{
}
- @Test(groups= {"Network"})
+ @Test(groups = { "Network" })
public void checkUniprotCanonicalFlagSet()
{
- // TODO - mock this - for moment it is a live request.
+ // TODO - mock this - for moment it is a live request.
SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
"MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
- + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
- + "LTA");
+ + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+ + "LTA");
DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
dbr.fetchDBRefs(true);
List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
assertNotNull(primRefs);
- assertTrue(primRefs.size()>0);
- boolean canonicalUp=false;
- for (DBRefEntry ref:primRefs) {
+ assertTrue(primRefs.size() > 0);
+ boolean canonicalUp = false;
+ for (DBRefEntry ref : primRefs)
+ {
assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
canonicalUp |= ref.isCanonical();
}
assertTrue("No Canonical Uniprot reference detected", canonicalUp);
}
+
/**
* Tests that standard protein database sources include Uniprot (as the first)
* and also PDB. (Additional sources are dependent on availability of DAS
public void testEmblUniprotProductRecovery() throws Exception
{
String retrievalId = "V00488";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
- DBRefSource.EMBL).get(0);
+ DbSourceProxy embl = new SequenceFetcher()
+ .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(
- DBRefSource.EMBLCDS).get(0);
+ DbSourceProxy embl = new SequenceFetcher()
+ .getSourceProxy(DBRefSource.EMBLCDS).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
}
assertEquals("Didn't retrieve right number of records", 1,
alsq.getHeight());
SequenceI seq = alsq.getSequenceAt(0);
- assertEquals("Wrong sequence name", embl.getDbSource() + "|"
- + retrievalId, seq.getName());
+ assertEquals("Wrong sequence name",
+ embl.getDbSource() + "|" + retrievalId, seq.getName());
List<SequenceFeature> sfs = seq.getSequenceFeatures();
assertFalse("Sequence features missing", sfs.isEmpty());
- assertTrue(
- "Feature not CDS",
- FeatureProperties.isCodingFeature(embl.getDbSource(),
- sfs.get(0).getType()));
+ assertTrue("Feature not CDS", FeatureProperties
+ .isCodingFeature(embl.getDbSource(), sfs.get(0).getType()));
assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT });
+ new String[]
+ { DBRefSource.UNIPROT });
assertNotNull(dr);
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.get(0)
- .getMap().getWidth(), 3);
+ 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.get(0).getMap().getWidth(), 3);
AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
.findXrefSequences(dr.get(0).getSource(), true);
assertNotNull(
assertEquals("Didn't xref right number of records", 1,
sprods.getHeight());
SequenceI proteinSeq = sprods.getSequenceAt(0);
- assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
- .getSequenceAsString());
+ assertEquals(proteinSeq.getSequenceAsString(),
+ dr.get(0).getMap().getTo().getSequenceAsString());
assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
proteinSeq.getName());
}