Package ru.autosome.ape.calculation.findPvalue

Examples of ru.autosome.ape.calculation.findPvalue.FindPvalueBsearchBuilder

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                                           new FindPvalueAPE<ModelType, BackgroundType>(pwm, collectionBackground, preciseDiscretizer, maxHashSize)));
      } else {
        result.add(new ThresholdEvaluator( pwm,
                                           new FindThresholdBsearchBuilder(thresholds_folder).thresholdCalculator(pwm),
                                           null,
                                           new FindPvalueBsearchBuilder(thresholds_folder).pvalueCalculator(pwm),
                                           null));
      }
    }
    return result;
  }
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    for (MotifType motif: motifList) {
      CanFindPvalue pvalueCalculator;
      if (thresholds_folder == null) {
        pvalueCalculator = new FindPvalueAPE<MotifType, BackgroundType>(motif, background, discretizer, max_hash_size);
      } else {
        pvalueCalculator = new FindPvalueBsearchBuilder(thresholds_folder).pvalueCalculator(motif);
      }
      pwmCollection.add(new ThresholdEvaluator(motif, pvalueCalculator, motif.getName()));
    }
  }
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  protected CanFindPvalue calculator() {
    if (cache_calculator == null) {
      if (thresholds_folder == null) {
        cache_calculator = new FindPvalueAPE<PWM, BackgroundModel>(motif, background, discretizer, max_hash_size);
      } else {
        cache_calculator = new FindPvalueBsearchBuilder(thresholds_folder).pvalueCalculator(motif);
      }
    }
    return cache_calculator;
  }
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  protected CanFindPvalue calculator() {
    if (cache_calculator == null) {
      if (thresholds_folder == null) {
        cache_calculator = new FindPvalueAPE<DiPWM, DiBackgroundModel>(motif, background, discretizer, max_hash_size);
      } else {
        cache_calculator = new FindPvalueBsearchBuilder(thresholds_folder).pvalueCalculator(motif);
      }
    }
    return cache_calculator;
  }
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Related Classes of ru.autosome.ape.calculation.findPvalue.FindPvalueBsearchBuilder

  • ru.autosome.ape.di.FindPvalue
  • ru.autosome.ape.FindPvalue
  • ru.autosome.ape.model.PvalueBsearchList
  • ru.autosome.macroape.cli.generalized.ScanCollection
  • ru.autosome.perfectosape.cli.generalized.MultiSNPScan
  • java.io.File
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