CMC { public CMCResult run(RealVector phenotype, RealMatrix genotype) { return run(phenotype, genotype, 0.05, 100); }  CMCResult run(RealVector phenotype, RealMatrix genotype); CMCResult run(RealVector phenotype, RealMatrix genotype, double maf, int numPermutations);  }
@Test public void test() { double[] phenotype = {1, 1, 1, 1, 1, 0, 0, 0, 0, 0}; double[][] genotype = { {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 1, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0}, {1, 0, 0, 0, 0, 0, 0, 0} }; CMC cmc = new CMC(); CMCResult result = cmc.run(new ArrayRealVector(phenotype), new BlockRealMatrix(genotype)); System.out.println(result.toString()); assertEquals("CMC statistic does not match", result.getStatistic(), 2.666666666666665, 0.1); }