ExperimentConfiguration { public List<AssayGroup> getAssayGroups() { ImmutableList.Builder<AssayGroup> b = ImmutableList.builder(); for (String assayGroupId : xmlReader.getStringArray("/analytics/assay_groups/assay_group/@id")) { b.add(getAssayGroup(assayGroupId)); } return b.build(); } ExperimentConfiguration(XmlReader xmlReader); List<Pair<Contrast, Boolean>> getContrastAndAnnotationPairs(); List<Contrast> getContrasts(); List<AssayGroup> getAssayGroups(); ExperimentType getExperimentType();  }
@Test public void testGetAssayGroups() { List<AssayGroup> assayGroups = testConfiguration(MICROARRAY_CONFIGURATION_XML).getAssayGroups(); assertThat(assayGroups, hasSize(5)); }
@Test public void replicatesIsSumOfUniqueTechnicalReplicatesAndUnqualifiedAssays() { List<AssayGroup> assayGroups = testConfiguration(MICROARRAY_CONFIGURATION_XML).getAssayGroups(); assertThat(assayGroups.get(0).getId(), is("g1")); assertThat(assayGroups.get(1).getId(), is("g2")); assertThat(assayGroups.get(2).getId(), is("g3")); assertThat(assayGroups.get(3).getId(), is("g4")); assertThat(assayGroups.get(4).getId(), is("g5")); assertThat(assayGroups.get(0).getReplicates(), is(1)); assertThat(assayGroups.get(1).getReplicates(), is(1)); assertThat(assayGroups.get(2).getReplicates(), is(2)); assertThat(assayGroups.get(3).getReplicates(), is(3)); assertThat(assayGroups.get(4).getReplicates(), is(5)); }