import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
public void testCopyConstructor() throws IOException
{
AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
+ // create sequence and alignment datasets
protein.setDataset(null);
AlignedCodonFrame acf = new AlignedCodonFrame();
protein.getDataset().setCodonFrames(Collections.singleton(acf));
.getSequenceAt(0).getDatasetSequence());
assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
.getSequenceAt(1).getDatasetSequence());
- // and the same alignment dataset (?)
- // or a new one with the same dataset sequences?
- assertSame(copy.getDataset(), protein.getDataset());
+
+ // TODO should the copy constructor copy the dataset?
+ // or make a new one referring to the same dataset sequences??
+ assertNull(copy.getDataset());
+ // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
+ // .getDataset().getSequencesArray());
+ }
+
+ /**
+ * Test behaviour of createDataset
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testCreateDatasetAlignment() throws IOException
+ {
+ AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
+ AppletFormatAdapter.PASTE, "FASTA");
+ /*
+ * create a dataset sequence on first sequence
+ * leave the second without one
+ */
+ protein.getSequenceAt(0).createDatasetSequence();
+ assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
+ assertNull(protein.getSequenceAt(1).getDatasetSequence());
+
+ /*
+ * add a mapping to the alignment
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ protein.addCodonFrame(acf);
+ assertNull(protein.getDataset());
+ assertTrue(protein.getCodonFrames().contains(acf));
+
+ /*
+ * create the alignment dataset
+ * note this creates sequence datasets where missing
+ * as a side-effect (in this case, on seq2
+ */
+ // TODO promote this method to AlignmentI
+ ((Alignment) protein).createDatasetAlignment();
+
+ // TODO this method should return AlignmentI not Alignment !!
+ Alignment ds = protein.getDataset();
+
+ // side-effect: dataset created on second sequence
+ assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
+ // dataset alignment has references to dataset sequences
+ assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
+ .getDatasetSequence());
+ assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
+ .getDatasetSequence());
+
+ // codon frames should have been moved to the dataset
+ // getCodonFrames() should delegate to the dataset:
+ assertTrue(protein.getCodonFrames().contains(acf));
+ // prove the codon frames are indeed on the dataset:
+ assertTrue(ds.getCodonFrames().contains(acf));
}
}