X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=b50e5af92191c7cd2df24696f40a95db15634d7a;hb=e44876a5a8801c0118b67793ebd57d21079be7b0;hp=bb634665c3f9c11e8b034b50b117b97a4ded2ae2;hpb=141eaf3859dbd8304fe664b37ef81848353406e0;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index bb63466..b50e5af 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -28,6 +28,7 @@ import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -59,8 +60,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -1424,12 +1423,12 @@ public class Sequence extends ASequence implements SequenceI
     }
     if (dbrefs==null || dbrefs.length==0)
     {
-      return Arrays.asList(new DBRefEntry[0]);
+      return Collections.emptyList();
     }
     synchronized (dbrefs)
     {
       List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
-      DBRefEntry tmp[] = new DBRefEntry[1], res[] = null;
+      DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
         if (!ref.isPrimary())
@@ -1451,13 +1450,12 @@ public class Sequence extends ASequence implements SequenceI
         {
           // PDB dbrefs imply there should be a PDBEntry associated
           // TODO: tighten PDB dbrefs
-          // formally imply Jalview has actually downlaoded and
+          // formally imply Jalview has actually downloaded 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"))
+          if (pdbentry != null && pdbentry.getFile() != null)
           {
             primaries.add(ref);
           }
@@ -1465,7 +1463,7 @@ public class Sequence extends ASequence implements SequenceI
         }
         // check standard protein or dna sources
         tmp[0] = ref;
-        res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+        DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
         if (res != null && res[0] == tmp[0])
         {
           primaries.add(ref);