Examples of countSureHits()

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

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    Alignment a = new Alignment(4,5);
    a.align(0, 1);
    a.align(1, 1);
    a.align(2, 4);
    a.align(1, 4);
    assertEquals(1,ra.countSureHits(a));
   
//    Alignment b = new Alignment(3,4);
//    try {
//      ra.countProbableHits(b);
//      fail("Should fail");
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Examples of edu.umd.hooka.alignment.aer.ReferenceAlignment.countSureHits()

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        PerplexityReporter pr = new PerplexityReporter();

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

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        value.setAlignmentPosteriorGrid(g);
      }

      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();
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