Examples of CanFindThreshold

Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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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);
      double preciseThreshold = preciseThresholdInfo.threshold;
      double preciseCount = preciseThresholdInfo.numberOfRecognizedWords(background, pwm.length());

      result.add(new PWMWithThreshold(pwm,
                                      roughThreshold, roughCount,
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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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  protected double thresholdFirst() throws HashOverflowException {
    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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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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  protected double thresholdSecond() throws HashOverflowException {
    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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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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                               secondCount(threshold_second),
                               position);
  }

  public CompareModelsCountsGiven.SimilarityInfo jaccard_by_pvalue(double pvalue) throws HashOverflowException {
    CanFindThreshold canFindThresholdFirst = new FindThresholdAPE<ModelType,BackgroundType>(firstPWM, firstBackground, discretizer, null);
    CanFindThreshold canFindThresholdSecond = new FindThresholdAPE<ModelType, BackgroundType>(secondPWM, secondBackground, discretizer, null);

    double threshold_first = canFindThresholdFirst.strongThresholdByPvalue(pvalue).threshold;
    double threshold_second = canFindThresholdSecond.strongThresholdByPvalue(pvalue).threshold;
    return jaccard(threshold_first, threshold_second);
  }
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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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    double threshold_second = canFindThresholdSecond.strongThresholdByPvalue(pvalue).threshold;
    return jaccard(threshold_first, threshold_second);
  }

  public CompareModelsCountsGiven.SimilarityInfo jaccard_by_weak_pvalue(double pvalue) throws HashOverflowException {
    CanFindThreshold canFindThresholdFirst = new FindThresholdAPE<ModelType,BackgroundType>(firstPWM, firstBackground, discretizer, null);
    CanFindThreshold canFindThresholdSecond = new FindThresholdAPE<ModelType,BackgroundType>(secondPWM, secondBackground, discretizer, null);

    double threshold_first = canFindThresholdFirst.weakThresholdByPvalue(pvalue).threshold;
    double threshold_second = canFindThresholdSecond.weakThresholdByPvalue(pvalue).threshold;
    return jaccard(threshold_first, threshold_second);
  }
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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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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;
    }
  }
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Examples of ru.autosome.ape.calculation.findThreshold.CanFindThreshold

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    BoundaryType pvalue_boundary = BoundaryType.LOWER;
    Integer max_hash_size = null;
    double pvalue = 0.0005;
    double[] pvalues = {0.0001, 0.0005, 0.001};

    CanFindThreshold calculator = new FindThresholdAPE<PWM, BackgroundModel>(pwm, background, discretizer, max_hash_size);

    // Single threshold
    {
      CanFindThreshold.ThresholdInfo info = null;
      try {
        info = calculator.thresholdByPvalue(pvalue, pvalue_boundary);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      print_result(info, background, pwm.length());
    }
    // Multiple thresholds
    {
      CanFindThreshold.ThresholdInfo[] infos = new CanFindThreshold.ThresholdInfo[0];
      try {
        infos = calculator.thresholdsByPvalues(pvalues, pvalue_boundary);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      for (CanFindThreshold.ThresholdInfo info : infos) {
        print_result(info, background, pwm.length());
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