuali.kfs.gl.batch.service.impl.PosterServiceImpl.java

/**
 * Post scrubbed GL entries to GL tables.
 *//*  w w w  .j a va  2 s .  co  m*/
@Override
public void postMainEntries() {
    LOG.debug("postMainEntries() started");
    Date runDate = dateTimeService.getCurrentSqlDate();
    try {
        FileReader INPUT_GLE_FILE = new FileReader(batchFileDirectoryName + File.separator
                + GeneralLedgerConstants.BatchFileSystem.POSTER_INPUT_FILE
                + GeneralLedgerConstants.BatchFileSystem.EXTENSION);
        File OUTPUT_ERR_FILE = new File(batchFileDirectoryName + File.separator
                + GeneralLedgerConstants.BatchFileSystem.POSTER_ERROR_OUTPUT_FILE
                + GeneralLedgerConstants.BatchFileSystem.EXTENSION);

        postEntries(PosterService.MODE_ENTRIES, INPUT_GLE_FILE, null, OUTPUT_ERR_FILE);

        INPUT_GLE_FILE.close();
    } catch (FileNotFoundException e1) {
        e1.printStackTrace();
        throw new RuntimeException("PosterMainEntries Stopped: " + e1.getMessage(), e1);
    } catch (IOException ioe) {
        LOG.error("postMainEntries stopped due to: " + ioe.getMessage(), ioe);
        throw new RuntimeException(ioe);
    }
}

From source file:org.kuali.kfs.gl.batch.service.impl.PosterServiceImpl.java

/**
 * Post ICR GL entries to GL tables.//from   w ww.  ja  v a  2s .co  m
 */
@Override
public void postIcrEntries() {
    LOG.debug("postIcrEntries() started");
    Date runDate = dateTimeService.getCurrentSqlDate();
    try {
        FileReader INPUT_GLE_FILE = new FileReader(batchFileDirectoryName + File.separator
                + GeneralLedgerConstants.BatchFileSystem.ICR_POSTER_INPUT_FILE
                + GeneralLedgerConstants.BatchFileSystem.EXTENSION);
        File OUTPUT_ERR_FILE = new File(batchFileDirectoryName + File.separator
                + GeneralLedgerConstants.BatchFileSystem.ICR_POSTER_ERROR_OUTPUT_FILE
                + GeneralLedgerConstants.BatchFileSystem.EXTENSION);

        postEntries(PosterService.MODE_ICR, INPUT_GLE_FILE, null, OUTPUT_ERR_FILE);

        INPUT_GLE_FILE.close();
    } catch (FileNotFoundException e1) {
        e1.printStackTrace();
        throw new RuntimeException("PosterIcrEntries Stopped: " + e1.getMessage(), e1);
    } catch (IOException ioe) {
        LOG.error("postIcrEntries stopped due to: " + ioe.getMessage(), ioe);
        throw new RuntimeException(ioe);
    }
}

From source file:ca.sqlpower.object.annotation.SPAnnotationProcessor.java

/**
 * Generates and returns the GPL license header in a comment, as Eclipse
 * does whenever a new source file is created. The license is taken from
 * src/license_in_comment.txt.//from w w  w.  ja v a2 s. co m
 */
private String generateLicense() {
    StringBuilder sb = new StringBuilder();
    try {
        FileReader fr = new FileReader(LICENSE_COMMENT_FILE_PATH);
        BufferedReader br = new BufferedReader(fr);
        String line;
        while ((line = br.readLine()) != null) {
            niprintln(sb, line);
        }
        fr.close();
        br.close();
    } catch (FileNotFoundException e) {
        throw new RuntimeException(e);
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
    return sb.toString();
}