// If one need to work with certain nucleotide background probabilities he should use:

    // BackgroundModel background = new Background(new double[]{pA, pC, pG, pT}); where {pA,... pT} are probabilities of respective nucleotides

    BackgroundModel background = new WordwiseBackground();

    // A actual pvalue will be less than requested. Not very important setting in this task

    // Setting max_hash_size allows one to restrict memory exhausting during Pvalue calculation (using APE algorithm, not binary search)

    // Reasonable value is about 10 millions elements. But actually only specially constructed matrices can reach such high hash sizes.

    // So in standalone calculation we use null (not to check hash size) and in web version we use 1e7

    Integer max_hash_size = null;

  public static void main(String[] args) {

    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");

    BackgroundModel background = new WordwiseBackground();

    Discretizer discretizer = new Discretizer(10000.0);

    Integer max_hash_size = null;

    double pvalue = 0.0005;

    double[] pvalues = {0.0001, 0.0005, 0.001};

    CanFindThreshold calculator = new FindThresholdAPE<PWM, BackgroundModel>(pwm, background, discretizer, max_hash_size);