// CountingPWM secondPWMCounting = new CountingPWM(secondPWM.discrete(discretizer), new WordwiseBackground(), null);
BackgroundModel background = new WordwiseBackground();
// BackgroundModel background = new Background(new double[]{0.25,0.25,0.25,0.25});
CompareModels comparator = new CompareModels(firstPWM, secondPWM, background, background, discretizer, null, null);
CompareModelsCountsGiven.SimilarityInfo similarityInfo = comparator.jaccard_by_weak_pvalue(0.0005);
System.out.println("\n----------\n" + similarityInfo.similarity());
System.out.println(similarityInfo.alignment);
System.out.println(similarityInfo.recognizedByBoth);
//System.out.println("\n----------\n" + new PairAligned(firstPWMCounting, secondPWMCounting, similarityInfo.alignment).firstModelAligned);
//System.out.println("\n----------\n" + new PairAligned(firstPWMCounting, secondPWMCounting, similarityInfo.alignment).secondModelAligned);