Examples of net.sourceforge.align.filter.Filter

net.sourceforge.align.filter.Filter

Represents alignment list filter (in a sense of UNIX filter).

Allows to perform any operation on alignment list (not only, like name suggests, filter elements from it) - for example it can modify segment contents, join or split alignments, etc.

Filter operation receives alignment list as a parameter and returns modified alignment list. Thanks to the fact that input and output has the same type filters can be connected together creating the operation pipeline.
@author Jarek Lipski (loomchild)

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


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

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    filterList.add(new OneToOneSelector());
    
    filterList.add(new FractionSelector(SELECT_FRACTION));
    
    Filter filter = new CompositeFilter(filterList);    
    
    return filter.apply(alignmentList);
    
  }

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


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

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


  }

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    ModifyAlgorithm sourceAlgorithm = 
      new UnifyRareWordsCleanAlgorithm(sourceVocabulary);
    ModifyAlgorithm targetAlgorithm = 
      new UnifyRareWordsCleanAlgorithm(targetVocabulary);


    Filter filter = new Modifier(sourceAlgorithm, targetAlgorithm);
    
    return filter.apply(alignmentList);
    
  }

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

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   */
  private List<Alignment> selectBestAlignments(List<Alignment> alignmentList) {
    List<Filter> filterList = new ArrayList<Filter>();
    filterList.add(new OneToOneSelector());
    filterList.add(new FractionSelector(SELECT_FRACTION));
    Filter filter = new CompositeFilter(filterList);    
    return filter.apply(alignmentList);
  }

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


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

View Full Code Here

   * @see UnifyAligner
   */
  private List<Alignment> unifyAlignments(List<Alignment> alignmentList, 
      List<Alignment> referenceAlignmentList) {
    
    Filter filter = new UnifyAligner(referenceAlignmentList);
    
    return filter.apply(alignmentList);
    
  }

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      throw new UnknownParameterException("part");
    }
    
    Formatter formatter = new AlFormatter(getOut());
    
    Filter filter = new Modifier(sourceAlgorithm, targetAlgorithm);
    filter = FilterDecorators.decorate(filter);


    if (alignmentList == null) {
      alignmentList = parser.parse();
    }
    
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }

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Related Classes of net.sourceforge.align.filter.Filter

net.sourceforge.align.filter.macro.GaleAndChurchMacro

net.sourceforge.align.filter.macro.MooreMacro

net.sourceforge.align.filter.macro.PoissonMacro

net.sourceforge.align.filter.macro.PoissonTranslationMacro

net.sourceforge.align.filter.macro.TranslationMacro

net.sourceforge.align.filter.meta.IgnoreInfiniteProbabilityAlignmentsFilterDecoratorTest

net.sourceforge.align.filter.selector.DifferenceSelectorTest

net.sourceforge.align.filter.selector.FractionSelectorTest

net.sourceforge.align.filter.selector.IntersectionSelectorTest

net.sourceforge.align.filter.selector.OneToOneSelectorTest

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