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)

   * @return
   */
  private List<Alignment> contentAlign(List<Alignment> alignmentList, 
      List<Alignment> bestAlignmentList) {
     
    Calculator calculator = 
      new TranslationCalculator(bestAlignmentList);


    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();

View Full Code Here

  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();

View Full Code Here

    Counter counter = new SplitCounter();
    calculatorList.add(new PoissonDistributionCalculator(counter, alignmentList));
    
    calculatorList.add(new TranslationCalculator(bestAlignmentList));


    Calculator calculator = new CompositeCalculator(calculatorList);
    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm =

View Full Code Here

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 =

View Full Code Here

   * @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();

View Full Code Here

    Counter counter = new SplitCounter();
    calculatorList.add(new PoissonDistributionCalculator(counter, alignmentList));
    
    calculatorList.add(new TranslationCalculator(bestAlignmentList));


    Calculator calculator = new CompositeCalculator(calculatorList);
    
    HmmAlignAlgorithmFactory algorithmFactory = 
      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm =

View Full Code Here

   * 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);
  }

View Full Code Here

0 1

TOP

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

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.