JAL-2106 tighten DBRefEntry primary seq test for PDB

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index fcd24dd..3ad309e 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -452,8 +452,10 @@ public class SequenceTest
     
     DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
     DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
-    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
-        pdb2pdb });
+
+    //FIXME pdb2pdb's matching PDBEntry has Type.MMCIF - but 2.10 only has PDBEntry with type==PDB to indicate ID is a real PDB entry
+    
+    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb });
 
     sq.getDatasetSequence().addDBRef(pdb1pdb);
     sq.getDatasetSequence().addDBRef(pdb2pdb);
@@ -763,4 +765,30 @@ public class SequenceTest
     assertSame(dbref3, sq.getDBRefs()[2]);
     assertEquals("3", dbref2.getVersion());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetPrimaryDBRefs()
+  {
+    /*
+     * test PDB relationships for for getPrimaryDBRefs
+     */
+    SequenceI seq = new Sequence("aseq", "ASDF");
+    DBRefEntry upentry = new DBRefEntry("UNIPROT", "0", "1qip");
+    // primary - uniprot
+    seq.addDBRef(upentry);
+    // primary - type is PDB
+    DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
+    seq.addDBRef(pdbentry);
+    // not primary - type of PDBEntry is not PDB
+    seq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
+    // not primary - no PDBEntry
+    seq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
+    seq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, null));
+    seq.addPDBId(new PDBEntry("1AAA", null, null, null));
+    assertTrue("Couldn't find simple primary reference (UNIPROT)", seq
+            .getPrimaryDBRefs().contains(upentry));
+    assertTrue("Couldn't find expected PDB primary reference", seq
+            .getPrimaryDBRefs().contains(pdbentry));
+    assertEquals(2, seq.getPrimaryDBRefs().size());
+  }
 }