/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
FeatureProperties.isCodingFeature(embl.getDbSource(),
sfs[0].getType()));
assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
- DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
+ DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
assertNotNull(dr);
.getMap().getMappedWidth(), 1);
assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
.getMap().getWidth(), 3);
- AlignmentI sprods = CrossRef.findXrefSequences(
- alsq.getSequencesArray(), true, dr[0].getSource(),
- alsq.getDataset());
+ AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+ .findXrefSequences(dr[0].getSource(), true);
assertNotNull(
"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
sprods);