JAL-1712 fixes/tests for Castor binding and 'show flanking regions'

[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
new file mode 100644 (file)
index 0000000..e89245c
--- /dev/null
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -0,0 +1,127 @@
+package jalview.datamodel.xdb.embl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.StringReader;
+import java.util.Vector;
+
+import org.junit.Test;
+
+import jalview.datamodel.DBRefEntry;
+
+public class EmblFileTest
+{
+  // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+  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\">"
+          + "<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\" />"
+          + "<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>"
+          + "<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>";
+
+  @Test
+  public void testGetEmblFile()
+  {
+    Vector<EmblEntry> entries = EmblFile.getEmblFile(
+            new StringReader(TESTDATA)).getEntries();
+    assertEquals(1, entries.size());
+    EmblEntry entry = entries.get(0);
+
+    assertEquals("X53828", entry.getAccession());
+    assertEquals(
+            "Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)",
+            entry.getDesc());
+    assertEquals("2005-04-18", entry.getLastUpdated());
+
+    /*
+     * FIXME these assertions fail - values are null - why?? Adding or removing
+     * attributes in the test XML modifies behaviour. eg. inserting an attribute
+     * _before_ lastUpdated results in a null value in this field.
+     */
+    // assertEquals("25", entry.getRCreated());
+    // assertEquals("83", entry.getRLastUpdated());
+
+    assertEquals(2, entry.getKeywords().size());
+    assertEquals("L-lactate dehydrogenase", entry.getKeywords().get(0));
+    assertEquals("chutney", entry.getKeywords().get(1));
+
+    /*
+     * dbrefs
+     */
+    assertEquals(1, entry.getDbRefs().size());
+    DBRefEntry dbref = entry.getDbRefs().get(0);
+    assertEquals("EuropePMC", dbref.getSource());
+    assertEquals("PMC1460223", dbref.getAccessionId());
+    assertEquals("9649548", dbref.getVersion());
+
+    /*
+     * sequence features
+     */
+    assertEquals(1, entry.getFeatures().size());
+    EmblFeature ef = entry.getFeatures().get(0);
+    assertEquals("CDS", ef.getName());
+    assertEquals(2, ef.getDbRefs().size());
+    dbref = ef.getDbRefs().get(0);
+    assertEquals("GOA", dbref.getSource());
+    assertEquals("P00340", dbref.getAccessionId());
+    assertEquals("2.1", dbref.getVersion());
+    dbref = ef.getDbRefs().get(1);
+    assertEquals("InterPro", dbref.getSource());
+    assertEquals("IPR001236", dbref.getAccessionId());
+    assertEquals("", dbref.getVersion());
+    assertEquals(2, ef.getQualifiers().size());
+
+    // feature qualifiers
+    Qualifier q = ef.getQualifiers().get(0);
+    assertEquals("note", q.getName());
+    assertEquals(2, q.getValues().length);
+    assertEquals("L-lactate dehydrogenase A-chain", q.getValues()[0]);
+    assertEquals("pickle", q.getValues()[1]);
+    assertNull(q.getEvidence());
+    q = ef.getQualifiers().get(1);
+    assertEquals("translation", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("MSLKDHLIHN", q.getValues()[0]);
+    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());
+  }
+}