Examples of AlignAlgorithm

net.sourceforge.align.filter.aligner.align.AlignAlgorithm
Represents alignment algorithm. @author Jarek Lipski (loomchild)

Examples of net.sourceforge.align.filter.aligner.align.AlignAlgorithm

      new PoissonDistributionCalculator(counter, alignmentList);
    
    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.AlignAlgorithm

    Calculator calculator = new CompositeCalculator(calculatorList);
    
    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.AlignAlgorithm

   * if the results are correct.
   */
  @Test
  public void testRunAllFilters() {
    SplitAlgorithm splitAlgorithm = new SplitAlgorithmMock(1);
    AlignAlgorithm alignAlgorithm = new AlignAlgorithmMock(2);
    MergeAlgorithm mergeAlgorithm = new SeparatorMergeAlgorithm();
    List<Filter> filterList = new ArrayList<Filter>();
    filterList.add(new Modifier(splitAlgorithm, splitAlgorithm));
    filterList.add(new Aligner(alignAlgorithm));
    filterList.add(new Modifier(mergeAlgorithm, mergeAlgorithm));

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Examples of net.sourceforge.align.filter.aligner.align.AlignAlgorithm

      List<Alignment> unificationAlignmentList = 
        loadAlignmentList(unificationCorpus);
      filter = new UnifyAligner(unificationAlignmentList);
    } else {
      alignmentList = parser.parse();
      AlignAlgorithm algorithm = createAlgorithm(commandLine, alignmentList);
      filter = new Aligner(algorithm);
    }
    filter = FilterDecorators.decorate(filter);
    Formatter formatter = new AlFormatter(getOut());
    if (alignmentList == null) {

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Examples of net.sourceforge.align.filter.aligner.align.AlignAlgorithm

  }
  
  private AlignAlgorithm createAlgorithm(CommandLine commandLine,
      List<Alignment> alignmentList) {
    String cls = commandLine.getOptionValue('c');
    AlignAlgorithm algorithm;
    if (cls.equals("fb") || cls.equals("viterbi")) {
      Calculator calculator = createCalculator(commandLine, 
          alignmentList);
      Map<Category, Float> categoryMap = 
        CategoryDefaults.BEST_CATEGORY_MAP;

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Examples of net.sourceforge.align.filter.aligner.align.AlignAlgorithm

  /**
   * Checks if {@link Aligner} uses {@link AlignAlgorithm} correctly.
   */
  @Test
  public void testAlign() {
    AlignAlgorithm algorithm = new AlignAlgorithmMock(2);
    Aligner aligner = new Aligner(algorithm);
    List<Alignment> alignmentList = createAlignmentList(
        SOURCE_SEGMENT_ARRAY, TARGET_SEGMENT_ARRAY);
    List<Alignment> resultAlignmentList = aligner.apply(alignmentList);
    assertAlignmentListEquals(EXPECTED_SOURCE_SEGMENT_ARRAY,

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