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:com.photon.phresco.framework.rest.api.RepositoryService.java

/**
 * Update latest project.//from w w  w  .j  a v  a  2 s .  c  o  m
 *
 * @param user the user
 * @param projectId the project id
 * @param appId the app id
 * @throws PhrescoException the phresco exception
 */
private void updateLatestProject(User user, String projectId, String appId) throws PhrescoException {
    try {
        File tempPath = new File(Utility.getPhrescoTemp() + File.separator + USER_PROJECT_JSON);
        JSONObject userProjJson = null;
        JSONParser parser = new JSONParser();
        if (tempPath.exists()) {
            FileReader reader = new FileReader(tempPath);
            userProjJson = (JSONObject) parser.parse(reader);
            reader.close();
        } else {
            userProjJson = new JSONObject();
        }

        userProjJson.put(user.getId(), projectId + Constants.STR_COMMA + appId);
        FileWriter writer = new FileWriter(tempPath);
        writer.write(userProjJson.toString());
        writer.close();
    } catch (IOException e) {
        throw new PhrescoException(e);
    } catch (ParseException e) {
        throw new PhrescoException(e);
    }
}

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

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

    NumberAxis sharedAxis = new NumberAxis("-log?(P)");
    sharedAxis.setTickMarkInsideLength(3.0f);
    CombinedRangeXYPlot combinedPlot = new CombinedRangeXYPlot(sharedAxis);
    combinedPlot.setGap(0);//  ww  w.j  a  v  a2 s .c om

    XYSeries series1 = null;
    XYSeries series2 = null;
    FileReader inputFileReader = null;
    BufferedReader inputBufferReader = null;
    try {
        inputFileReader = new FileReader(plinkReport);
        inputBufferReader = new BufferedReader(inputFileReader);

        // Getting data from file and subdividing to series all points by chromosome
        String l;
        String tempChr = "";
        // read but ignore the header
        /*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 pValue = Double.parseDouble(s_pVal); // P value

                if (cVals[0].toString().equals(tempChr)) {
                    if (redMarkers.contains(markerId)) { // Insert in alternate color series
                        series2.add(position, pValue);
                    } else {
                        series1.add(position, pValue);
                    }

                    //                  series1.add(position, logPValue);
                } else {
                    if (!tempChr.isEmpty()) { // Not the first time round!
                        XYSeriesCollection tempChrData = new XYSeriesCollection();
                        tempChrData.addSeries(series1);
                        tempChrData.addSeries(series2);
                        appendToCombinedRangePlot(combinedPlot, tempChr, tempChrData, false);
                    }

                    tempChr = cVals[0];
                    series1 = new XYSeries("Imputed");
                    series2 = new XYSeries("Observed"); // Alternate color series
                    if (redMarkers.contains(markerId)) { // Insert inlternate color series
                        series2.add(position, pValue);
                    } else {
                        series1.add(position, pValue);
                    }

                    //                  series1 = new XYSeries(cVals[0]);
                    //                  series1.add(position, logPValue);
                }
            }
        }
        // Append last chromosome to combined plot
        XYSeriesCollection tempChrData = new XYSeriesCollection();
        tempChrData.addSeries(series1);
        tempChrData.addSeries(series2);
        appendToCombinedRangePlot(combinedPlot, tempChr, tempChrData, true);
    } finally {
        try {
            if (inputBufferReader != null) {
                inputBufferReader.close();
            } else if (inputFileReader != null) {
                inputFileReader.close();
            }
        } catch (Exception ex) {
            log.warn(null, ex);
        }
    }

    return combinedPlot;
}

From source file:com.sec.ose.osi.ui.frm.main.identification.codematch.JPanCodeMatchMain.java

private void setMySourceCode(String fileName) {
    sbMySourceNum.delete(0, sbMySourceNum.length());
    sbMySourceText.delete(0, sbMySourceText.length());

    log.debug("setMySourceCode: " + fileName);

    String projectName = IdentifyMediator.getInstance().getSelectedProjectName();
    File mySourceCode = new File(protexSDK.getSourceLocation(projectName) + File.separator + fileName);

    log.debug("mySourceCode: " + mySourceCode.getAbsolutePath());

    getJPanMatchedSourceViewLeft().clear();
    if (mySourceCode.exists()) {
        FileReader fr = null;
        try {/*  ww  w  .j ava2  s  . c  o m*/
            fr = new FileReader(mySourceCode);
            BufferedReader br = new BufferedReader(fr);
            String tmpStr = null;
            int curLine = 1;
            while ((tmpStr = br.readLine()) != null) {
                sbMySourceNum.append(String.valueOf(curLine) + "\n");
                sbMySourceText.append(tmpStr + "\n");
                curLine++;
            }

            getJPanMatchedSourceViewLeft().setText(sbMySourceText.toString(), sbMySourceNum.toString());
        } catch (Exception e) {
            log.warn(e.getMessage());
            getJPanMatchedSourceViewLeft().clear();
            getJPanMatchedSourceViewLeft()
                    .setText(mySourceCode.getAbsolutePath() + "\n" + NO_SOURCE_CODE_NOT_EXIST_IN_LOCAL);
        } finally {
            try {
                if (fr != null) {
                    fr.close();
                }
            } catch (Exception e) {
                log.warn(e);
            }
        }
    } else {
        getJPanMatchedSourceViewLeft()
                .setText(mySourceCode.getAbsolutePath() + "\n" + NO_SOURCE_CODE_NOT_EXIST_IN_LOCAL);
    }

    getJPanMatchedSourceViewLeft().clearStyle();

}

From source file:org.dspace.app.statistics.LogAnalyser.java

/**
 * Read in the given config file and populate the class globals.
 *
 * @param   configFile  the config file to read in
 * @throws IOException if IO error/*from w w w .ja  v a  2s  .co m*/
 */
public static void readConfig(String configFile) throws IOException {
    //instantiate aggregators
    actionAggregator = new HashMap<String, Integer>();
    searchAggregator = new HashMap<String, Integer>();
    userAggregator = new HashMap<String, Integer>();
    itemAggregator = new HashMap<String, Integer>();
    archiveStats = new HashMap<String, Integer>();

    //instantiate lists
    generalSummary = new ArrayList<String>();
    excludeWords = new ArrayList<String>();
    excludeTypes = new ArrayList<String>();
    excludeChars = new ArrayList<String>();
    itemTypes = new ArrayList<String>();

    // prepare our standard file readers and buffered readers
    FileReader fr = null;
    BufferedReader br = null;

    String record = null;
    try {
        fr = new FileReader(configFile);
        br = new BufferedReader(fr);
    } catch (IOException e) {
        System.out.println("Failed to read config file: " + configFile);
        System.exit(0);
    }

    // read in the config file and set up our instance variables
    while ((record = br.readLine()) != null) {
        // check to see what kind of line we have
        Matcher matchComment = comment.matcher(record);
        Matcher matchReal = real.matcher(record);

        // if the line is not a comment and is real, read it in
        if (!matchComment.matches() && matchReal.matches()) {
            // lift the values out of the matcher's result groups
            String key = matchReal.group(1).trim();
            String value = matchReal.group(2).trim();

            // read the config values into our instance variables (see 
            // documentation for more info on config params)
            if (key.equals("general.summary")) {
                actionAggregator.put(value, Integer.valueOf(0));
                generalSummary.add(value);
            }

            if (key.equals("exclude.word")) {
                excludeWords.add(value);
            }

            if (key.equals("exclude.type")) {
                excludeTypes.add(value);
            }

            if (key.equals("exclude.character")) {
                excludeChars.add(value);
            }

            if (key.equals("item.type")) {
                itemTypes.add(value);
            }

            if (key.equals("item.floor")) {
                itemFloor = Integer.parseInt(value);
            }

            if (key.equals("search.floor")) {
                searchFloor = Integer.parseInt(value);
            }

            if (key.equals("item.lookup")) {
                itemLookup = Integer.parseInt(value);
            }

            if (key.equals("user.email")) {
                userEmail = value;
            }
        }
    }

    // close the inputs
    br.close();
    fr.close();

    return;
}

From source file:big.BigZip.java

/**
 * Looks inside a textWeird file to discover the line that contains a given
keyword. When the line is discovered then it returns an array where
 * the first long represents the start of data and the second represents
 * its end./*ww w.  j  ava  2 s  .com*/
 * @param file      A file on disk
 * @param keyword   A keyword that must be present on the file
 * @return          An array with the start and end position of a given
 * file inside our BIG archive. If we don't have a match, the result is NULL
 */
private long[] getFileCoordinates(final File file, final String keyword) {
    // what we provide as answer
    long[] result = null;
    BufferedReader reader;
    try {
        FileReader fileReader = new FileReader(file);
        reader = new BufferedReader(fileReader);
        String line = "";
        while (line != null) {
            // do we have a match? Yes, let's proceed
            if (line.endsWith(keyword)) {
                // an example of what we are reading:
                // 000000000180411 3f1f0990b8200b5e9b5de461a7fa7f7640ae16f7 /C/HappyNuno.txt
                final String startValue = line.substring(0, 15);
                // get the coordinate and ignore the magic signature size to get the raw binary contents
                final long val1 = Long.parseLong(startValue) + magicSignature.length();
                // now read the next line to get the end value
                line = reader.readLine();
                final String endValue = line.substring(0, 15);
                final long val2 = Long.parseLong(endValue);
                // deliver the value
                result = new long[] { val1, val2 };
                break;
            }
            line = reader.readLine();
        }
        fileReader.close();
        reader.close();
    } catch (IOException ex) {
        Logger.getLogger(files.class.getName()).log(Level.SEVERE, null, ex);
    }
    // all done    
    return result;
}

From source file:base.BasePlayer.AddGenome.java

static void makeGenomes() {
    try {//from   w  w  w.ja  v  a 2s  . c  o m
        FileReader freader = null;
        File file = new File(Main.genomeDir.getCanonicalPath() + "/ensembl.txt");
        if (file.exists()) {
            freader = new FileReader(file);

            BufferedReader reader = new BufferedReader(freader);
            String line, name;
            String[] split;

            while ((line = reader.readLine()) != null) {
                split = line.split("\t");
                name = split[0].substring(split[0].lastIndexOf("/") + 1, split[0].indexOf(".dna."));
                organisms.add(name);
                if (split[0].contains("GRCh38")) {
                    split[0] = split[0].replace("toplevel", "primary_assembly");
                }
                if (split.length == 5) {
                    URL[] urls = { new URL(split[0]), new URL(split[2]), new URL(split[4]) };
                    genomeHash.put(name, urls);
                } else {
                    URL[] urls = { new URL(split[0]), new URL(split[2]) };
                    genomeHash.put(name, urls);
                }
                Integer[] sizes = { Integer.parseInt(split[1]), Integer.parseInt(split[3]) };
                sizeHash.put(name, sizes);
            }

            freader.close();
            reader.close();
        }
        file = new File(Main.genomeDir.getCanonicalPath() + "/ensembl_fetched.txt");
        if (file.exists()) {

            freader = new FileReader(file);

            BufferedReader reader = new BufferedReader(freader);
            String line, name;
            String[] split;
            while ((line = reader.readLine()) != null) {
                split = line.split("\t");
                name = split[0].substring(split[0].lastIndexOf("/") + 1, split[0].indexOf(".dna."));
                organisms.add(name);
                if (split[0].contains("GRCh38")) {
                    split[0] = split[0].replace("toplevel", "primary_assembly");
                }
                if (split.length == 5) {
                    URL[] urls = { new URL(split[0]), new URL(split[2]), new URL(split[4]) };
                    genomeHash.put(name, urls);
                } else {
                    URL[] urls = { new URL(split[0]), new URL(split[2]) };
                    genomeHash.put(name, urls);
                }
                Integer[] sizes = { Integer.parseInt(split[1]), Integer.parseInt(split[3]) };
                sizeHash.put(name, sizes);
            }
            freader.close();
            reader.close();
        }
        /*      URL[] urls = {new URL("ftp://ftp.ensembl.org/pub/grch37/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz"),
            new URL("ftp://ftp.ensembl.org/pub/grch37/update/gff3/homo_sapiens/Homo_sapiens.GRCh37.82.gff3.gz"),
            new URL("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz")};
              Integer[] sizes = new Integer[2];
              sizes[0] = 900;
              sizes[1] = 40;
              sizeHash.put("Homo_sapiens_GRCh37", sizes);
              genomeHash.put("Homo_sapiens_GRCh37", urls);
                      
           /*   URL[] urls2 = {new URL("ftp://ftp.ensembl.org/pub/grch37/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz"),
         new URL("ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.3/GFF/ref_GRCh37.p5_top_level.gff3.gz"),
         new URL("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz") };
              sizes = new Integer[2];
              sizes[0] = 900;
              sizes[1] = 35;
              sizeHash.put("Homo_sapiens_GRCh37:RefSeq_genes", sizes);
              genomeHash.put("Homo_sapiens_GRCh37:RefSeq_genes", urls2);
              */
        /*   URL[] urls3 = { new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/ciona_intestinalis/dna/Ciona_intestinalis.KH.dna.toplevel.fa.gz"),
          new URL("ftp://ftp.ensembl.org/pub/release-85/gff3/ciona_intestinalis/Ciona_intestinalis.KH.85.gff3.gz")
           };
           sizes = new Integer[2];
           sizes[0] = 34;
           sizes[1] = 5;
           sizeHash.put("Ciona_intestinalis", sizes);
           genomeHash.put("Ciona_intestinalis", urls3);
                   
           URL[] urls4 = { new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz"),
                 new URL("ftp://ftp.ensembl.org/pub/release-85/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.85.gff3.gz")
           };
           sizes = new Integer[2];
           sizes[0] = 4;
           sizes[1] = 1;
           sizeHash.put("Saccharomyces_cerevisiae", sizes);
           genomeHash.put("Saccharomyces_cerevisiae", urls4);
                   
           URL[] urls5 = {new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz"),
         new URL("ftp://ftp.ensembl.org/pub/release-85/gff3/mus_musculus/Mus_musculus.GRCm38.85.gff3.gz"),
         new URL("http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBand.txt.gz")};
                   
           sizes = new Integer[2];
           sizes[0] = 801;
           sizes[1] = 58;
           sizeHash.put("Mus_musculus_GRCm38", sizes);
           genomeHash.put("Mus_musculus_GRCm38", urls5);
                   
        /*   URL[] urls6 = {new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz"),
         new URL("ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz") };
           sizes = new Integer[2];
           sizes[0] = 801;
           sizes[1] = 28;
           sizeHash.put("Mus_musculus_GRCm38:RefSeq_genes", sizes);
           genomeHash.put("Mus_musculus_GRCm38:RefSeq_genes", urls6);
                   
           URL[] urls7 = {new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz"),
         new URL("ftp://ftp.ensembl.org/pub/release-85/gff3/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.85.gff3.gz") };
           sizes = new Integer[2];
           sizes[0] = 812;
           sizes[1] = 15;
           sizeHash.put("Rattus_norvegicus", sizes);
           genomeHash.put("Rattus_norvegicus", urls7);
                   
                   
           URL[] urls8 = {new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"),
         new URL("ftp://ftp.ensembl.org/pub/release-85/gff3/homo_sapiens/Homo_sapiens.GRCh38.85.gff3.gz"),
         new URL("http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz")};
           sizes = new Integer[2];
           sizes[0] = 860;
           sizes[1] = 38;
           sizeHash.put("Homo_sapiens_GRCh38", sizes);
           genomeHash.put("Homo_sapiens_GRCh38", urls8);
                
           /*URL[] urls9 = {new URL("ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"),
         new URL("ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p7_top_level.gff3.gz"),
         new URL("http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz")};
           sizes = new Integer[2];
           sizes[0] = 860;
           sizes[1] = 41;
           sizeHash.put("Homo_sapiens_GRCh38:RefSeq_genes", sizes);
           genomeHash.put("Homo_sapiens_GRCh38:RefSeq_genes", urls9);
        */
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

From source file:com.xoriant.akka.mongodb.bulkimport.actor.FileReaderActor.java

private void readAndInsertCSV(String filePath) {
    FileReader fileReader = null;

    CSVParser csvFileParser = null;/*from  w  ww  .  j av a  2  s  . co  m*/

    // Create the CSVFormat object with the header mapping
    CSVFormat csvFileFormat = CSVFormat.EXCEL.withHeader(FILE_HEADER_MAPPING);

    try {

        fileReader = new FileReader(filePath);

        csvFileParser = new CSVParser(fileReader, csvFileFormat);

        List<CSVRecord> csvRecords = csvFileParser.getRecords();
        CSVRecordBatchMsg csvRecordBatch = new CSVRecordBatchMsg();
        boolean batchSent = false;
        // Skip the header row and start reading CSV records
        for (int i = 1; i < csvRecords.size(); i++) {
            CSVRecord record = csvRecords.get(i);
            BasicDBObject person = new BasicDBObject();
            person.put(PERSON_GENDER, record.get(PERSON_GENDER));
            person.put(PERSON_TITLE, record.get(PERSON_TITLE));
            person.put(PERSON_NAMESET, record.get(PERSON_NAMESET));
            person.put(PERSON_SURNAME, record.get(PERSON_SURNAME));
            person.put(PERSON_CITY, record.get(PERSON_CITY));
            person.put(PERSON_STATE, record.get(PERSON_STATE));
            person.put(PERSON_ZIPCODE, record.get(PERSON_ZIPCODE));
            csvRecordBatch.add(person);
            batchSent = false;
            if (i % batchSize == 0) {
                batchSentCounter++;
                csvRecordBatch.setBatchNo(batchSentCounter);
                mongoInsertionActor.tell(csvRecordBatch, getSelf());
                csvRecordBatch = new CSVRecordBatchMsg();
                batchSent = true;
            }

        }

        // Last batch maybe pending if there are less than batch size left over records. Sending last batch of such records explicitly
        if (!batchSent) {
            batchSentCounter++;
            csvRecordBatch.setBatchNo(batchSentCounter);
            mongoInsertionActor.tell(csvRecordBatch, getSelf());
        }
        mongoInsertionActor.tell(new EndOfFileMsg(), getSelf());
        System.out.println("FileReaderActor: EOF sent");

    } catch (Exception e) {
        System.out.println("Error in CsvFileReader !!!" + e.getMessage());
    } finally {
        try {
            fileReader.close();
            csvFileParser.close();
        } catch (IOException e) {
            System.out.println("Error while closing fileReader/csvFileParser : " + e.getMessage());
        }
    }

}

From source file:org.apache.jetspeed.modules.actions.portlets.PsmlManagerAction.java

/**
 * Load a PSMLDOcument from disk// ww w .  j a va 2  s. co m
 *
 * @param fileOrUrl a String representing either an absolute URL or an
 * absolute filepath
 */
private PSMLDocument loadDocument(String fileOrUrl) {
    PSMLDocument doc = null;

    if (fileOrUrl != null) {

        // we'll assume the name is the the location of the file
        File f = null;

        f = new File(fileOrUrl);

        if (!f.exists()) {
            return null;
        }

        doc = new BasePSMLDocument();
        doc.setName(fileOrUrl);

        // now that we have a file reference, try to load the serialized PSML
        Portlets portlets = null;
        FileReader reader = null;
        try {
            reader = new FileReader(f);

            Unmarshaller unmarshaller = new Unmarshaller(this.loadMapping());
            portlets = (Portlets) unmarshaller.unmarshal(reader);

            doc.setPortlets(portlets);

        } catch (IOException e) {
            logger.error("PsmlManagerAction: Could not load the file " + f.getAbsolutePath(), e);
        } catch (MarshalException e) {
            logger.error("PsmlManagerAction: Could not unmarshal the file " + f.getAbsolutePath(), e);
        } catch (MappingException e) {
            logger.error("PsmlManagerAction: Could not unmarshal the file " + f.getAbsolutePath(), e);
        } catch (ValidationException e) {
            logger.error("PsmlManagerAction: document " + f.getAbsolutePath() + " is not valid", e);
        } catch (Exception e) {
            logger.error("PsmlManagerAction: Error while loading  " + f.getAbsolutePath(), e);
        } finally {
            try {
                reader.close();
            } catch (IOException e) {
            }
        }
    }

    return doc;
}

From source file:SWTFileViewerDemo.java

/**
 * Copies a file or entire directory structure.
 * //  w w  w .  j ava  2s.  c o m
 * @param oldFile
 *            the location of the old file or directory
 * @param newFile
 *            the location of the new file or directory
 * @return true iff the operation succeeds without errors
 */
boolean copyFileStructure(File oldFile, File newFile) {
    if (oldFile == null || newFile == null)
        return false;

    // ensure that newFile is not a child of oldFile or a dupe
    File searchFile = newFile;
    do {
        if (oldFile.equals(searchFile))
            return false;
        searchFile = searchFile.getParentFile();
    } while (searchFile != null);

    if (oldFile.isDirectory()) {
        /*
         * Copy a directory
         */
        if (progressDialog != null) {
            progressDialog.setDetailFile(oldFile, ProgressDialog.COPY);
        }
        if (simulateOnly) {
            // System.out.println(getResourceString("simulate.DirectoriesCreated.text",
            // new Object[] { newFile.getPath() }));
        } else {
            if (!newFile.mkdirs())
                return false;
        }
        File[] subFiles = oldFile.listFiles();
        if (subFiles != null) {
            if (progressDialog != null) {
                progressDialog.addWorkUnits(subFiles.length);
            }
            for (int i = 0; i < subFiles.length; i++) {
                File oldSubFile = subFiles[i];
                File newSubFile = new File(newFile, oldSubFile.getName());
                if (!copyFileStructure(oldSubFile, newSubFile))
                    return false;
                if (progressDialog != null) {
                    progressDialog.addProgress(1);
                    if (progressDialog.isCancelled())
                        return false;
                }
            }
        }
    } else {
        /*
         * Copy a file
         */
        if (simulateOnly) {
            // System.out.println(getResourceString("simulate.CopyFromTo.text",
            // new Object[] { oldFile.getPath(), newFile.getPath() }));
        } else {
            FileReader in = null;
            FileWriter out = null;
            try {
                in = new FileReader(oldFile);
                out = new FileWriter(newFile);

                int count;
                while ((count = in.read()) != -1)
                    out.write(count);
            } catch (FileNotFoundException e) {
                return false;
            } catch (IOException e) {
                return false;
            } finally {
                try {
                    if (in != null)
                        in.close();
                    if (out != null)
                        out.close();
                } catch (IOException e) {
                    return false;
                }
            }
        }
    }
    return true;
}

From source file:org.fhaes.jsea.JSEAFrame.java

/**
 * Parse the events file to extract years with events
 * //  w ww.  ja v  a2s  . c om
 * @return
 */
public Boolean parseEventListFile() {

    File f = new File(this.txtEventListFile.getText());
    if (!f.exists()) {
        log.error("Event list file does not exist");
        return false;
    }

    FileReader fr = null;
    BufferedReader br = null;
    String record = null;
    events = new ArrayList<Integer>();

    try {
        fr = new FileReader(txtEventListFile.getText());
        br = new BufferedReader(fr);

        while ((record = br.readLine()) != null) {
            if (!record.contains("*")) {

                try {
                    events.add(new Integer(record));
                } catch (NumberFormatException e) {
                    JOptionPane.showMessageDialog(this,
                            "The event file must contain a list of integer values after any comment lines.\nPlease check the file and try again.",
                            "Warning", JOptionPane.ERROR_MESSAGE);
                    txtEventListFile.setText("");
                    fr.close();
                    br.close();
                    return false;
                }

            }
        }
    } catch (IOException ex) {
        JOptionPane.showMessageDialog(this, "Error reading events file.\nPlease check the file and try again.",
                "Warning", JOptionPane.ERROR_MESSAGE);
        txtEventListFile.setText("");

        return false;
    } finally {
        try {
            fr.close();
            br.close();
        } catch (IOException e) {
            e.printStackTrace();
        }

    }

    Collections.sort(events);

    return true;
}