import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.testng.annotations.AfterClass;
@Test(groups = { "Functional" })
public void testStandardProtDbs()
{
- String[] defdb = DBRefSource.PROTEINDBS;
+ List<String> defdb = new ArrayList<String>();
+ defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+ defdb.add(DBRefSource.PDB);
List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
SequenceFetcher sfetcher = new SequenceFetcher();
boolean pdbFound = false;
sfs[0].getType()));
assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
- DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+ new String[] { DBRefSource.UNIPROT });
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
assertEquals("Expected cross reference map to be one amino acid", dr[0]
.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);
+ 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);