import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import jalview.analysis.CrossRef;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.util.DBRefUtils;
-import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
import java.util.List;
import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.util.DBRefUtils;
+import jalview.ws.SequenceFetcher;
+
/**
* @author jimp
*
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Cache.initLogger();
}
/**
{
String retrievalId = "CAA23748"; // "V00488";
DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
- assertNotNull("Couldn't find the EMBL retrieval client",embl);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ @Test
+ 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);
+ }
+
+ 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());
DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+ assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+ .getMap().getMappedWidth(), 1);
+ assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+ .getMap().getWidth(), 3);
AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
assertNotNull(
"Couldn't recover cross reference sequence from dataset. Was it ever added ?",