@Test(groups = { "Functional" })
public void testStandardProtDbs()
{
- List<String> defdb = new ArrayList<String>();
+ List<String> defdb = new ArrayList<>();
defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
defdb.add(DBRefSource.PDB);
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- SequenceFetcher sfetcher = new SequenceFetcher();
+ List<DbSourceProxy> srces = new ArrayList<>();
+ SequenceFetcher sfetcher = SequenceFetcher.getInstance();
boolean pdbFound = false;
for (String ddb : defdb)
public void testEmblUniprotProductRecovery() throws Exception
{
String retrievalId = "V00488";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DbSourceProxy embl = SequenceFetcher.getInstance().getSourceProxy(
DBRefSource.EMBL).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
public void testEmblCDSUniprotProductRecovery() throws Exception
{
String retrievalId = "AAH29712";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DbSourceProxy embl = SequenceFetcher.getInstance()
+ .getSourceProxy(
DBRefSource.EMBLCDS).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
FeatureProperties.isCodingFeature(embl.getDbSource(),
sfs.get(0).getType()));
assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
- DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
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]
+ assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
+ assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
.getMap().getMappedWidth(), 1);
- assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
+ assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
.getMap().getWidth(), 3);
AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
- .findXrefSequences(dr[0].getSource(), true);
+ .findXrefSequences(dr.get(0).getSource(), true);
assertNotNull(
"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
sprods);
assertEquals("Didn't xref right number of records", 1,
sprods.getHeight());
SequenceI proteinSeq = sprods.getSequenceAt(0);
- assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo()
+ assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
.getSequenceAsString());
- assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+ assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
proteinSeq.getName());
}
}