Package net.sourceforge.align.calculator.length

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

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   * but based on Forward Backward method instead of Viterbi method.
   */
  @Before
  public void setUp() {
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
    MatrixFactory matrixFactory = new FullMatrixFactory();
   
    algorithm = new ForwardBackwardAlgorithm(calculator,
        CategoryDefaults.BEST_CATEGORY_MAP, matrixFactory);
  }
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  private Calculator createNormalCalculator(CommandLine commandLine) {
    Counter counter = createCounter(commandLine);
    if (counter == null) {
      throw new MissingParameterException("counter");
    }
    Calculator calculator = new NormalDistributionCalculator(counter);
    return calculator;
  }
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  private List<Alignment> lengthAlign(List<Alignment> alignmentList) {

    List<Filter> filterList = new ArrayList<Filter>();
   
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
   
    AlignAlgorithm algorithm =
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public class GaleAndChurchMacro implements Macro {

  public List<Alignment> apply(List<Alignment> alignmentList) {
   
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ViterbiAlgorithmFactory();
   
    AlignAlgorithm algorithm =
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   * Constructs algorithm object. It is similar to Gale and Church algorithm.
   */
  @Before
  public void setUp() {
    Counter counter = new CharCounter();
    Calculator calculator = new NormalDistributionCalculator(counter);
    MatrixFactory matrixFactory = new FullMatrixFactory();
   
    algorithm = new ViterbiAlgorithm(calculator,
        CategoryDefaults.BEST_CATEGORY_MAP, matrixFactory);
  }
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Related Classes of net.sourceforge.align.calculator.length.NormalDistributionCalculator

  • net.sourceforge.align.filter.aligner.align.hmm.fb.ForwardBackwardAlgorithmTest
  • net.sourceforge.align.filter.aligner.align.hmm.viterbi.ViterbiAlgorithmTest
  • net.sourceforge.align.filter.macro.GaleAndChurchMacro
  • net.sourceforge.align.filter.macro.TranslationMacro
  • net.sourceforge.align.ui.console.command.AlignCommand
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