Package ru.autosome.commons.importer

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

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  @Override
  protected DiPWM loadQueryMotif() {
    if (queryFromMononucleotide) {
      BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
      PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
      return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
    } else {
      DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
      return importer.loadMotif(queryPMFilename);
    }
  }
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      BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
      PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
      return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
    } else {
      DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
      return importer.loadMotif(queryPMFilename);
    }
  }

  protected ru.autosome.macroape.calculation.di.ScanCollection calculator() {
    ru.autosome.macroape.calculation.di.ScanCollection calculator;
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  @Override
  protected DiPWM loadFirstPWM(String filename) {
    if (firstPWMFromMononucleotide) {
      BackgroundModel firstBackgroundMononucleotide = Background.fromDiBackground(firstBackground);
      PWMImporter firstMotifImporter = new PWMImporter(firstBackgroundMononucleotide, dataModelFirst, effectiveCountFirst, transposeFirst);
      return DiPWM.fromPWM( firstMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter firstMotifImporter = new DiPWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
      return firstMotifImporter.loadMotif(filename);
    }
  }
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      BackgroundModel firstBackgroundMononucleotide = Background.fromDiBackground(firstBackground);
      PWMImporter firstMotifImporter = new PWMImporter(firstBackgroundMononucleotide, dataModelFirst, effectiveCountFirst, transposeFirst);
      return DiPWM.fromPWM( firstMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter firstMotifImporter = new DiPWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
      return firstMotifImporter.loadMotif(filename);
    }
  }
  @Override
  protected DiPWM loadSecondPWM(String filename) {
    if (secondPWMFromMononucleotide) {
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  @Override
  protected DiPWM loadSecondPWM(String filename) {
    if (secondPWMFromMononucleotide) {
      BackgroundModel secondBackgroundMononucleotide = Background.fromDiBackground(secondBackground);
      PWMImporter secondMotifImporter = new PWMImporter(secondBackgroundMononucleotide, dataModelSecond, effectiveCountSecond, transposeSecond);
      return DiPWM.fromPWM( secondMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter secondMotifImporter = new DiPWMImporter(secondBackground, dataModelSecond, effectiveCountSecond, transposeSecond);
      return secondMotifImporter.loadMotif(filename);
    }
  }
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      BackgroundModel secondBackgroundMononucleotide = Background.fromDiBackground(secondBackground);
      PWMImporter secondMotifImporter = new PWMImporter(secondBackgroundMononucleotide, dataModelSecond, effectiveCountSecond, transposeSecond);
      return DiPWM.fromPWM( secondMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter secondMotifImporter = new DiPWMImporter(secondBackground, dataModelSecond, effectiveCountSecond, transposeSecond);
      return secondMotifImporter.loadMotif(filename);
    }
  }

  private EvalSimilarity() {
    initialize_defaults();
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    return importer.loadMotifCollection(pathToCollectionOfPWMs);
  }

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


  protected ru.autosome.macroape.calculation.mono.ScanCollection calculator() {
    ru.autosome.macroape.calculation.mono.ScanCollection calculator;
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  }

  @Override
  protected PWM loadFirstPWM(String filename) {
    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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    return firstMotifImporter.loadMotif(filename);
  }
  @Override
  protected PWM loadSecondPWM(String filename) {
    PWMImporter secondMotifImporter = new PWMImporter(secondBackground, dataModelSecond, effectiveCountSecond, transposeSecond);
    return secondMotifImporter.loadMotif(filename);
  }


  private EvalSimilarity() {
    initialize_defaults();
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  }

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

  protected FindPvalue() {
    initialize_defaults();
  }
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