X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFileTest.java;h=906436fd755265bce8e67144ac0420ad54980408;hb=02d6aa2077a261d41db77a0158f2b4b779a36398;hp=fda25e3d6709b344e6b28e642ba757c217299dc3;hpb=5071850e8470077a8ac2bdc6a53908c70ad5526d;p=jalview.git

diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index fda25e3..906436f 100644
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -25,59 +25,45 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.DBRefEntry;
 
-import java.io.StringReader;
 import java.util.Vector;
 
 import org.testng.annotations.Test;
 
 public class EmblFileTest
 {
-  // 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\" ?>"
-          + "<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>"
-          + "<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>"
-          + "</feature>"
-          + "<sequence>GTGACG</sequence></entry></ROOT>";
 
   @Test(groups = { "Functional" })
   public void testGetEmblFile()
   {
-    Vector<EmblEntry> entries = EmblFile.getEmblFile(
-            new StringReader(TESTDATA)).getEntries();
+    Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().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());
-    assertEquals("mRNA", entry.getMoleculeType());
+    assertEquals("X07547", entry.getAccession());
+    assertEquals("C. trachomatis plasmid", entry.getDescription());
+    assertEquals("STD", entry.getDataClass());
+    assertEquals("PRO", entry.getTaxonomicDivision());
+    assertEquals("1999-02-10", entry.getLastUpdatedDate());
+    assertEquals("58", entry.getLastUpdatedRelease());
+    assertEquals("1988-11-10", entry.getFirstPublicDate());
+    assertEquals("18", entry.getFirstPublicRelease());
+    assertEquals("genomic DNA", entry.getMoleculeType());
     assertEquals("1", entry.getSequenceVersion());
-    assertEquals("3", entry.getEntryVersion());
+    assertEquals("8", entry.getEntryVersion());
     assertEquals("linear", entry.getTopology());
-    assertEquals("1575", entry.getSequenceLength());
+    assertEquals("7499", entry.getSequenceLength());
 
     /*
      * 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("1988-11-10", entry.getFirstPublicDate());
+    assertEquals("18", entry.getFirstPublicRelease());
 
     assertEquals(2, entry.getKeywords().size());
-    assertEquals("L-lactate dehydrogenase", entry.getKeywords().get(0));
-    assertEquals("chutney", entry.getKeywords().get(1));
+    assertEquals("plasmid", entry.getKeywords().get(0));
+    assertEquals("unidentified reading frame", entry.getKeywords().get(1));
 
     /*
      * dbrefs
@@ -85,52 +71,98 @@ public class EmblFileTest
     assertEquals(2, entry.getDbRefs().size());
     DBRefEntry dbref = entry.getDbRefs().get(0);
     assertEquals("EuropePMC", dbref.getSource());
-    assertEquals("PMC1460223", dbref.getAccessionId());
-    assertEquals("9649548", dbref.getVersion());
+    assertEquals("PMC107176", dbref.getAccessionId());
+    assertEquals("9573186", dbref.getVersion());
     dbref = entry.getDbRefs().get(1);
     assertEquals("MD5", dbref.getSource());
-    assertEquals("d3b68", dbref.getAccessionId());
+    assertEquals("ac73317", dbref.getAccessionId());
     // blank version has been converted to "0"
     assertEquals("0", dbref.getVersion());
 
     /*
-     * sequence feature for CDS
+     * three sequence features for CDS
+     */
+    assertEquals(3, entry.getFeatures().size());
+    /*
+     * first CDS
      */
-    assertEquals(1, entry.getFeatures().size());
     EmblFeature ef = entry.getFeatures().get(0);
     assertEquals("CDS", ef.getName());
-    assertEquals("60..1058", ef.getLocation());
+    assertEquals("complement(46..57)", ef.getLocation());
     assertEquals(2, ef.getDbRefs().size());
     dbref = ef.getDbRefs().get(0);
-    assertEquals("GOA", dbref.getSource());
-    assertEquals("P00340", dbref.getAccessionId());
+    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+    assertEquals("B0BCM4", dbref.getAccessionId());
     assertEquals("2.1", dbref.getVersion());
     dbref = ef.getDbRefs().get(1);
-    assertEquals("InterPro", dbref.getSource());
-    assertEquals("IPR001236", dbref.getAccessionId());
-    // blank version converted to "0":
+    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+    assertEquals("P0CE20", dbref.getAccessionId());
+    // blank version gets converted to "0":
     assertEquals("0", dbref.getVersion());
-    assertEquals(2, ef.getQualifiers().size());
-
-    // feature qualifiers
+    // CDS feature qualifiers
+    assertEquals(3, ef.getQualifiers().size());
     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("ORF 8 (AA 1-330)", q.getValues()[0]);
     assertEquals("pickle", q.getValues()[1]);
     assertNull(q.getEvidence());
     q = ef.getQualifiers().get(1);
+    assertEquals("protein_id", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("CAA30420.1", q.getValues()[0]);
+    q = ef.getQualifiers().get(2);
     assertEquals("translation", q.getName());
     assertEquals(1, q.getValues().length);
-    assertEquals("MSLKDHLIHN", q.getValues()[0]);
+    assertEquals("MLCF", q.getValues()[0]);
     assertEquals(1, q.getEvidence().length);
     assertEquals("Keith", q.getEvidence()[0]);
 
     /*
-     * Sequence
+     * second CDS
+     */
+    ef = entry.getFeatures().get(1);
+    assertEquals("CDS", ef.getName());
+    assertEquals("4..15", ef.getLocation());
+    assertEquals(1, ef.getDbRefs().size());
+    dbref = ef.getDbRefs().get(0);
+    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+    assertEquals("B0BCM3", dbref.getAccessionId());
+    assertEquals("0", dbref.getVersion());
+    assertEquals(2, ef.getQualifiers().size());
+    q = ef.getQualifiers().get(0);
+    assertEquals("protein_id", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("CAA30421.1", q.getValues()[0]);
+    q = ef.getQualifiers().get(1);
+    assertEquals("translation", q.getName());
+    assertEquals(1, q.getValues().length);
+    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();
-    assertEquals("GTGACG", seq.getSequence());
+    assertEquals(
+            "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+            seq.getSequence());
 
     /*
      * getSequence() converts empty DBRefEntry.version to "0"