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

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

diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index 6955833..6afdced 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -21,12 +21,11 @@
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.DBRefEntry;
 
-import java.util.Vector;
-
 import org.testng.annotations.Test;
 
 public class EmblFileTest
@@ -35,9 +34,10 @@ public class EmblFileTest
   @Test(groups = { "Functional" })
   public void testGetEmblFile()
   {
-    Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
-    assertEquals(1, entries.size());
-    EmblEntry entry = entries.get(0);
+    EmblEntry entry = EmblTestHelper.getEmblFile();
+    assertNotNull(entry);
+    // assertEquals(1, entries.size());
+    // EmblEntry entry = entries.get(0);
 
     assertEquals("X07547", entry.getAccession());
     assertEquals("C. trachomatis plasmid", entry.getDescription());
@@ -80,9 +80,9 @@ public class EmblFileTest
     assertEquals("0", dbref.getVersion());
 
     /*
-     * two sequence features for CDS
+     * three sequence features for CDS
      */
-    assertEquals(2, entry.getFeatures().size());
+    assertEquals(3, entry.getFeatures().size());
     /*
      * first CDS
      */
@@ -140,6 +140,23 @@ public class EmblFileTest
     assertEquals("MSSS", q.getValues()[0]);
 
     /*
+     * third CDS
+     */
+    ef = entry.getFeatures().get(2);
+    assertEquals("CDS", ef.getName());
+    assertEquals("join(4..6,10..15)", ef.getLocation());
+    assertNull(ef.getDbRefs());
+    assertEquals(2, ef.getQualifiers().size());
+    q = ef.getQualifiers().get(0);
+    assertEquals("protein_id", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("CAA12345.6", q.getValues()[0]);
+    q = ef.getQualifiers().get(1);
+    assertEquals("translation", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("MSS", q.getValues()[0]);
+
+    /*
      * Sequence - verify newline not converted to space (JAL-2029)
      */
     EmblSequence seq = entry.getSequence();