Examples of net.sourceforge.align.calculator.Calculator

Package net.sourceforge.align.calculator

Examples of net.sourceforge.align.calculator.Calculator

net.sourceforge.align.calculator.Calculator

Represents method of calculating probability of an alignment of given source segments to given target segments. It's the heart of alignment algorithm.

The actual implementation can calculate the result using just segment lengths (package length) or contents of the segments (package content).
@author Jarek Lipski (loomchild)

   * 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);
  }

View Full Code Here

   */
  @Test
  public void calculate() {
    List<Calculator> calculatorList = Arrays.asList(new Calculator[] {
        new CalculatorMock(0.5f), new CalculatorMock(0.25f)});
    Calculator calculator = new CompositeCalculator(calculatorList);
    assertEquals(0.75f, calculator.calculateScore(null, null), 0.75f);
  }

View Full Code Here

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();

View Full Code Here

  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;
      String search = commandLine.getOptionValue('s');
      if (search == null) {

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    List<Calculator> calculatorList = new ArrayList<Calculator>();
    Iterator<String> calculatorStringIterator = calculatorStringList.iterator();
    while (calculatorStringIterator.hasNext()) {
      String calculatorString = calculatorStringIterator.next();
      Calculator calculator;
      if (calculatorString.equals("normal")) {
        calculator = createNormalCalculator(commandLine);
      } else if(calculatorString.equals("poisson")) {
        calculator = createPoissonCalculator(commandLine, alignmentList);
      } else if(calculatorString.equals("translation")) {
        calculator = createTranslationCalculator(commandLine);
      } else if(calculatorString.equals("oracle")) {
        List<String> remainingCalculatorStringList = 
          new ArrayList<String>();
        while (calculatorStringIterator.hasNext()) {
          remainingCalculatorStringList.add(calculatorStringIterator.next());
        }
        Calculator remainingCalculator = createCalculator(
            commandLine, alignmentList, remainingCalculatorStringList);
        calculator = createOracleCalculator(commandLine, remainingCalculator);
      } else {
        throw new UnknownParameterException("calculator");
      }
      calculatorList.add(calculator);
    }
    
    Calculator calculator;
    if (calculatorList.size() == 1) {
      calculator = calculatorList.get(0);
    } else {
      calculator = new CompositeCalculator(calculatorList);
    }

View Full Code Here

  private Calculator createNormalCalculator(CommandLine commandLine) {
    Counter counter = createCounter(commandLine);
    if (counter == null) {
      throw new MissingParameterException("counter");
    }
    Calculator calculator = new NormalDistributionCalculator(counter);
    return calculator;
  }

View Full Code Here

    if (lengthCorpus != null) {
      lengthAlignmentList = loadAlignmentList(lengthCorpus);
    } else {
      lengthAlignmentList = alignmentList;
    }
    Calculator calculator = new PoissonDistributionCalculator(counter, 
        lengthAlignmentList);
    return calculator;
  }

View Full Code Here

        lengthAlignmentList);
    return calculator;
  }


  private Calculator createTranslationCalculator(CommandLine commandLine) {
    Calculator calculator;
    int iterations = createInt(commandLine, "iterations", 
        TranslationModelUtil.DEFAULT_TRAIN_ITERATION_COUNT);
    String translationCorpus = commandLine.getOptionValue('t');
    String languageModels = commandLine.getOptionValue("x");
    String transModel = commandLine.getOptionValue("y");

View Full Code Here

    return calculator;
  }


  private Calculator createOracleCalculator(CommandLine commandLine,
      Calculator calculator) {
    Calculator resultCalculator;
    String oracleCorpus = commandLine.getOptionValue("oracle-corpus");
    if (oracleCorpus == null) {
      throw new MissingParameterException("oracle-corpus");
    }
    List<Alignment> oracleAlignmentList = loadAlignmentList(oracleCorpus);

View Full Code Here

  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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Related Classes of net.sourceforge.align.calculator.Calculator

net.sourceforge.align.calculator.meta.CompositeCalculatorTest

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.MooreMacro

net.sourceforge.align.filter.macro.PoissonMacro

net.sourceforge.align.filter.macro.PoissonTranslationMacro

net.sourceforge.align.filter.macro.TranslationMacro

net.sourceforge.align.ui.console.command.AlignCommand

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