import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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.EBIAlfaFold;
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;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
/**
* @author jimp
*
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
}
/**
{
}
+ @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
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());
}
+
+ /**
+ * 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.CONTACT_MAP)
+ {
+ 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.");
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff