Package ru.autosome.ape.model

Examples of ru.autosome.ape.model.ScoreDistributionTop

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      scores = recalc_score_hash(scores, pwm.matrix[pos], threshold - pwm.best_suffix(pos + 1));
      if (exceedHashSizeLimit(scores)) {
        throw new HashOverflowException("Hash overflow in PWM::ThresholdByPvalue#score_distribution_above_threshold");
      }
    }
    ScoreDistributionTop result = new ScoreDistributionTop(scores, vocabularyVolume(), threshold);
    result.setWorstScore(pwm.worst_score());
    result.setBestScore(pwm.best_score());
    return result;
  }
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  }

  private ScoreDistributionTop score_distribution_under_pvalue(double pvalue) throws HashOverflowException {
    final int maxNumberOfAttempts = 2;
    int numberOfAttempts = 0;
    ScoreDistributionTop scoreDistribution;
    CanFindThresholdApproximation gaussianThresholdEstimation = gaussianThresholdEstimator();
    double pvalue_to_estimate_threshold = pvalue;
    try {
      do {
        numberOfAttempts += 1;
        if (numberOfAttempts > maxNumberOfAttempts) {
          return score_distribution(); // calculate whole distribution
        }
        // calculate only top part of distribution cause it's faster
        double approximate_threshold = gaussianThresholdEstimation.thresholdByPvalue(pvalue_to_estimate_threshold);
        scoreDistribution = score_distribution_above_threshold(approximate_threshold);
        pvalue_to_estimate_threshold *= 2;
      } while (scoreDistribution.top_part_pvalue() < pvalue);
      return scoreDistribution;

    } catch (ArithmeticException e) {
      return score_distribution();
    }
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      return score_distribution();
    }
  }

  public TDoubleDoubleMap counts_above_thresholds(double[] thresholds) throws HashOverflowException {
    ScoreDistributionTop scoreDistribution = score_distribution_above_threshold(ArrayExtensions.min(thresholds));
    try {
      return scoreDistribution.counts_above_thresholds(thresholds);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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      throw new RuntimeException("Should never be here", exception);
    }
  }

  public Double count_above_threshold(double threshold) throws HashOverflowException {
    ScoreDistributionTop scoreDistribution = score_distribution_above_threshold(threshold);
    try {
      return scoreDistribution.count_above_threshold(threshold);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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      throw new RuntimeException("Should never be here", exception);
    }
  }

  TDoubleObjectMap<ScoreDistributionTop.ThresholdsRange> thresholds_by_pvalues(double[] pvalues) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(ArrayExtensions.max(pvalues));
    try {
      return scores_hash.thresholds_by_pvalues(pvalues);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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    }
  }

  // "strong" means that threshold has real pvalue not more than requested one
  public CanFindThreshold.ThresholdInfo[] strong_thresholds(double[] pvalues) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(ArrayExtensions.max(pvalues));
    try {
      return scores_hash.strong_thresholds(pvalues);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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      throw new RuntimeException("Should never be here", exception);
    }
  }

  public CanFindThreshold.ThresholdInfo strong_threshold(double pvalue) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(pvalue);
    try {
      return scores_hash.strong_threshold(pvalue);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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    }
  }

  // "strong" means that threshold has real pvalue not less than requested one
  public CanFindThreshold.ThresholdInfo[] weak_thresholds(double[] pvalues) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(ArrayExtensions.max(pvalues));
    try {
      return scores_hash.weak_thresholds(pvalues);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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      throw new RuntimeException("Should never be here", exception);
    }
  }

  public CanFindThreshold.ThresholdInfo weak_threshold(double pvalue) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(pvalue);
    try {
      return scores_hash.weak_threshold(pvalue);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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      throw new RuntimeException("Should never be here", exception);
    }
  }

  public CanFindThreshold.ThresholdInfo[] thresholds(double[] pvalues, BoundaryType pvalueBoundary) throws HashOverflowException {
    ScoreDistributionTop scores_hash = score_distribution_under_pvalue(ArrayExtensions.max(pvalues));
    try {
      return scores_hash.thresholds(pvalues, pvalueBoundary);
    } catch (ScoreDistributionTop.NotRepresentativeDistribution exception) {
      throw new RuntimeException("Should never be here", exception);
    }
  }
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TOP

Related Classes of ru.autosome.ape.model.ScoreDistributionTop

  • gnu.trove.iterator.TDoubleDoubleIterator
  • gnu.trove.map.hash.TDoubleDoubleHashMap
  • gnu.trove.map.TDoubleDoubleMap
  • ru.autosome.perfectosape.calculation.ScoringModelDistributions.CountingDiPWM
  • ru.autosome.perfectosape.calculation.ScoringModelDistributions.CountingPWM
  • ru.autosome.perfectosape.calculation.ScoringModelDistributions.ScoringModelDistibutions
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