X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=e6aa47246536da0f8e6a6e950c08df3ff2264a5e;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2d09088051d0a580419bb46094aadeaee4c54d7b;hpb=4699d1858999c49dfbab4d98004b20df974fdc57;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 2d09088..e6aa472 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -29,7 +29,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -508,9 +507,7 @@ public class DBRefUtils
           PDBEntry pdbr = new PDBEntry();
           pdbr.setId(pdbid);
           pdbr.setType(PDBEntry.Type.PDB);
-          pdbr.setProperty(new Hashtable());
           pdbr.setChainCode(chaincode);
-          // pdbr.getProperty().put("CHAIN", chaincode);
           seq.addPDBId(pdbr);
         }
         else
@@ -618,21 +615,21 @@ public class DBRefUtils
    * sequences if they have an appropriate primary ref
    * <table>
    * <tr>
-   * <td>Seq Type</td>
-   * <td>Primary DB</td>
-   * <td>Direct which will be promoted</td>
+   * <th>Seq Type</th>
+   * <th>Primary DB</th>
+   * <th>Direct which will be promoted</th>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>peptides</td>
    * <td>Ensembl</td>
    * <td>Uniprot</td>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>peptides</td>
    * <td>Ensembl</td>
    * <td>Uniprot</td>
    * </tr>
-   * <tr>
+   * <tr align=center>
    * <td>dna</td>
    * <td>Ensembl</td>
    * <td>ENA</td>
@@ -650,8 +647,16 @@ public class DBRefUtils
       return;
     }
     List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
-    selfs.addAll(Arrays.asList(selectDbRefs(!sequence.isProtein(),
-            sequence.getDBRefs())));
+    {
+      DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+              sequence.getDBRefs());
+      if (selfArray == null || selfArray.length == 0)
+      {
+        // nothing to do
+        return;
+      }
+      selfs.addAll(Arrays.asList(selfArray));
+    }
 
     // filter non-primary refs
     for (DBRefEntry p : pr)