JAL-2245 Castor mapping and code changes for change to ENA XML format

[jalview.git] / test / jalview / datamodel / xdb / embl / EmblEntryTest.java

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index abe5099..f332fa6 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,6 +1,7 @@
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 
@@ -40,20 +41,21 @@ public class EmblEntryTest
     // not the whole sequence but enough for this test...
     List<SequenceI> peptides = new ArrayList<SequenceI>();
     SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
-    EmblFile ef = EmblTestHelper.getEmblFile();
-    assertEquals(1, ef.getEntries().size());
-    EmblEntry testee = ef.getEntries().get(0);
+    EmblEntry ef = EmblTestHelper.getEmblFile();
+    assertNotNull(ef);
+    // assertEquals(1, ef.getEntries().size());
+    // EmblEntry testee = ef.getEntries().get(0);
     String sourceDb = "EMBL";
-    SequenceI dna = testee.makeSequence(sourceDb);
+    SequenceI dna = ef.makeSequence(sourceDb);
 
     /*
      * parse three CDS features, with two/one/no Uniprot cross-refs
      */
-    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+    for (EmblFeature feature : ef.getFeatures())
     {
       if ("CDS".equals(feature.getName()))
       {
-        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+        ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
       }
     }