/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.seqfetcher;
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
-import jalview.ws.DBRefFetcher;
+import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
/**
* @author jimp
- *
+ *
*/
public class DbRefFetcherTest
{
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Cache.initLogger();
}
/**
{
}
- @Test
+ @Test(groups ={ "Functional" })
public void testStandardProtDbs()
{
String[] defdb = DBRefSource.PROTEINDBS;
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- for (String ddb : defdb)
- {
- SequenceFetcher sfetcher= new SequenceFetcher();
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-
- if (srcesfordb != null)
- {
- srces.addAll(srcesfordb);
- }
- }
- DbSourceProxy uniprot=null;
- int i=0;
- // append the selected sequence sources to the default dbs
- for (DbSourceProxy s:srces)
- {
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ for (String ddb : defdb)
{
- i++;
+ SequenceFetcher sfetcher = new SequenceFetcher();
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+
+ if (srcesfordb != null)
+ {
+ srces.addAll(srcesfordb);
+ }
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
+ DbSourceProxy uniprot = null;
+ int i = 0;
+ // append the selected sequence sources to the default dbs
+ for (DbSourceProxy s : srces)
{
- uniprot = s;
- break;
+ if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ i++;
+ }
+
+ if (s instanceof jalview.ws.dbsources.Uniprot)
+ {
+ uniprot = s;
+ break;
+ }
}
+
+ assertTrue("Failed to find Uniprot source as first source amongst "
+ + srces.size() + " sources (source was at position " + i + ")",
+ uniprot != null && i < 2);
}
-
- assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+
+ @Test(groups =
+ { "External" })
+ public void testEmblUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "CAA23748"; // "V00488";
+ DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
}
+ @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);
+ }
+
+ 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 ?",
+ sprods);
+
+
+ }
}