JAL-2113 embl_mapping.xml and code updated for EMBL XML v1.2

[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 c6a94d7..fda25e3 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -21,9 +21,7 @@
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
 
@@ -34,22 +32,21 @@ import org.testng.annotations.Test;
 
 public class EmblFileTest
 {
-  // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+  // adapted from http://www.ebi.ac.uk/ena/data/view/x53828&display=xml
   private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
-          + "<EMBL_Services>"
-          + "<entry accession=\"X53828\" version=\"3\" lastUpdated=\"2005-04-18\" releaseCreated=\"25\" releaseLastUpdated=\"83\">"
+          + "<ROOT>"
+          + "<entry accession=\"X53828\" entryVersion=\"3\" lastUpdated=\"2005-04-18\" releaseCreated=\"25\" releaseLastUpdated=\"83\""
+          + " version=\"1\" moleculeType=\"mRNA\" topology=\"linear\" sequenceLength=\"1575\">"
           + "<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\" />"
+          + "<xref db=\"EuropePMC\" id=\"PMC1460223\" secondaryId=\"9649548\" />"
+          + "<xref db=\"MD5\" id=\"d3b68\" />"
+          + "<feature name=\"CDS\" location=\"60..1058\">"
+          + "<xref db=\"GOA\" id=\"P00340\" secondaryId=\"2.1\" /><xref db=\"InterPro\" id=\"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>"
-          + "<location type=\"single\" complement=\"true\">"
-          + "<locationElement type=\"range\" accession=\"X53828\" version=\"1\" complement=\"false\">"
-          + "<basePosition type=\"simple\">60</basePosition><basePosition type=\"join\">1058</basePosition>"
-          + "</locationElement></location></feature>"
-          + "<sequence type=\"mRNA\" version=\"2\">GTGACG</sequence></entry></EMBL_Services>";
+          + "</feature>"
+          + "<sequence>GTGACG</sequence></entry></ROOT>";
 
   @Test(groups = { "Functional" })
   public void testGetEmblFile()
@@ -64,6 +61,11 @@ public class EmblFileTest
             "Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)",
             entry.getDesc());
     assertEquals("2005-04-18", entry.getLastUpdated());
+    assertEquals("mRNA", entry.getMoleculeType());
+    assertEquals("1", entry.getSequenceVersion());
+    assertEquals("3", entry.getEntryVersion());
+    assertEquals("linear", entry.getTopology());
+    assertEquals("1575", entry.getSequenceLength());
 
     /*
      * FIXME these assertions fail - values are null - why?? Adding or removing
@@ -92,11 +94,12 @@ public class EmblFileTest
     assertEquals("0", dbref.getVersion());
 
     /*
-     * sequence features
+     * sequence feature for CDS
      */
     assertEquals(1, entry.getFeatures().size());
     EmblFeature ef = entry.getFeatures().get(0);
     assertEquals("CDS", ef.getName());
+    assertEquals("60..1058", ef.getLocation());
     assertEquals(2, ef.getDbRefs().size());
     dbref = ef.getDbRefs().get(0);
     assertEquals("GOA", dbref.getSource());
@@ -123,31 +126,10 @@ public class EmblFileTest
     assertEquals(1, q.getEvidence().length);
     assertEquals("Keith", q.getEvidence()[0]);
 
-    // feature locations
-    assertEquals(1, ef.getLocations().size());
-    EmblFeatureLocations fl = ef.getLocations().get(0);
-    assertEquals("single", fl.getLocationType());
-    assertTrue(fl.isLocationComplement());
-    assertEquals(1, fl.getLocElements().size());
-    EmblFeatureLocElement le = fl.getLocElements().get(0);
-    assertEquals("range", le.getType());
-    assertEquals("X53828", le.getAccession());
-    assertEquals("1", le.getVersion());
-    assertFalse(le.isComplement());
-    assertEquals(2, le.getBasePositions().length);
-    BasePosition bp = le.getBasePositions()[0];
-    assertEquals("simple", bp.getType());
-    assertEquals("60", bp.getPos());
-    bp = le.getBasePositions()[1];
-    assertEquals("join", bp.getType());
-    assertEquals("1058", bp.getPos());
-
     /*
      * Sequence
      */
     EmblSequence seq = entry.getSequence();
-    assertEquals("mRNA", seq.getType());
-    assertEquals("2", seq.getVersion());
     assertEquals("GTGACG", seq.getSequence());
 
     /*