Examples of PoissonDistributionCalculator

net.sourceforge.align.calculator.length.PoissonDistributionCalculator
Represents length-base calculator that computes alignment score assuming that alignment lengths have Poisson distribution. Calculates length models (models based on frequency of occurrence of segment lengths) using training corpus (can be the same as the input corpus). @author loomchild

Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator


  public List<Alignment> apply(List<Alignment> alignmentList) {
    
    Counter counter = new SplitCounter();
    Calculator calculator = 
      new PoissonDistributionCalculator(counter, alignmentList);
    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm =

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Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator

    if (lengthCorpus != null) {
      lengthAlignmentList = loadAlignmentList(lengthCorpus);
    } else {
      lengthAlignmentList = alignmentList;
    }
    Calculator calculator = new PoissonDistributionCalculator(counter, 
        lengthAlignmentList);
    return calculator;
  }

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Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator


    List<Filter> filterList = new ArrayList<Filter>();
    
    Counter counter = new SplitCounter();
    Calculator calculator = 
      new PoissonDistributionCalculator(counter, alignmentList);
    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm =

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Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator

      List<Alignment> bestAlignmentList) {
    
    List<Calculator> calculatorList = new ArrayList<Calculator>();
    
    Counter counter = new SplitCounter();
    calculatorList.add(new PoissonDistributionCalculator(counter, alignmentList));
    
    calculatorList.add(new TranslationCalculator(bestAlignmentList));


    Calculator calculator = new CompositeCalculator(calculatorList);

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Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator

   * @return aligned list
   */
  private List<Alignment> lengthAlign(List<Alignment> alignmentList) {
    Counter counter = new SplitCounter();
    Calculator calculator = 
      new PoissonDistributionCalculator(counter, alignmentList);
    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm =

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Examples of net.sourceforge.align.calculator.length.PoissonDistributionCalculator

      List<Alignment> bestAlignmentList) {
    
    List<Calculator> calculatorList = new ArrayList<Calculator>();
    
    Counter counter = new SplitCounter();
    calculatorList.add(new PoissonDistributionCalculator(counter, alignmentList));
    
    calculatorList.add(new TranslationCalculator(bestAlignmentList));


    Calculator calculator = new CompositeCalculator(calculatorList);

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