public boolean matches(Base b1, Base b2) { HashSet<Base> dbsnp_bases = new HashSet<Base>(); char[] norm = get_normalized_observed_bases().toCharArray(); for (int i = 0; i < norm.length; i++) { if (norm[i] != '/') dbsnp_bases.add(Base.valueOf(norm[i])); } HashSet<Base> query = new HashSet<Base>(); query.add(b1); query.add(b2); return dbsnp_bases.equals(query); }