Package ru.autosome.commons.model

Examples of ru.autosome.commons.model.Position

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    return cache_score_by_position;
  }

  public Position best_position() {
    Double max_score = Double.NEGATIVE_INFINITY;
    Position best_position = null;
    for (Position position : scores_by_position().keySet()) {
      if (scores_by_position().get(position) > max_score) {
        best_position = position;
        max_score = scores_by_position().get(position);
      }
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      Character allele = sequenceWithSNP.mid[allele_number];
      EstimateAffinityMinPvalue affinity_calculator =  new EstimateAffinityMinPvalue(pwm,
                                                                                     sequence,
                                                                                     pvalueCalculator,
                                                                                     positionsToCheck());
      Position pos = affinity_calculator.bestPosition();
      double pvalue = affinity_calculator.affinity();
      Sequence word = sequence.substring(pos, pwm.length());

      Position pos_centered = new Position(pos.position - sequenceWithSNP.left.length(), pos.directStrand);
      return new RegionAffinityVariantInfo(pos_centered, allele, pvalue, word);
  }
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    } else if (opt.equals("--position")) {
      String pos_string = argv.remove(0);
      String[] pos_tokens = pos_string.split(",");
      Integer shift = Integer.valueOf(pos_tokens[0]);
      String orientation = pos_tokens[1];
      alignment = new Position(shift, orientation);
    } else if (opt.equals("--transpose")) {
      transposeFirst = true;
      transposeSecond = true;
    } else if (opt.equals("--first-transpose")) {
      transposeFirst = true;
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  }

  private List<Position> relative_alignments() {
    List<Position> result = new ArrayList<Position>();
    for(int shift = -secondPWM.length(); shift <= firstPWM.length(); ++shift) {
      result.add(new Position(shift, true));
      result.add(new Position(shift, false));
    }
    return result;
  }
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Related Classes of ru.autosome.commons.model.Position

  • ru.autosome.macroape.calculation.generalized.CompareModelsCountsGiven
  • ru.autosome.macroape.cli.generalized.EvalSimilarity
  • ru.autosome.perfectosape.calculation.ScanSequence
  • ru.autosome.perfectosape.calculation.SNPScan
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