Package ru.autosome.ape.model

Examples of ru.autosome.ape.model.PvalueBsearchList

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      if (!silence) {
        System.err.println(file);
      }
      ModelType motif = loadMotif(file);
      File result_filename = new File(results_dir, motif.getName() + ".thr");
      PvalueBsearchList bsearchList = calculator().bsearch_list_for_pwm(motif);
      bsearchList.save_to_file(result_filename);
    }
  }
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  }

  public CanFindThreshold thresholdCalculator(Named motif) {
    try {
      File thresholds_file = new File(pathToThresholds, motif.getName() + ".thr");
      PvalueBsearchList pvalueBsearchList = PvalueBsearchList.load_from_file(thresholds_file);
      return new FindThresholdBsearch(pvalueBsearchList);
    } catch (FileNotFoundException e) {
      return null;
    }
  }
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    List<PvalueBsearchList.ThresholdPvaluePair> pairs = new ArrayList<PvalueBsearchList.ThresholdPvaluePair>();
    for (CanFindThreshold.ThresholdInfo info: infos) {
      pairs.add(new PvalueBsearchList.ThresholdPvaluePair(info));
    }

    return new PvalueBsearchList(pairs);
  }
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  }

  public CanFindPvalue pvalueCalculator(Named motif) {
    try {
      File thresholds_file = new File(pathToThresholds, motif.getName() + ".thr");
      PvalueBsearchList pvalueBsearchList = PvalueBsearchList.load_from_file(thresholds_file);
      return new FindPvalueBsearch(pvalueBsearchList);
    } catch (FileNotFoundException e) {
      return null;
    }
  }
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Related Classes of ru.autosome.ape.model.PvalueBsearchList

  • ru.autosome.ape.calculation.findPvalue.FindPvalueBsearchBuilder
  • ru.autosome.ape.calculation.findThreshold.FindThresholdBsearchBuilder
  • ru.autosome.ape.calculation.PrecalculateThresholdList
  • ru.autosome.ape.cli.generalized.PrecalculateThresholdLists
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