X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;fp=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=33a917e2f5fc3a2a8d3284a67d298848a9de0518;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=23924769d7a80c2344c35da8c1474852f7c0a6c8;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 2392476..33a917e 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -55,7 +55,7 @@ public class ASequenceFetcher
   /**
    * Constructor
    */
-  public ASequenceFetcher()
+  protected ASequenceFetcher()
   {
     super();
 
@@ -125,20 +125,20 @@ public class ASequenceFetcher
    *          if true, only fetch from nucleotide data sources, else peptide
    * @return
    */
-  public SequenceI[] getSequences(DBRefEntry[] refs, boolean dna)
+  public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
   {
     Vector<SequenceI> rseqs = new Vector<SequenceI>();
     Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
-    for (int r = 0; r < refs.length; r++)
+    for (DBRefEntry ref : refs)
     {
-      if (!queries.containsKey(refs[r].getSource()))
+      if (!queries.containsKey(ref.getSource()))
       {
-        queries.put(refs[r].getSource(), new ArrayList<String>());
+        queries.put(ref.getSource(), new ArrayList<String>());
       }
-      List<String> qset = queries.get(refs[r].getSource());
-      if (!qset.contains(refs[r].getAccessionId()))
+      List<String> qset = queries.get(ref.getSource());
+      if (!qset.contains(ref.getAccessionId()))
       {
-        qset.add(refs[r].getAccessionId());
+        qset.add(ref.getAccessionId());
       }
     }
     Enumeration<String> e = queries.keys();
@@ -205,15 +205,12 @@ public class ASequenceFetcher
                 for (int is = 0; is < seqs.length; is++)
                 {
                   rseqs.addElement(seqs[is]);
-                  DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
+                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(seqs[is]
                           .getDBRefs(), new DBRefEntry(db, null, null));
-                  if (frefs != null)
+                  for (DBRefEntry dbr : frefs)
                   {
-                    for (DBRefEntry dbr : frefs)
-                    {
-                      queriesFound.add(dbr.getAccessionId());
-                      queriesMade.remove(dbr.getAccessionId());
-                    }
+                    queriesFound.add(dbr.getAccessionId());
+                    queriesMade.remove(dbr.getAccessionId());
                   }
                   seqs[is] = null;
                 }