Package ru.autosome.commons.importer

Examples of ru.autosome.commons.importer.DiPWMImporter

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      for(PWM monoPWM: monoCollection) {
        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, dataModel, effectiveCount, transpose);
      return importer.loadMotifCollection(path_to_collection_of_pwms);
    }
  }
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      for(PWM monoPWM: monoCollection) {
        diCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return diCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(collectionBackground, dataModel, effectiveCount, collectionTranspose);
      return importer.loadMotifCollection(pathToCollectionOfPWMs);
    }
  }
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    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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      for(PWM monoPWM: monoCollection) {
        pwmCollection.add(DiPWM.fromPWM(monoPWM));
      }
      return pwmCollection;
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, dataModel, effectiveCount, transpose);
      return importer.loadMotifCollection(path_to_collection);
    }
  }
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    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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    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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    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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    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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    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.DiPWMImporter

  • ru.autosome.ape.di.FindPvalue
  • ru.autosome.ape.di.FindThreshold
  • ru.autosome.ape.di.PrecalculateThresholdLists
  • ru.autosome.commons.motifModel.di.DiPCM
  • ru.autosome.commons.motifModel.di.DiPPM
  • ru.autosome.commons.motifModel.di.DiPWM
  • ru.autosome.macroape.di.CollectDistanceMatrix
  • ru.autosome.macroape.di.EvalSimilarity
  • ru.autosome.macroape.di.ScanCollection
  • ru.autosome.perfectosape.di.MultiSNPScan
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