Package ru.autosome.commons.backgroundModel.di

Examples of ru.autosome.commons.backgroundModel.di.DiWordwiseBackground

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  protected void extract_background(String str) {
    background = DiBackground.fromString(str);
  }
  @Override
  protected void initialize_default_background() {
    background = new DiWordwiseBackground();
  }
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  public PCM2PWM() {
    super();
  }

  protected DiBackgroundModel defaultBackground() {
    return new DiWordwiseBackground();
  }
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    fromMononucleotide = false;
  }

  @Override
  protected void initialize_default_background() {
    background = new DiWordwiseBackground();
  }
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    secondPWMFromMononucleotide = false;
  }

  @Override
  protected void initialize_default_background() {
    firstBackground = new DiWordwiseBackground();
    secondBackground = new DiWordwiseBackground();
  }
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      //System.out.println("\n----------\n" + new PairAligned(firstPWMCounting, secondPWMCounting, similarityInfo.alignment).firstModelAligned);
      //System.out.println("\n----------\n" + new PairAligned(firstPWMCounting, secondPWMCounting, similarityInfo.alignment).secondModelAligned);

      DiPWM firstDiPWM = DiPWM.fromPWM(firstPWM);
      DiPWM secondDiPWM = DiPWM.fromPWM(secondPWM);
      DiBackgroundModel dibackground = new DiWordwiseBackground();
//      DiBackgroundModel dibackground = new DiBackground(new double[]{ 0.0625,0.0625,0.0625,0.0625,
//                                                                      0.0625,0.0625,0.0625,0.0625,
//                                                                      0.0625,0.0625,0.0625,0.0625,
//                                                                      0.0625,0.0625,0.0625,0.0625});
      ru.autosome.macroape.calculation.di.CompareModels dicomparator;
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    return DiBackground.fromString(str);
  }

  @Override
  protected void initialize_default_background() {
    queryBackground = new DiWordwiseBackground();
    collectionBackground = new DiWordwiseBackground();
  }
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    fromMononucleotide = false;
  }

  @Override
  protected void initialize_default_background() {
    background = new DiWordwiseBackground();
  }
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    fromMononucleotide = false;
  }

  @Override
  protected void initialize_default_background() {
    background = new DiWordwiseBackground();
  }
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    fromMononucleotide = false;
  }

  @Override
  protected void initialize_default_background() {
    background = new DiWordwiseBackground();
  }
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    return score(word.sequence, background);
  }

  @Override
  public double score(Sequence word) throws IllegalArgumentException {
    return score(word, new DiWordwiseBackground());
  }
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Related Classes of ru.autosome.commons.backgroundModel.di.DiWordwiseBackground

  • ru.autosome.ape.di.FindPvalue
  • ru.autosome.ape.di.FindThreshold
  • ru.autosome.ape.di.PrecalculateThresholdLists
  • ru.autosome.commons.converter.di.PCM2PWM
  • ru.autosome.commons.motifModel.di.DiPWM
  • ru.autosome.macroape.di.CollectDistanceMatrix
  • ru.autosome.macroape.di.EvalSimilarity
  • ru.autosome.macroape.di.ScanCollection
  • ru.autosome.macroape.example.EvaluateSimilarity
  • ru.autosome.perfectosape.di.MultiSNPScan
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