Examples of HmmAlignAlgorithmFactory

Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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    List<Filter> filterList = new ArrayList<Filter>();
   
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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      List<Alignment> bestAlignmentList) {
    
    Calculator calculator =
      new TranslationCalculator(bestAlignmentList);

    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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    calculatorList.add(new TranslationCalculator(bestAlignmentList));

    Calculator calculator = new CompositeCalculator(calculatorList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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  public List<Alignment> apply(List<Alignment> alignmentList) {
   
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ViterbiAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
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Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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  private List<Alignment> lengthAlign(List<Alignment> alignmentList) {
    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
View Full Code Here

Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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    calculatorList.add(new TranslationCalculator(bestAlignmentList));

    Calculator calculator = new CompositeCalculator(calculatorList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
View Full Code Here

Examples of net.sourceforge.align.filter.aligner.align.hmm.HmmAlignAlgorithmFactory

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            BandMatrixFactory.DEFAULT_BAND_RADIUS);
        int margin = createInt(commandLine, "margin",
            AdaptiveBandAlgorithm.DEFAULT_MIN_BAND_MARGIN);
        float increment = createFloat(commandLine, "increment",
            AdaptiveBandAlgorithm.DEFAULT_BAND_INCREMENT_RATIO);
        HmmAlignAlgorithmFactory algorithmFactory;
        if (cls.equals("viterbi")) {
          algorithmFactory = new ViterbiAlgorithmFactory();
        } else if (cls.equals("fb")) {
          algorithmFactory = new ForwardBackwardAlgorithmFactory();
        } else {
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