Package ru.autosome.commons.importer

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

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  }

  @Override
  protected List<PWM> load_collection_of_pwms() {
    PWMImporter importer = new PWMImporter(background, dataModel, effectiveCount, transpose);
    return importer.loadMotifCollection(path_to_collection_of_pwms);
  }

  protected static ru.autosome.perfectosape.cli.generalized.MultiSNPScan from_arglist(ArrayList<String> argv) {
    MultiSNPScan result = new MultiSNPScan();
    Helper.print_help_if_requested(argv, result.documentString());
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  @Override
  protected List<DiPWM> load_collection_of_pwms() {
    if (fromMononucleotide) {
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, dataModel, effectiveCount, transpose);
      List<PWM> monoCollection = importer.loadMotifCollection(path_to_collection_of_pwms);
      List<DiPWM> diCollection = new ArrayList<DiPWM>(monoCollection.size());
      for(PWM monoPWM: monoCollection) {
        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
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        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, dataModel, effectiveCount, transpose);
      return importer.loadMotifCollection(path_to_collection_of_pwms);
    }
  }

  protected static ru.autosome.perfectosape.cli.generalized.MultiSNPScan from_arglist(ArrayList<String> argv) {
    MultiSNPScan result = new MultiSNPScan();
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  @Override
  protected List<DiPWM> loadMotifCollection() {
    if (collectionFromMononucleotide) {
      BackgroundModel collectionBackgroundMononucleotide = Background.fromDiBackground(collectionBackground);
      PWMImporter importer = new PWMImporter(collectionBackgroundMononucleotide, dataModel, effectiveCount, collectionTranspose);
      List<PWM> monoCollection = importer.loadMotifCollection(pathToCollectionOfPWMs);
      List<DiPWM> diCollection = new ArrayList<DiPWM>(monoCollection.size());
      for(PWM monoPWM: monoCollection) {
        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
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        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(collectionBackground, dataModel, effectiveCount, collectionTranspose);
      return importer.loadMotifCollection(pathToCollectionOfPWMs);
    }
  }

  @Override
  protected DiPWM loadQueryMotif() {
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  @Override
  protected List<DiPWM> loadMotifCollection(File path_to_collection) {
    if (fromMononucleotide) {
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, dataModel, effectiveCount, transpose);
      List<PWM> monoCollection = importer.loadMotifCollection(path_to_collection);
      pwmCollection = new ArrayList<DiPWM>(monoCollection.size());
      for(PWM monoPWM: monoCollection) {
        pwmCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return pwmCollection;
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        pwmCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return pwmCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, dataModel, effectiveCount, transpose);
      return importer.loadMotifCollection(path_to_collection);
    }
  }

  @Override
  protected void initialize_defaults() {
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    return from_arglist(argv);
  }

  protected List<PWM> loadMotifCollection() {
    PWMImporter importer = new PWMImporter(collectionBackground, dataModel, effectiveCount, collectionTranspose);
    return importer.loadMotifCollection(pathToCollectionOfPWMs);
  }

  protected PWM loadQueryMotif() {
    PWMImporter importer = new PWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
    return importer.loadMotif(queryPMFilename);
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  }

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

  @Override
  protected CompareModelsCountsGiven calculator(PWM firstModel, PWM secondModel) {
    return new CompareModelsCountsGiven(firstModel, secondModel,
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