Examples with StringBuilder java.lang.StringBuilder used on opensource projects

Example 1 with StringBuilder

use of java.lang.StringBuilder in project MSEC by Tencent.

the class MysqlSink method createTable.

private int createTable() throws IOException, SQLException {
    SimpleDateFormat formatter = new SimpleDateFormat("MMdd");
    String curTableName = "t_dailylog_" + formatter.format(new Date());
    if (curTableName.compareTo(tableName) == 0) {
        return 0;
    }
    DatabaseMetaData md = conn.getMetaData();
    ResultSet rs = md.getTables(null, null, curTableName, null);
    if (rs.next()) {
        tableName = curTableName;
        return 1;
    }
    //create table
    File file = new File(createTableSqlFile);
    BufferedReader bf = new BufferedReader(new FileReader(file));
    StringBuilder sb = new StringBuilder();
    String line = "";
    while (line != null) {
        line = bf.readLine();
        if (line == null)
            break;
        sb.append(line);
    }
    String createTableSql = sb.toString().replace("$TABLENAME$", curTableName);
    Statement stmt = conn.createStatement();
    stmt.executeUpdate(createTableSql);
    LOG.info("Create table " + curTableName + " using sql statement: " + createTableSql);
    tableName = curTableName;
    return 2;
}

Example 2 with StringBuilder

use of java.lang.StringBuilder in project android_frameworks_base by DirtyUnicorns.

the class VrManagerService method formatSettings.

private static String formatSettings(Collection<String> c) {
    if (c == null || c.isEmpty()) {
        return "";
    }
    StringBuilder b = new StringBuilder();
    boolean start = true;
    for (String s : c) {
        if ("".equals(s)) {
            continue;
        }
        if (!start) {
            b.append(':');
        }
        b.append(s);
        start = false;
    }
    return b.toString();
}

Example 3 with StringBuilder

use of java.lang.StringBuilder in project polyGembler by c-zhou.

the class Population method formatOutput.

private String formatOutput(String dnaSEQ) {
    // TODO Auto-generated method stub
    Pattern p = Pattern.compile("(.{" + CHUNK_SIZE + "})", Pattern.DOTALL);
    Matcher m = p.matcher(dnaSEQ);
    StringBuilder os = new StringBuilder();
    os.append(m.replaceAll("$1" + "\n"));
    if (os.charAt(os.length() - 1) != '\n')
        os.append("\n");
    return os.toString();
}

Example 4 with StringBuilder

use of java.lang.StringBuilder in project polyGembler by c-zhou.

the class Population method generateChromosome.

public Chromosome0[] generateChromosome(String fastaFilePath) {
    List<String> chroms = new ArrayList<String>();
    double physicaL = 0.0;
    try {
        BufferedReader br = getBufferedReader(fastaFilePath);
        StringBuilder sb = new StringBuilder();
        String line = br.readLine();
        while (line != null) {
            if (line.startsWith(">")) {
                sb.setLength(0);
                while ((line = br.readLine()) != null && !line.startsWith(">")) sb.append(line);
                chroms.add(sb.toString());
                physicaL += sb.length();
            }
        }
        br.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    double CHROM_BASE_LENGTH = GENETIC_LENGTH > 0 ? GENETIC_LENGTH / physicaL : 1e-6;
    int N = chroms.size();
    Chromosome0[] chromosome = new Chromosome0[N];
    for (int i = 0; i < N; i++) {
        double cm = chroms.get(i).length() * CHROM_BASE_LENGTH;
        chromosome[i] = new Chromosome0("CHROM" + (i + 1), chroms.get(i), chroms.get(i).length(), cm, CENTROMERE_POS * cm, random.nextFloat() / 2 + 0.5, 0.0);
    }
    return chromosome;
}

Example 5 with StringBuilder

use of java.lang.StringBuilder in project polyGembler by c-zhou.

the class GBS method simulate.

public void simulate(final int sim_sample_index) {
    try {
        // GBSFastqFileBufferedWriter = getGZIPBufferedWriter(GBSFastqFilePath);
        String name, line, fastaFilePath;
        ArrayList<Integer> cut, recognization;
        StringBuilder chromosome;
        FastqRead fastq;
        int l;
        Digest digestion;
        fastaFilePath = fastaFileList.get(sim_sample_index);
        StringBuilder oos = new StringBuilder();
        // try{
        BufferedWriter GBSFastqFileBufferedWriter = getGZIPBufferedWriter(GBSFastqFilePath + "_" + sim_sample_index + ".gz", 65536);
        BufferedReader br = getBufferedReader(fastaFilePath);
        line = br.readLine();
        while (line != null) {
            name = parseSampleName(fastaFilePath) + "|" + line.replaceFirst(">", "");
            chromosome = new StringBuilder();
            while ((line = br.readLine()) != null && !line.startsWith(">")) {
                chromosome.append(line);
            }
            l = chromosome.length();
            // System.out.println(getSystemTime()+">>> digest starting...");
            digestion = new Digest(enzyme, chromosome.toString());
            // System.out.println(getSystemTime()+">>> done.");
            cut = digestion.getCutsite();
            recognization = digestion.getRecognization();
            // System.out.println(getSystemTime()+">>> simulate starting...");
            // simulate 5'-3' end genome
            int coverage;
            for (int i = 2; i < cut.size(); i++) {
                if (cut.get(i) - cut.get(i - 1) < MIN_FRAGMENT_SIZE)
                    continue;
                coverage = (int) Math.round(meanDepth + random.nextGaussian() * sdDepth);
                for (int j = 0; j < coverage; j++) {
                    fastq = generateFastqRead(chromosome.substring(cut.get(i - 1), cut.get(i)), recognization.get(i - 1), fastaFileBarcodeMap.get(fastaFilePath), "@" + name + "|" + cut.get(i - 1) + "|" + j, false);
                    // writeFastqRead(fastq);
                    oos.setLength(0);
                    oos.append(fastq.identifier);
                    oos.append(NLS);
                    oos.append(fastq.sequence);
                    oos.append(NLS);
                    oos.append(fastq.plus);
                    oos.append(NLS);
                    oos.append(fastq.quality);
                    oos.append(NLS);
                    GBSFastqFileBufferedWriter.write(oos.toString());
                }
            }
            // simulate reverse complementary genome
            chromosome.reverse();
            for (int i = 0; i < l; i++) chromosome.setCharAt(i, baseComplementaryMap.get(chromosome.charAt(i)));
            for (int i = 0; i < cut.size(); i++) cut.set(i, l - cut.get(i));
            Collections.reverse(cut);
            for (int i = 2; i < cut.size(); i++) {
                if (cut.get(i) - cut.get(i - 1) < MIN_FRAGMENT_SIZE)
                    continue;
                coverage = (int) Math.round(meanDepth + random.nextGaussian() * sdDepth);
                for (int j = 0; j < coverage; j++) {
                    fastq = generateFastqRead(chromosome.substring(cut.get(i - 1), cut.get(i)), recognization.get(i - 1), fastaFileBarcodeMap.get(fastaFilePath), "@" + name + "|" + cut.get(i - 1) + "|1", true);
                    // writeFastqRead(fastq);
                    oos.setLength(0);
                    oos.append(fastq.identifier);
                    oos.append(NLS);
                    oos.append(fastq.sequence);
                    oos.append(NLS);
                    oos.append(fastq.plus);
                    oos.append(NLS);
                    oos.append(fastq.quality);
                    oos.append(NLS);
                    GBSFastqFileBufferedWriter.write(oos.toString());
                }
            }
            // System.out.println(getSystemTime()+">>> done.");
            System.out.println(getSystemTime() + ">>> " + name + " done.");
        }
        br.close();
        GBSFastqFileBufferedWriter.close();
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
    }
// GBSFastqFileBufferedWriter.close();
// } catch (IOException | InterruptedException e) {
// } catch (InterruptedException e) {
// e.printStackTrace();
// System.exit(1);
// }
}