Package ru.autosome.ape.calculation.findPvalue

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

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    Map<PWM, Map<SequenceWithSNP, SNPScan.RegionAffinityInfos>> result;
    setStatus(Status.RUNNING);
    try {
      result = new HashMap<PWM, Map<SequenceWithSNP, SNPScan.RegionAffinityInfos>>();
      for (PWM pwm: parameters.pvalueCalculator.keySet()) {
        CanFindPvalue pvalueCalculator = parameters.pvalueCalculator.get(pwm);

        Map<SequenceWithSNP,SNPScan.RegionAffinityInfos> result_part = new HashMap<SequenceWithSNP, SNPScan.RegionAffinityInfos>();

        for (SequenceWithSNP sequenceWithSNP: parameters.sequencesWithSNP) {
          if (interrupted()) {
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  protected void load_collection_of_pwms_with_evaluators() {
    List<MotifType> motifList = load_collection_of_pwms();

    pwmCollection = new ArrayList<ThresholdEvaluator>();
    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);
      }
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Related Classes of ru.autosome.ape.calculation.findPvalue.CanFindPvalue

  • ru.autosome.perfectosape.api.MultiSNPScan
  • ru.autosome.perfectosape.cli.generalized.MultiSNPScan
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