Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...

[jalview.git] / test / jalview / ws / dbsources / UniprotTest.java

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 24f62bc..7eb3b75 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -26,6 +26,16 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.math.BigInteger;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -37,16 +47,6 @@ import jalview.xml.binding.uniprot.FeatureType;
 import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
-import java.math.BigInteger;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class UniprotTest
 {
 
@@ -224,11 +224,25 @@ public class UniprotTest
     res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
             DBRefSource.UNIPROT);
     assertEquals(2, res.size());
+    res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
+    assertEquals(1, res.size());
+    assertTrue("1".equals(res.get(0).getVersion()));
     /*
      * NB this test fragile - relies on ordering being preserved
      */
     assertTrue(res.get(0).isCanonical());
     assertFalse(res.get(1).isCanonical());
+
+    // check version is preserved for EMBLCDS
+    res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
+    assertEquals(1, res.size());
+    // Ideally we would expect AAK85932.1 -> AAK85932
+    // assertTrue("1".equals(res.get(0).getVersion()));
+    // but it also passes through DBrefUtils.ensurePrimaries which adds
+    // (promoted) to the version string
+    // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
+    // ignore it !
+    assertEquals("1 (promoted)", (res.get(0).getVersion()));
   }
 
   /**