Examples of countAlignmentPoints()

Examples of edu.umd.hooka.Alignment.countAlignmentPoints()

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    float den = 0.0f;
    while (refi.hasNext()) {
      ReferenceAlignment ref = refi.next();
      Alignment test = testi.next();
      num += (ref.countProbableHits(test) + ref.countSureHits(test));
      den += (test.countAlignmentPoints() + ref.countAlignmentPoints());
    }
    if (testi.hasNext())
      throw new RuntimeException("Mismatch in lengths");
    return num / den;
  }
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Examples of edu.umd.hooka.Alignment.countAlignmentPoints()

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        Alignment a = trainer.viterbiAlign(value, pr);
        a = trainer.computeAlignmentPosteriors(value).alignPosteriorThreshold(0.5f);
        ReferenceAlignment ref = (ReferenceAlignment)value.getAlignment();
        reporter.incrCounter(AlignmentEvalEnum.SURE_HITS, ref.countSureHits(a));
        reporter.incrCounter(AlignmentEvalEnum.PROBABLE_HITS, ref.countProbableHits(a));
        reporter.incrCounter(AlignmentEvalEnum.HYPOTHESIZED_ALIGNMENT_POINTS, a.countAlignmentPoints());
        reporter.incrCounter(AlignmentEvalEnum.REF_ALIGNMENT_POINTS, ref.countSureAlignmentPoints());
      }
      hasCounts = true;
    }
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