JAL-2037 set DBRefEntry.version to "0" not "" in EMBL xrefs

[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 d7fd7e4..c6a94d7 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -41,6 +41,7 @@ public class EmblFileTest
           + "<description>Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)</description>"
           + "<keyword>L-lactate dehydrogenase</keyword><keyword>chutney</keyword>"
           + "<dbreference db=\"EuropePMC\" primary=\"PMC1460223\" secondary=\"9649548\" />"
+          + "<dbreference db=\"MD5\" primary=\"d3b68\" />"
           + "<feature name=\"CDS\"><dbreference db=\"GOA\" primary=\"P00340\" secondary=\"2.1\" /><dbreference db=\"InterPro\" primary=\"IPR001236\" />"
           + "<qualifier name=\"note\"><value>L-lactate dehydrogenase A-chain</value><value>pickle</value></qualifier>"
           + "<qualifier name=\"translation\"><value>MSLKDHLIHN</value><evidence>Keith</evidence></qualifier>"
@@ -79,11 +80,16 @@ public class EmblFileTest
     /*
      * dbrefs
      */
-    assertEquals(1, entry.getDbRefs().size());
+    assertEquals(2, entry.getDbRefs().size());
     DBRefEntry dbref = entry.getDbRefs().get(0);
     assertEquals("EuropePMC", dbref.getSource());
     assertEquals("PMC1460223", dbref.getAccessionId());
     assertEquals("9649548", dbref.getVersion());
+    dbref = entry.getDbRefs().get(1);
+    assertEquals("MD5", dbref.getSource());
+    assertEquals("d3b68", dbref.getAccessionId());
+    // blank version has been converted to "0"
+    assertEquals("0", dbref.getVersion());
 
     /*
      * sequence features
@@ -99,7 +105,8 @@ public class EmblFileTest
     dbref = ef.getDbRefs().get(1);
     assertEquals("InterPro", dbref.getSource());
     assertEquals("IPR001236", dbref.getAccessionId());
-    assertEquals("", dbref.getVersion());
+    // blank version converted to "0":
+    assertEquals("0", dbref.getVersion());
     assertEquals(2, ef.getQualifiers().size());
 
     // feature qualifiers
@@ -142,5 +149,12 @@ public class EmblFileTest
     assertEquals("mRNA", seq.getType());
     assertEquals("2", seq.getVersion());
     assertEquals("GTGACG", seq.getSequence());
+
+    /*
+     * getSequence() converts empty DBRefEntry.version to "0"
+     */
+    assertEquals("0", entry.getDbRefs().get(1).getVersion());
+    assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)
+            .getVersion());
   }
 }