Package ru.autosome.commons.backgroundModel.mono

Examples of ru.autosome.commons.backgroundModel.mono.BackgroundModel

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  }

  @Override
  protected DiPWM loadMotif(String filename) {
    if (fromMononucleotide) {
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
      return DiPWM.fromPWM( importer.loadMotif(filename) );
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
      return importer.loadMotif(filename);
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  }

  @Override
  protected DiPWM loadMotif(File file){
    if (fromMononucleotide) {
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
      return DiPWM.fromPWM( importer.loadMotif(file) );
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
      return importer.loadMotif(file);
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     "number of recognized words: " + info.numberOfRecognizedWords(background, pwmLength) + "\n------------\n");
  }

  public static void main(String[] args) {
    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    BackgroundModel background = new WordwiseBackground();
    Discretizer discretizer = new Discretizer(10000.0);
    Integer max_hash_size = null;
    double threshold = 3;
    double[] thresholds = {3,5,7};
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                         "number of recognized words: " + info.numberOfRecognizedWords(background, pwmLength) + "\n------------\n");
  }

  public static void main(String[] args) {
    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    BackgroundModel background = new WordwiseBackground();
    Discretizer discretizer = new Discretizer(10000.0);
    BoundaryType pvalue_boundary = BoundaryType.LOWER;
    Integer max_hash_size = null;
    double pvalue = 0.0005;
    double[] pvalues = {0.0001, 0.0005, 0.001};
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Related Classes of ru.autosome.commons.backgroundModel.mono.BackgroundModel

  • ru.autosome.ape.di.FindPvalue
  • ru.autosome.ape.di.FindThreshold
  • ru.autosome.ape.di.PrecalculateThresholdLists
  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.commons.backgroundModel.di.DiBackground
  • ru.autosome.macroape.di.CollectDistanceMatrix
  • ru.autosome.macroape.di.EvalSimilarity
  • ru.autosome.macroape.di.ScanCollection
  • ru.autosome.macroape.example.EvaluateSimilarity
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