Examples of AdaptiveBandAlgorithm

net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

Represents meta-alignment algorithm. It uses given alignment algorithm and by increasing width of the diagonal band in {@link BandMatrix} tries to findreasonable alignment.

The idea is that it first creates a matrix with narrow band and performs the alignment using the algorithm. It evaluates it by checking if the result is not closer to the band edge than the given margin (this suggests that there might be better alignment outside the band). If it is then it increases the size of band and tries again. The whole process is repeated until alignment is not within the margin.

This improves overall performance of the alignment because the whole matrix does not need to be calculated, just the elements on the narrow band around diagonal.
@author loomchild

Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    filterList.add(new Aligner(algorithm));
    
    filterList.add(new OneToOneSelector());

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm


    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);


    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    filterList.add(new Aligner(algorithm));
    
    filterList.add(new OneToOneSelector());

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);


    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ViterbiAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    Filter filter = new Aligner(algorithm);  
    
    return filter.apply(alignmentList);
  }

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);


    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.align.hmm.adaptive.AdaptiveBandAlgorithm

        } else if (cls.equals("fb")) {
          algorithmFactory = new ForwardBackwardAlgorithmFactory();
        } else {
          throw new UnknownParameterException("class");
        }
        algorithm = new AdaptiveBandAlgorithm(algorithmFactory,
            calculator, radius, increment, margin, 
            categoryMap);
      } else {
        throw new UnknownParameterException("search");
      }

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