// but may be in latter implementations we'll use more information so it's better to keep, say 50 nucleotides from each side where possible).

    // Another way is to construct object from string in this way:

    List<SequenceWithSNP> snpCollection = new ArrayList<SequenceWithSNP>();

    snpCollection.add(SequenceWithSNP.fromString("AAGGTCAATACTCAACATCATAAAAACAGACAAAAGTATAAAACTTACAG[C/G]GTCTTACAAAAAGGATGATCCAGTAATATGCTGCTTACAAGAAACCCACC"));

                                          new char[]{'G','T'},

                                          "TTTTTAAGTGAAAAGTGTATAGTTCAGAGTGTAATATTTATTACCAGTAT"));

    //////////////////////////////////////////////////////////////////////////////////////////////////

  }

  protected void process_snp(String snp_input) throws HashOverflowException {

    String snp_name = first_part_of_string(snp_input);

    for (ThresholdEvaluator motifEvaluator: pwmCollection) {

      SNPScan.RegionAffinityInfos result;

      result = new SNPScan(motifEvaluator.pwm, seq_w_snp, motifEvaluator.pvalueCalculator).affinityInfos();

      boolean pvalueSignificant = (result.getInfo_1().getPvalue() <= max_pvalue_cutoff ||