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

Example 26 with StringBuilder

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

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 27 with StringBuilder

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

the class GBS method generateFastqRead.

public FastqRead generateFastqRead(String dnaInsert, int recognization, String barcode, String identifier, boolean reverse) {
    int i = reverse ? 1 : 0;
    String toSequence = barcode + enzymeOverhang[recognization][i] + dnaInsert + enzymeRemainWithCommanAdapter[recognization][i];
    StringBuilder sequence = new StringBuilder();
    StringBuilder quality = new StringBuilder();
    Character prev_base = null, prev_qual = null;
    int b = 0, p = 0, indel, l = toSequence.length(), u;
    while (b < readLength && p < l) {
        if (random.nextFloat() < baseSubIndelErrorRate) {
            indel = random.nextInt(3);
            if (indel == 0) {
                /**
                 * substitution
                 */
                prev_base = baseSubstitutionErrorProbabilityMap.get(toSequence.charAt(p)).get(random.nextInt(INV_PROBS_PRECISION));
                prev_qual = qualityTransitionProbabilityMap.get(b).get(prev_qual).get(random.nextInt(INV_PROBS_PRECISION));
                sequence.append(prev_base);
                quality.append(prev_qual);
                p++;
                b++;
            } else if (indel == 1) {
                /**
                 * insertion
                 */
                u = (int) Math.ceil(-Math.log(1.0 - random.nextFloat()) / baseIndelErrorProbabilityLambda);
                u = Math.min(u, readLength - b);
                sequence.append(insertionSeqFactory(u));
                for (int t = 0; t < u; t++) {
                    prev_qual = qualityTransitionProbabilityMap.get(b).get(prev_qual).get(random.nextInt(INV_PROBS_PRECISION));
                    quality.append(prev_qual);
                    b++;
                }
                prev_base = sequence.charAt(b - 1);
            } else {
                /**
                 * deletion
                 */
                p += Math.ceil(-Math.log(1.0 - random.nextFloat()) / baseIndelErrorProbabilityLambda);
            }
        } else {
            if (prev_base == MISSING_BASE_SYMBOL && random.nextFloat() < probabilityBaseMissingSucceeding[b]) {
                sequence.append(MISSING_BASE_SYMBOL);
                quality.append(MISSING_QUAL_SCORE);
            } else if (random.nextFloat() < probabilityBaseMissingInitialization[b]) {
                prev_base = MISSING_BASE_SYMBOL;
                prev_qual = null;
                sequence.append(MISSING_BASE_SYMBOL);
                quality.append(MISSING_QUAL_SCORE);
            } else {
                prev_base = toSequence.charAt(p);
                prev_qual = qualityTransitionProbabilityMap.get(b).get(prev_qual).get(random.nextInt(INV_PROBS_PRECISION));
                sequence.append(prev_base);
                quality.append(prev_qual);
            }
            p++;
            b++;
        }
    }
    while (b++ < readLength) {
        sequence.append(MISSING_BASE_SYMBOL);
        quality.append(MISSING_QUAL_SCORE);
    }
    return new FastqRead(identifier, sequence.toString(), "+", quality.toString());
}

Example 28 with StringBuilder

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

the class Population method writeGenomeFile.

public void writeGenomeFile(int sim_sample_index) {
    final int N = popData.chromCount();
    String[][] indall;
    // StringBuilder chr;
    ArrayList<Locus> loci;
    int pos;
    String str2write;
    Individual indiv = popData.getIndiv(sim_sample_index);
    try (BufferedWriter bw = getGZIPBufferedWriter(filePath + SEP + scenario + SEP + indiv.getIndivName() + ".fasta.gz")) {
        for (int c = 0; c < N; c++) {
            Chromosome chrom = popData.getChrom(c);
            Chromosome0 chr = chromosome[c];
            loci = chrom.getLocus();
            indall = new String[PLOIDY][loci.size()];
            for (int l = 0; l < loci.size(); l++) {
                String[] inds = indiv.getLocusAllele(c, l);
                for (int h = 0; h < PLOIDY; h++) {
                    indall[h][l] = inds[h];
                }
            }
            for (int h = 0; h < PLOIDY; h++) {
                // debug
                // println(getSystemTime()+" >>> StringBulder starting...");
                /**
                 * String builder is slow
                 *                        chr = new StringBuilder(ref.substring(cutsite[c],cutsite[c+1]));
                 *                        for(int l=0; l<loci.size(); l++) {
                 *                            pos = SNPs2PosMap.get(loci.get(l).getLocusName());
                 *                            chr.replace(pos,pos+indall[h][l].length(),indall[h][l]);
                 *                        }
                 */
                // debug
                // println(getSystemTime()+" >>> Done. BufferedWriter Start writing...");
                String header = ">" + chr.getName() + "|" + (h + 1) + ":" + PLOIDY;
                bw.write(header + NLS);
                final StringBuilder oos = new StringBuilder();
                int j0 = 0, j1 = chr.getLBasePairs();
                for (int l = 0; l < loci.size(); l++) {
                    pos = SNPs2PosMap.get(loci.get(l).getLocusName());
                    str2write = indall[h][l];
                    oos.append(chr.getDnaSEQ().substring(j0, pos - str2write.length() + 1));
                    oos.append(str2write);
                    j0 = pos + str2write.length();
                }
                if (j0 < j1)
                    oos.append(chr.getDnaSEQ().substring(j0, j1));
                bw.write(this.formatOutput(oos.toString()));
                // debug
                myLogger.info(getSystemTime() + " " + header + " >>> done.");
            }
        }
        bw.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }
}

Example 29 with StringBuilder

use of java.lang.StringBuilder in project android_packages_apps_Snap by LineageOS.

the class SettingsManager method getSupportedQcfaDimension.

public String getSupportedQcfaDimension(int cameraId) {
    int[] qcfaDimension = mCharacteristics.get(cameraId).get(CaptureModule.QCFA_SUPPORT_DIMENSION);
    if (qcfaDimension == null) {
        return null;
    }
    StringBuilder sb = new StringBuilder();
    for (int i = 0; i < qcfaDimension.length; i++) {
        sb.append(qcfaDimension[i]);
        if (i == 0) {
            sb.append("x");
        }
    }
    return sb.toString();
}

Example 30 with StringBuilder

use of java.lang.StringBuilder in project MassBank-web by MassBank.

the class MSDBUpdateUtil method updateSubStructData.

/**
 */
public static boolean updateSubStructData(String serverUrl) {
    boolean ret = true;
    String cgiUrl = serverUrl + "cgi-bin/GenSubstructure.cgi";
    try {
        URL url = new URL(cgiUrl);
        HttpURLConnection con = (HttpURLConnection) url.openConnection();
        con.setConnectTimeout(10 * 1000);
        con.setReadTimeout(60 * 1000);
        BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
        String line = "";
        StringBuilder res = new StringBuilder();
        while ((line = in.readLine()) != null) {
            res.append(line);
        }
        if (res.indexOf("OK") == -1) {
            ret = false;
        }
    } catch (IOException e) {
        e.printStackTrace();
        ret = false;
    }
    return ret;
}