From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Sep 2016 14:15:03 +0000 (+0100)
Subject: JAL-1803 JAL-2106 patch tests for tighter PDB Primary DBRef definition
X-Git-Tag: Release_2_10_0~47^2~4^2~15
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=bbcafe66766773929c15cbe80d7e7c731f743946

JAL-1803 JAL-2106 patch tests for tighter PDB Primary DBRef definition
---

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 3ad309e..0a1ca67 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -31,6 +31,7 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.util.MapList;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -453,9 +454,9 @@ public class SequenceTest
     DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
     DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
 
-    //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 });
+    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
+        pdb2pdb });
 
     sq.getDatasetSequence().addDBRef(pdb1pdb);
     sq.getDatasetSequence().addDBRef(pdb2pdb);
@@ -779,11 +780,15 @@ public class SequenceTest
     // primary - type is PDB
     DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
     seq.addDBRef(pdbentry);
-    // not primary - type of PDBEntry is not PDB
+    // not primary - PDBEntry has no file
     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));
+    // add corroborating PDB entry for primary DBref - needs to have a file as
+    // well as matching ID
+    seq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
+            .toString()));
+    // not valid DBRef - no file..
     seq.addPDBId(new PDBEntry("1AAA", null, null, null));
     assertTrue("Couldn't find simple primary reference (UNIPROT)", seq
             .getPrimaryDBRefs().contains(upentry));