コード例 #1
0
  @Override
  public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2) {
    int[] positions = correctPositions(pos1, pos2, sequences.getDuplexLength());
    pos1 = positions[0];
    pos2 = positions[1];

    NucleotidSequences newSequences = sequences.getEquivalentSequences("rna");

    String sequence =
        NucleotidSequences.convertToPyr_Pur(sequences.getSequenceContainig("-", pos1, pos2));
    String complementary =
        NucleotidSequences.convertToPyr_Pur(
            sequences.getComplementaryTo(
                sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2));

    if (sequence.charAt(0) == '-') {

      if (complementary.charAt(1) == 'Y'
          || (complementary.charAt(1) != 'Y' && complementary.charAt(2) == 'Y')) {
        complementary = complementary.substring(1, 3);
      }
    } else {
      if (complementary.charAt(1) == 'Y'
          || (complementary.charAt(1) != 'Y' && complementary.charAt(0) == 'Y')) {
        complementary = complementary.substring(0, 2);
      }
    }

    if (sequences
        .getSequenceSens(sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2)
        .equals("5'3'")) {

      if (this.collector.getDanglingValue(sequence, complementary) == null) {
        OptionManagement.logWarning(
            "\n The thermodymamic parameters for "
                + sequence
                + "/"
                + complementary
                + " are missing. Check the second dangling ends parameters.");

        return true;
      }
    } else {

      if (this.collector.getDanglingValue(complementary, sequence) == null) {
        OptionManagement.logWarning(
            "\n The thermodymamic parameters for "
                + complementary
                + "/"
                + sequence
                + " are missing. Check the second dangling ends parameters.");

        return true;
      }
    }

    return super.isMissingParameters(newSequences, pos1, pos2);
  }
コード例 #2
0
  @Override
  public ThermoResult computeThermodynamics(
      NucleotidSequences sequences, int pos1, int pos2, ThermoResult result) {
    int[] positions = super.correctPositions(pos1, pos2, sequences.getDuplexLength());
    pos1 = positions[0];
    pos2 = positions[1];

    NucleotidSequences newSequences = sequences.getEquivalentSequences("rna");

    OptionManagement.logMessage("\n The nearest neighbor model for double" + " dangling end is");
    OptionManagement.logMethodName(methodName);
    OptionManagement.logFileName(this.fileName);

    result = super.computeThermodynamics(newSequences, pos1, pos2, result);

    double enthalpy = result.getEnthalpy();
    double entropy = result.getEntropy();

    String sequence =
        NucleotidSequences.convertToPyr_Pur(sequences.getSequenceContainig("-", pos1, pos2));
    String complementary =
        NucleotidSequences.convertToPyr_Pur(
            sequences.getComplementaryTo(
                sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2));
    Thermodynamics doubleDanglingValue;

    if (sequence.charAt(0) == '-') {
      if (complementary.charAt(1) == 'Y'
          || (complementary.charAt(1) != 'Y' && complementary.charAt(2) == 'Y')) {
        complementary = complementary.substring(1, 3);
      }
    } else {
      if (complementary.charAt(1) == 'Y'
          || (complementary.charAt(1) != 'Y' && complementary.charAt(0) == 'Y')) {
        complementary = complementary.substring(0, 2);
      }
    }

    if (sequences
        .getSequenceSens(sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2)
        .equals("5'3'")) {
      doubleDanglingValue = this.collector.getDanglingValue(sequence, complementary);
    } else {
      doubleDanglingValue = this.collector.getDanglingValue(complementary, sequence);
    }

    OptionManagement.logMessage(
        "\n"
            + sequences.getSequence(pos1, pos2)
            + "/"
            + sequences.getComplementary(pos1, pos2)
            + ": incremented enthalpy = "
            + doubleDanglingValue.getEnthalpy()
            + "  incremented entropy = "
            + doubleDanglingValue.getEntropy());

    enthalpy += doubleDanglingValue.getEnthalpy();
    entropy += doubleDanglingValue.getEntropy();

    result.setEnthalpy(enthalpy);
    result.setEntropy(entropy);

    return result;
  }