package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
// not the whole sequence but enough for this test...
List<SequenceI> peptides = new ArrayList<SequenceI>();
SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- EmblFile ef = EmblTestHelper.getEmblFile();
- assertEquals(1, ef.getEntries().size());
- EmblEntry testee = ef.getEntries().get(0);
+ EmblEntry ef = EmblTestHelper.getEmblFile();
+ assertNotNull(ef);
+ // assertEquals(1, ef.getEntries().size());
+ // EmblEntry testee = ef.getEntries().get(0);
String sourceDb = "EMBL";
- SequenceI dna = testee.makeSequence(sourceDb);
+ SequenceI dna = ef.makeSequence(sourceDb);
/*
* parse three CDS features, with two/one/no Uniprot cross-refs
*/
- for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+ for (EmblFeature feature : ef.getFeatures())
{
if ("CDS".equals(feature.getName()))
{
- testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+ ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
}
}
assertEquals(5, dbrefs.length);
assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+ // TODO: verify getPrimaryDBRefs() for peptide products
assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
assertEquals("CAA30420.1", dbrefs[1].getAccessionId());