Package net.sourceforge.align.calculator.length.counter

Examples of net.sourceforge.align.calculator.length.counter.SplitCounter

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*/
public class PoissonMacro implements Macro {

  public List<Alignment> apply(List<Alignment> alignmentList) {
   
    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
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   */
  private List<Alignment> lengthAlign(List<Alignment> alignmentList) {

    List<Filter> filterList = new ArrayList<Filter>();
   
    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
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  private List<Alignment> contentAlign(List<Alignment> alignmentList,
      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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   * method to the one used in {@link PoissonMacro}).
   * @param alignmentList input alignment list
   * @return aligned list
   */
  private List<Alignment> lengthAlign(List<Alignment> alignmentList) {
    Counter counter = new SplitCounter();
    Calculator calculator =
      new PoissonDistributionCalculator(counter, alignmentList);
   
    HmmAlignAlgorithmFactory algorithmFactory =
      new ForwardBackwardAlgorithmFactory();
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  private List<Alignment> contentAlign(List<Alignment> alignmentList,
      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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    String ctr = commandLine.getOptionValue('n');
    Counter counter;
    if (ctr == null) {
      counter = null;
    } else if (ctr.equals("word")) {
      counter = new SplitCounter();
    } else if (ctr.equals("char")) {
      counter = new CharCounter();
    } else {
      throw new UnknownParameterException("counter");
    }
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Related Classes of net.sourceforge.align.calculator.length.counter.SplitCounter

  • net.sourceforge.align.filter.macro.MooreMacro
  • net.sourceforge.align.filter.macro.PoissonMacro
  • net.sourceforge.align.filter.macro.PoissonTranslationMacro
  • net.sourceforge.align.ui.console.command.AlignCommand
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