X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=f58ead5ad9c73852801eab3324c332882896a441;hb=9ad1e437d5d6366f0b06fbfbdb446a720ca57104;hp=afaadbb23cb3e47198ae0e271f1fd719bb0a78e2;hpb=a3ea406406be52a773560fedc4d93f07bfd69f5d;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index afaadbb..f58ead5 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -50,6 +50,7 @@ public class DbRefFetcherTest
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
@@ -102,13 +103,33 @@ public class DbRefFetcherTest
   {
     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 ?",