JAL-2113 additions to embl_mapping.xml / data models / tests

[jalview.git] / test / jalview / datamodel / xdb / embl / EmblEntryTest.java

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index c36b7d3..e8760bd 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,7 +1,9 @@
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
 
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -36,17 +38,79 @@ public class EmblEntryTest
     SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT");
     List<SequenceI> peptides = new ArrayList<SequenceI>();
     EmblFile ef = EmblTestHelper.getEmblFile();
-    EmblFeature feature = null;
-    for (EmblFeature feat : ef.getEntries().get(0).getFeatures())
+
+    /*
+     * parse two CDS features, one with two Uniprot cross-refs,
+     * the other with one
+     */
+    EmblEntry testee = new EmblEntry();
+    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
     {
-      if ("CDS".equals(feat.getName()))
+      if ("CDS".equals(feature.getName()))
       {
-        feature = feat;
-        break;
+        testee.parseCodingFeature(feature, "EMBL", dna, peptides);
       }
     }
 
-    EmblEntry testee = new EmblEntry();
-    testee.parseCodingFeature(feature, "EMBL", dna, peptides);
+    /*
+     * peptides should now have five entries:
+     * EMBL product and two Uniprot accessions for the first CDS / translation
+     * EMBL product and one Uniprot accession for the second CDS / translation
+     */
+    assertEquals(5, peptides.size());
+    assertEquals("CAA30420.1", peptides.get(0).getName());
+    assertEquals("MLCF", peptides.get(0).getSequenceAsString());
+    assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
+    assertEquals("MLCF", peptides.get(1).getSequenceAsString());
+    assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
+    assertEquals("MLCF", peptides.get(2).getSequenceAsString());
+    assertEquals("CAA30421.1", peptides.get(3).getName());
+    assertEquals("MSSS", peptides.get(3).getSequenceAsString());
+    assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
+    assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+
+    /*
+     * verify dna sequence has dbrefs with mappings to the peptide 'products'
+     */
+    DBRefEntry[] dbrefs = dna.getDBRefs();
+    assertEquals(3, dbrefs.length);
+    DBRefEntry dbRefEntry = dbrefs[0];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+    List<int[]> fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(57, fromRanges.get(0)[0]);
+    assertEquals(46, fromRanges.get(0)[1]);
+    List<int[]> toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
+
+    dbRefEntry = dbrefs[1];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("P0CE20", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(57, fromRanges.get(0)[0]);
+    assertEquals(46, fromRanges.get(0)[1]);
+    toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
+
+    dbRefEntry = dbrefs[2];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(4, fromRanges.get(0)[0]);
+    assertEquals(15, fromRanges.get(0)[1]);
+    toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
   }
 }