import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
import java.util.List;
/**
* Tests that standard protein database sources include Uniprot (as the first)
- * and also PDB. (Additional sources are dependent on available of DAS
+ * and also PDB. (Additional sources are dependent on availability of DAS
* services.)
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testStandardProtDbs()
{
String[] defdb = DBRefSource.PROTEINDBS;
List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ SequenceFetcher sfetcher = new SequenceFetcher();
+ boolean pdbFound = false;
+
for (String ddb : defdb)
{
- SequenceFetcher sfetcher = new SequenceFetcher();
List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
if (srcesfordb != null)
{
+ // TODO is this right? get duplicate entries
srces.addAll(srcesfordb);
}
}
int i = 0;
int uniprotPos = -1;
- int pdbPos = -1;
- // append the selected sequence sources to the default dbs
for (DbSourceProxy s : srces)
{
- if (s instanceof jalview.ws.dbsources.Uniprot)
+ if (s instanceof Uniprot && uniprotPos == -1)
{
uniprotPos = i;
}
- if (s instanceof jalview.ws.dbsources.Pdb)
+ if (s instanceof Pdb)
{
- pdbPos = i;
+ pdbFound = true;
}
i++;
}
+ srces.size() + " sources (source was at position "
+ uniprotPos + ")", uniprotPos == 0);
assertTrue("Failed to find PDB source amongst " + srces.size()
- + " sources", pdbPos >= 0);
+ + " sources", pdbFound);
}
/**
*
* @throws Exception
*/
- @Test(groups =
- { "External" })
+ @Test(groups = { "External" })
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);
}
*
* @throws Exception
*/
- @Test(groups =
- { "External" })
+ @Test(groups = { "External" })
public void testEmblCDSUniprotProductRecovery() throws Exception
{
String retrievalId = "AAH29712";
{
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());
+ 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());
FeatureProperties.isCodingFeature(embl.getDbSource(),
sfs[0].getType()));
assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
- DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(), DBRefSource.PROTEINSEQ);
+ DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
+ DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
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.getDataset());
+ AlignmentI sprods = CrossRef.findXrefSequences(
+ alsq.getSequencesArray(), true, dr[0].getSource(), alsq);
assertNotNull(
"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
sprods);