package jalview.ws.seqfetcher;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
+import jalview.ws.DBRefFetcher;
import jalview.ws.SequenceFetcher;
import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.testng.annotations.AfterClass;
public class DbRefFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
+ @Test(groups= {"Network"})
+ public void checkUniprotCanonicalFlagSet()
+ {
+ // TODO - mock this - for moment it is a live request.
+ SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
+ "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
+ + "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) {
+ 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
@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;
SequenceI seq = alsq.getSequenceAt(0);
assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+ retrievalId, seq.getName());
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- assertNotNull("Sequence features missing", sfs);
+ List<SequenceFeature> sfs = seq.getSequenceFeatures();
+ assertFalse("Sequence features missing", sfs.isEmpty());
assertTrue(
"Feature not CDS",
FeatureProperties.isCodingFeature(embl.getDbSource(),
- 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 });
+ 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.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 = CrossRef.findXrefSequences(
- alsq.getSequencesArray(), true, dr[0].getSource(), alsq);
+ 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[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());
}
}