Package ru.autosome.ape.calculation.findThreshold

Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold.thresholdByPvalue()

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  protected List<PWMWithThreshold> collectThreshold() throws HashOverflowException {
    List<PWMWithThreshold> result = new ArrayList<PWMWithThreshold>();
    for (ModelType pwm: pwmCollection) {
      CanFindThreshold roughThresholdCalculator = new FindThresholdAPE<ModelType, BackgroundType>(pwm, background, roughDiscretizer, maxHashSize);
      CanFindThreshold.ThresholdInfo roughThresholdInfo = roughThresholdCalculator.thresholdByPvalue(pvalue, pvalueBoundary);
      double roughThreshold = roughThresholdInfo.threshold;
      double roughCount = roughThresholdInfo.numberOfRecognizedWords(background, pwm.length());

      CanFindThreshold preciseThresholdCalculator = new FindThresholdAPE<ModelType, BackgroundType>(pwm, background, preciseDiscretizer, maxHashSize);
      CanFindThreshold.ThresholdInfo preciseThresholdInfo = preciseThresholdCalculator.thresholdByPvalue(pvalue, pvalueBoundary);
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      CanFindThreshold.ThresholdInfo roughThresholdInfo = roughThresholdCalculator.thresholdByPvalue(pvalue, pvalueBoundary);
      double roughThreshold = roughThresholdInfo.threshold;
      double roughCount = roughThresholdInfo.numberOfRecognizedWords(background, pwm.length());

      CanFindThreshold preciseThresholdCalculator = new FindThresholdAPE<ModelType, BackgroundType>(pwm, background, preciseDiscretizer, maxHashSize);
      CanFindThreshold.ThresholdInfo preciseThresholdInfo = preciseThresholdCalculator.thresholdByPvalue(pvalue, pvalueBoundary);
      double preciseThreshold = preciseThresholdInfo.threshold;
      double preciseCount = preciseThresholdInfo.numberOfRecognizedWords(background, pwm.length());

      result.add(new PWMWithThreshold(pwm,
                                      roughThreshold, roughCount,
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    if (cacheFirstThreshold == null) {
      if (predefinedFirstThreshold != null) {
        cacheFirstThreshold = predefinedFirstThreshold;
      } else {
        CanFindThreshold pvalue_calculator = new FindThresholdAPE<ModelType, BackgroundType>(firstPWM, firstBackground, discretizer, maxHashSize);
        cacheFirstThreshold = pvalue_calculator.thresholdByPvalue(pvalue, pvalueBoundary).threshold;
      }
    }
    return cacheFirstThreshold;
  }
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    if (cacheSecondThreshold == null) {
      if (predefinedSecondThreshold != null) {
        cacheSecondThreshold = predefinedSecondThreshold;
      } else {
        CanFindThreshold pvalue_calculator = new FindThresholdAPE<ModelType, BackgroundType>(secondPWM, secondBackground, discretizer, maxHashSize);
        cacheSecondThreshold = pvalue_calculator.thresholdByPvalue(pvalue, pvalueBoundary).threshold;
      }
    }
    return cacheSecondThreshold;
  }
}
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  double queryThreshold(Discretizer discretizer) throws HashOverflowException {
    if (queryPredefinedThreshold != null) {
      return queryPredefinedThreshold;
    } else {
      CanFindThreshold pvalue_calculator = new FindThresholdAPE<ModelType, BackgroundType>(queryPWM, queryBackground, discretizer, maxHashSize);
      return pvalue_calculator.thresholdByPvalue(pvalue, pvalueBoundaryType).threshold;
    }
  }

  public class SimilarityInfo extends CompareModelsCountsGiven.SimilarityInfo<ModelType> {
    public final ModelType collectionPWM;
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    // Single threshold
    {
      CanFindThreshold.ThresholdInfo info = null;
      try {
        info = calculator.thresholdByPvalue(pvalue, pvalue_boundary);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      print_result(info, background, pwm.length());
    }
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