Examples of Aligner

align.aligner.Aligner
net.sourceforge.align.filter.aligner.Aligner
Represents aligner - for each alignment on input list aligns source segments with target segments and appends obtained list of alignments to the result. This implies that resulting list can have more alignments than input list but cannot have less. Does not change alignment contents. @author Jarek Lipski (loomchild)
org.broadinstitute.gatk.engine.alignment.Aligner
Create perfect alignments from the read to the genome represented by the given BWT / suffix array. @author mhanna @version 0.1

Examples of align.aligner.Aligner

public class SimpleTaskTest extends TestCase {
  
  public void testUseDifferentSplitters() throws AlignmentImpossibleException {
    Splitter sourceSplitter = new SplitterMock(1);
    Splitter targetSplitter = new SplitterMock(2);
    Aligner aligner = new AlignerMock();    
    SimpleTask task = 
      new SimpleTask(sourceSplitter, targetSplitter, aligner);
    List<Alignment> alignmentList = task.run("abcd", "efgh");
    assertEquals(1, alignmentList.size());
    Alignment alignment = alignmentList.get(0);

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Examples of align.aligner.Aligner

  private SimpleTask task;
  
  public void setUp() {
    Splitter sourceSplitter = new SplitterMock(1);
    Splitter targetSplitter = new SplitterMock(2);
    Aligner aligner = new AlignerMock();    
    task = new SimpleTask(sourceSplitter, targetSplitter, aligner);
  }

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

      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.Aligner

      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    filterList.add(new Aligner(algorithm));
    
    filterList.add(new OneToOneSelector());
    
    filterList.add(new FractionSelector(SELECT_FRACTION));

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

      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.Aligner

      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
    
    filterList.add(new Aligner(algorithm));
    
    filterList.add(new OneToOneSelector());
    
    filterList.add(new FractionSelector(SELECT_FRACTION));

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

      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.Aligner

      new ViterbiAlgorithmFactory();
    
    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.Aligner

      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.Aligner

      new ForwardBackwardAlgorithmFactory();
    
    AlignAlgorithm algorithm = 
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);


    Filter filter = new Aligner(algorithm);
    
    return filter.apply(alignmentList);
     
  }

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