Package ru.autosome.commons.importer

Examples of ru.autosome.commons.importer.PWMImporter.loadMotif()

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  }

  @Override
  protected PWM loadMotif(String filename) {
    PWMImporter importer = new PWMImporter(background, data_model, effective_count, transpose);
    return importer.loadMotif(filename);
  }

  @Override
  protected void extract_background(String str) {
    background = Background.fromString(str);
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  }

  @Override
  protected PWM loadMotif(File file){
    PWMImporter importer = new PWMImporter(background, data_model, effective_count, transpose);
    return importer.loadMotif(file);
  }

  @Override
  protected String DOC_background_option() {
    return "ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25";
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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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      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);
    }
  }

  protected FindPvalue() {
    initialize_defaults();
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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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      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);
    }
  }

  @Override
  protected void extract_background(String str) {
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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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      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);
    }
  }

  @Override
  protected String DOC_background_option() {
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