test_class.declarator: EPSILON=0.00001
test_class.modifier: private static final
test_class.original_string: private static final double EPSILON=0.00001;
test_class.type: double
test_class.var_name: EPSILON
test_class.declarator: pvallist
test_class.modifier: private static
test_class.original_string: private static List<PValue> pvallist;
test_class.type: List<PValue>
test_class.var_name: pvallist
test_class.file: phenol-analysis/src/test/java/org/monarchinitiative/phenol/stats/mtc/BenjaminiHochbergTest.java
test_class.identifier: BenjaminiHochbergTest
test_case.body: @Test
    void testA() {
      MultipleTestingCorrection bonf = new BenjaminiHochberg();
      bonf.adjustPvals(pvallist);
      // index 0
      PValue item = getResult(MadeUpPValues.A,pvallist);
      assertNotNull(item);
      double adjpval = item.getAdjustedPValue(); // raw value was 0.0001 // raw value was 0.0001
      assertEquals(0.00150000,adjpval,EPSILON);
    }
test_case.class_method_signature: BenjaminiHochbergTest.testA()
test_case.full_signature: @Test void testA()
test_case.identifier: testA
test_case.invocations: adjustPvals getResult assertNotNull getAdjustedPValue assertEquals
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testA()
focal_class.file: phenol-analysis/src/main/java/org/monarchinitiative/phenol/stats/mtc/BenjaminiHochberg.java
focal_class.identifier: BenjaminiHochberg
focal_class.interfaces: implements MultipleTestingCorrection
focal_class.class_method_signature: BenjaminiHochberg.adjustPvals(List<? extends PValue> pvals)
focal_class.full_signature: @Override public void adjustPvals(List<? extends PValue> pvals)
focal_class.identifier: adjustPvals
focal_class.modifiers: @Override public
focal_class.parameters: (List<? extends PValue> pvals)
focal_class.return: void
focal_class.signature: void adjustPvals(List<? extends PValue> pvals)
focal_class.class_method_signature: BenjaminiHochberg.getName()
focal_class.full_signature: @Override public String getName()
focal_class.identifier: getName
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getName()
focal_method.body: @Override
    public void adjustPvals(List<? extends PValue> pvals) {
      Collections.sort(pvals);
      int N=pvals.size();
      for (int r=0;r<N;r++) {
        PValue item = pvals.get(r);
        double raw_p = item.getRawPValue();
        item.setAdjustedPValue(raw_p * N/(r+1));
      }
      enforcePValueMonotony(pvals);
    }
focal_method.class_method_signature: BenjaminiHochberg.adjustPvals(List<? extends PValue> pvals)
focal_method.full_signature: @Override public void adjustPvals(List<? extends PValue> pvals)
focal_method.identifier: adjustPvals
focal_method.invocations: sort size get getRawPValue setAdjustedPValue enforcePValueMonotony
focal_method.modifiers: @Override public
focal_method.parameters: (List<? extends PValue> pvals)
focal_method.return: void
focal_method.signature: void adjustPvals(List<? extends PValue> pvals)