- assertSame(dna.getCodonFrames(), cds.getCodonFrames());
- List<AlignedCodonFrame> cdsMappings = cds.getCodonFrames();
- assertEquals(2, cdsMappings.size());
-
+ List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+ /*
+ * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
+ */
+ assertEquals(6, cdsMappings.size());
+ /*
+ * verify that mapping sets for dna and cds alignments are different
+ */
+ Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+ assertEquals(4, dna.getCodonFrames());
+ assertEquals(4, cds.getCodonFrames());