Examples of edu.umd.hooka.alignment.aer.ReferenceAlignment.countSureAlignmentPoints()

        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;
    }


    public void close() {

      if (ref != null) {
        a = trainer.computeAlignmentPosteriors(value).alignPosteriorThreshold(0.5f);
        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());
        if (gmodel1!=null) {
          StringBuffer sb=new StringBuffer();
          for (int i =0; i<ref.getELength(); i++)
            for (int j=0; j<ref.getFLength(); j++) {
              if (ref.isProbableAligned(j, i) || ref.isSureAligned(j, i))

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