From 141eaf3859dbd8304fe664b37ef81848353406e0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 25 Aug 2016 20:53:46 +0100
Subject: [PATCH] JAL-2106 tighten DBRefEntry primary seq test for PDB

---
 src/jalview/datamodel/Sequence.java      |    9 ++++++++-
 test/jalview/datamodel/SequenceTest.java |   32 ++++++++++++++++++++++++++++--
 2 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 620bcc1..bb63466 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1450,7 +1450,14 @@ public class Sequence extends ASequence implements SequenceI
                 DBRefUtils.getCanonicalName(ref.getSource())))
         {
           // PDB dbrefs imply there should be a PDBEntry associated
-          if (getPDBEntry(ref.getAccessionId()) != null)
+          // TODO: tighten PDB dbrefs
+          // formally imply Jalview has actually downlaoded and
+          // parsed the pdb file. That means there should be a cached file
+          // handle on the PDBEntry, and a real mapping between sequence and
+          // extracted sequence from PDB file
+          PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+          if (pdbentry != null && pdbentry.getType() != null
+                  && pdbentry.getType().equalsIgnoreCase("PDB"))
           {
             primaries.add(ref);
           }
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index fcd24dd..3ad309e 100644
--- 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());
+  }
 }
-- 
1.7.10.2