+ + srces.size() + " sources (source was at position "
+ + uniprotPos + ")", uniprotPos == 0);
+ assertTrue("Failed to find PDB source amongst " + srces.size()
+ + " sources", pdbFound);
+ }
+
+ /**
+ * Tests retrieval of one entry from EMBL. Test is dependent on availability
+ * of network and the EMBL service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testEmblUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "V00488";
+ DbSourceProxy embl = new SequenceFetcher()
+ .getSourceProxy(DBRefSource.EMBL).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ /**
+ * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+ * availability of network and the EMBLCDS service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testEmblCDSUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "AAH29712";
+ DbSourceProxy embl = new SequenceFetcher()
+ .getSourceProxy(DBRefSource.EMBLCDS).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ /**
+ * Helper method to perform database retrieval and verification of results.
+ *
+ * @param retrievalId
+ * @param embl
+ * @throws Exception
+ */
+ private void verifyProteinNucleotideXref(String retrievalId,
+ DbSourceProxy embl) throws Exception
+ {
+ AlignmentI alsq = embl.getSequenceRecords(retrievalId);
+ assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
+ 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());
+ List<SequenceFeature> sfs = seq.getSequenceFeatures();
+ assertFalse("Sequence features missing", sfs.isEmpty());
+ 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 });
+ 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);
+ AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+ .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.get(0).getMap().getTo().getSequenceAsString());
+ assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
+ proteinSeq.getName());
+ }
+
+ /**
+ * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+ * availability of network and the EMBLCDS service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testAlphaFoldClien() throws Exception
+ {
+ DbSourceProxy alphafold = new EBIAlfaFold();
+ AlignmentI resp = alphafold
+ .getSequenceRecords(alphafold.getTestQuery());
+ assertNotNull(resp);
+ assertEquals("One sequence only", resp.getHeight(), 1);
+ for (AlignmentAnnotation aa : resp.getAlignmentAnnotation())
+ {
+ if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ {
+ assertTrue("Contact map didn't provide valid contact",
+ resp.getContactListFor(aa, 1).getContactAt(1) != -1d);
+ // test passes
+ return;
+ }
+ }
+ Assert.fail("No pAE matrix found for alphafold structure.");