Package ru.autosome.commons.importer

Examples of ru.autosome.commons.importer.PWMImporter

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    return from_arglist(argv);
  }

  @Override
  protected List<PWM> loadMotifCollection(File path_to_collection) {
    PWMImporter importer = new PWMImporter(background, dataModel, effectiveCount, transpose);
    return importer.loadMotifCollection(path_to_collection);
  }
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    return Background.fromString(str);
  }

  @Override
  protected PWM loadFirstPWM(String filename) {
    PWMImporter firstMotifImporter = new PWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
    return firstMotifImporter.loadMotif(filename);
  }
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    PWMImporter firstMotifImporter = new PWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
    return firstMotifImporter.loadMotif(filename);
  }
  @Override
  protected PWM loadSecondPWM(String filename) {
    PWMImporter secondMotifImporter = new PWMImporter(secondBackground, dataModelSecond, effectiveCountSecond, transposeSecond);
    return secondMotifImporter.loadMotif(filename);
  }
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import ru.autosome.macroape.calculation.generalized.CompareModelsCountsGiven;
import ru.autosome.macroape.calculation.mono.CompareModels;

public class EvaluateSimilarity {
  public static void main(String[] args){
    PWM firstPWM = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    PWM secondPWM = new PWMImporter().loadMotif("test_data/pwm/SP1_f1.pwm");
    try {
      Discretizer discretizer = new Discretizer(100.0);

//      CountingPWM firstPWMCounting = new CountingPWM(firstPWM.discrete(discretizer), new WordwiseBackground(), null);
//      CountingPWM secondPWMCounting = new CountingPWM(secondPWM.discrete(discretizer), new WordwiseBackground(), null);
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    background = Background.fromString(str);
  }

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

  @Override
  protected PWM loadMotif(String filename) {
    PWMImporter importer = new PWMImporter(background, data_model, effective_count, transpose);
    return importer.loadMotif(filename);
  }
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    return new PrecalculateThresholdList<PWM,BackgroundModel>(pvalues, discretizer, background, pvalue_boundary, max_hash_size);
  }

  @Override
  protected PWM loadMotif(File file){
    PWMImporter importer = new PWMImporter(background, data_model, effective_count, transpose);
    return importer.loadMotif(file);
  }
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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(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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Related Classes of ru.autosome.commons.importer.PWMImporter

  • ru.autosome.ape.di.FindPvalue
  • ru.autosome.ape.di.FindThreshold
  • ru.autosome.ape.di.PrecalculateThresholdLists
  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindPvalueDinucleotide
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.ape.FindPvalue
  • ru.autosome.ape.FindThreshold
  • ru.autosome.ape.PrecalculateThresholdLists
  • ru.autosome.commons.motifModel.mono.PCM
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