test_class.file: hpg-bigdata-analysis/src/test/java/org/opencb/hpg/bigdata/analysis/variant/statistics/CMCTest.java
test_class.identifier: CMCTest
test_case.body: @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);
      }
test_case.class_method_signature: CMCTest.test()
test_case.full_signature: @Test public void test()
test_case.identifier: test
test_case.invocations: run println toString assertEquals getStatistic
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void test()
focal_class.declarator: result = new CMCResult()
focal_class.modifier: private
focal_class.original_string: private CMCResult result = new CMCResult();
focal_class.type: CMCResult
focal_class.var_name: result
focal_class.file: hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/statistics/CMC.java
focal_class.identifier: CMC
focal_class.class_method_signature: CMC.run(RealVector phenotype, RealMatrix genotype)
focal_class.full_signature: public CMCResult run(RealVector phenotype, RealMatrix genotype)
focal_class.identifier: run
focal_class.modifiers: public
focal_class.parameters: (RealVector phenotype, RealMatrix genotype)
focal_class.return: CMCResult
focal_class.signature: CMCResult run(RealVector phenotype, RealMatrix genotype)
focal_class.class_method_signature: CMC.run(RealVector phenotype, RealMatrix genotype, double maf, int numPermutations)
focal_class.full_signature: public CMCResult run(RealVector phenotype, RealMatrix genotype, double maf, int numPermutations)
focal_class.identifier: run
focal_class.modifiers: public
focal_class.parameters: (RealVector phenotype, RealMatrix genotype, double maf, int numPermutations)
focal_class.return: CMCResult
focal_class.signature: CMCResult run(RealVector phenotype, RealMatrix genotype, double maf, int numPermutations)
focal_class.class_method_signature: CMC.computeStatistic(RealVector phenotype, RealMatrix genotype)
focal_class.full_signature: private double computeStatistic(RealVector phenotype, RealMatrix genotype)
focal_class.identifier: computeStatistic
focal_class.modifiers: private
focal_class.parameters: (RealVector phenotype, RealMatrix genotype)
focal_class.return: double
focal_class.signature: double computeStatistic(RealVector phenotype, RealMatrix genotype)
focal_class.class_method_signature: CMC.colMeans(RealMatrix matrix)
focal_class.full_signature: private double[] colMeans(RealMatrix matrix)
focal_class.identifier: colMeans
focal_class.modifiers: private
focal_class.parameters: (RealMatrix matrix)
focal_class.return: double[]
focal_class.signature: double[] colMeans(RealMatrix matrix)
focal_class.class_method_signature: CMC.substractVector(RealMatrix matrix, double[] vector)
focal_class.full_signature: private RealMatrix substractVector(RealMatrix matrix, double[] vector)
focal_class.identifier: substractVector
focal_class.modifiers: private
focal_class.parameters: (RealMatrix matrix, double[] vector)
focal_class.return: RealMatrix
focal_class.signature: RealMatrix substractVector(RealMatrix matrix, double[] vector)
focal_method.body: public CMCResult run(RealVector phenotype, RealMatrix genotype) {
          return run(phenotype, genotype, 0.05, 100);
      }
focal_method.class_method_signature: CMC.run(RealVector phenotype, RealMatrix genotype)
focal_method.full_signature: public CMCResult run(RealVector phenotype, RealMatrix genotype)
focal_method.identifier: run
focal_method.invocations: run
focal_method.modifiers: public
focal_method.parameters: (RealVector phenotype, RealMatrix genotype)
focal_method.return: CMCResult
focal_method.signature: CMCResult run(RealVector phenotype, RealMatrix genotype)