Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110

[jalview.git] / test / jalview / ws / seqfetcher / DbRefFetcherTest.java

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 5265a72..8ee4f40 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -62,7 +62,7 @@ public class DbRefFetcherTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
@@ -169,17 +169,17 @@ public class DbRefFetcherTest
             FeatureProperties.isCodingFeature(embl.getDbSource(),
                     sfs[0].getType()));
     assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
-            DBRefSource.PROTEINSEQ);
+    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+            new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
+                DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
     assertEquals("Expected cross reference map to be one amino acid", dr[0]
             .getMap().getMappedWidth(), 1);
     assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
-    AlignmentI sprods = CrossRef.findXrefSequences(
-            alsq.getSequencesArray(), true, dr[0].getSource(),
-            alsq.getDataset());
+    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+            .findXrefSequences(dr[0].getSource());
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);