X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=94aa5c9f6c4b663c07f2f59f469fe6b87f68ad39;hb=171ca8730ea146d50b2eb00701d8df986d88f519;hp=629850511fefc57400d34c9e07753c938e442c3e;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 6298505..94aa5c9 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,23 +1,24 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
 
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 import java.util.Hashtable;
 
@@ -34,15 +35,15 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
- * 
+ *
  * @author JimP
- * 
+ *
  */
 public class CrossRef
 {
   /**
    * get the DNA or protein references for a protein or dna sequence
-   * 
+   *
    * @param dna
    * @param rfs
    * @return
@@ -90,7 +91,7 @@ public class CrossRef
   /**
    * Indirect references are references from other sequences from the dataset to
    * any of the direct DBRefEntrys on the given sequences.
-   * 
+   *
    * @param dna
    *          true if seqs are DNA seqs
    * @param seqs
@@ -201,7 +202,7 @@ public class CrossRef
   }
 
   /**
-   * 
+   *
    * @param dna
    * @param seqs
    * @return
@@ -213,7 +214,7 @@ public class CrossRef
   }
 
   /**
-   * 
+   *
    * @param seqs
    * @param dna
    * @param source
@@ -415,7 +416,7 @@ public class CrossRef
    * find references to lrfs in the cross-reference set of each sequence in
    * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
    * based on source and accession string only - Map and Version are nulled.
-   * 
+   *
    * @param sequenceI
    * @param lrfs
    * @param dataset
@@ -443,7 +444,7 @@ public class CrossRef
   /**
    * search a given sequence dataset for references matching cross-references to
    * the given sequence
-   * 
+   *
    * @param sequenceI
    * @param xrf
    * @param dataset
@@ -462,7 +463,7 @@ public class CrossRef
    * TODO: generalise to different protein classifications Search dataset for
    * DBRefEntrys matching the given one (xrf) and add the associated sequence to
    * rseq.
-   * 
+   *
    * @param sequenceI
    * @param xrf
    * @param dataset
@@ -486,10 +487,10 @@ public class CrossRef
       System.err.println("Empty dataset sequence set - NO VECTOR");
       return false;
     }
-    Enumeration e = dataset.getSequences().elements();
-    while (e.hasMoreElements())
+    List<SequenceI> ds;
+    synchronized (ds=dataset.getSequences())
     {
-      SequenceI nxt = (SequenceI) e.nextElement();
+      for (SequenceI nxt:ds)
       if (nxt != null)
       {
         if (nxt.getDatasetSequence() != null)
@@ -566,7 +567,7 @@ public class CrossRef
   /**
    * precalculate different products that can be found for seqs in dataset and
    * return them.
-   * 
+   *
    * @param dna
    * @param seqs
    * @param dataset