X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=6c63f1c009a3078751f15f09ec02c9995f761e21;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=8682e8abe7bc34c8a92e00c5b46f139134a469d9;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 8682e8a..6c63f1c 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
+ * 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;
 
@@ -486,79 +487,82 @@ 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();
-      if (nxt != null)
-      {
-        if (nxt.getDatasetSequence() != null)
-        {
-          System.err
-                  .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
-        }
-        if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+      for (SequenceI nxt : ds)
+        if (nxt != null)
         {
-          // check if this is the correct sequence type
+          if (nxt.getDatasetSequence() != null)
           {
-            typer[0] = nxt;
-            boolean isDna = jalview.util.Comparison.isNucleotide(typer);
-            if ((direct && isDna == dna) || (!direct && isDna != dna))
+            System.err
+                    .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+          }
+          if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+          {
+            // check if this is the correct sequence type
             {
-              // skip this sequence because it is same molecule type
-              continue;
+              typer[0] = nxt;
+              boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+              if ((direct && isDna == dna) || (!direct && isDna != dna))
+              {
+                // skip this sequence because it is same molecule type
+                continue;
+              }
             }
-          }
 
-          // look for direct or indirect references in common
-          DBRefEntry[] poss = nxt.getDBRef(), cands = null;
-          if (direct)
-          {
-            cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
-          }
-          else
-          {
-            poss = CrossRef.findXDbRefs(dna, poss); //
-            cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
-          }
-          if (cands != null)
-          {
-            if (!rseqs.contains(nxt))
+            // look for direct or indirect references in common
+            DBRefEntry[] poss = nxt.getDBRef(), cands = null;
+            if (direct)
+            {
+              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+            }
+            else
             {
-              rseqs.addElement(nxt);
-              boolean foundmap = cf != null; // don't search if we aren't given
-              // a codon map object
-              for (int r = 0; foundmap && r < cands.length; r++)
+              poss = CrossRef.findXDbRefs(dna, poss); //
+              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+            }
+            if (cands != null)
+            {
+              if (!rseqs.contains(nxt))
               {
-                if (cands[r].hasMap())
+                rseqs.addElement(nxt);
+                boolean foundmap = cf != null; // don't search if we aren't
+                                               // given
+                // a codon map object
+                for (int r = 0; foundmap && r < cands.length; r++)
                 {
-                  if (cands[r].getMap().getTo() != null
-                          && cands[r].getMap().getMap().getFromRatio() != cands[r]
-                                  .getMap().getMap().getToRatio())
+                  if (cands[r].hasMap())
                   {
-                    foundmap = true;
-                    // get sense of map correct for adding to product alignment.
-                    if (dna)
-                    {
-                      // map is from dna seq to a protein product
-                      cf.addMap(sequenceI, nxt, cands[r].getMap().getMap());
-                    }
-                    else
+                    if (cands[r].getMap().getTo() != null
+                            && cands[r].getMap().getMap().getFromRatio() != cands[r]
+                                    .getMap().getMap().getToRatio())
                     {
-                      // map should be from protein seq to its coding dna
-                      cf.addMap(nxt, sequenceI, cands[r].getMap().getMap()
-                              .getInverse());
+                      foundmap = true;
+                      // get sense of map correct for adding to product
+                      // alignment.
+                      if (dna)
+                      {
+                        // map is from dna seq to a protein product
+                        cf.addMap(sequenceI, nxt, cands[r].getMap()
+                                .getMap());
+                      }
+                      else
+                      {
+                        // map should be from protein seq to its coding dna
+                        cf.addMap(nxt, sequenceI, cands[r].getMap()
+                                .getMap().getInverse());
+                      }
                     }
                   }
                 }
+                // TODO: add mapping between sequences if necessary
+                found = true;
               }
-              // TODO: add mapping between sequences if necessary
-              found = true;
             }
-          }
 
+          }
         }
-      }
     }
     return found;
   }